From manju.rawat2 at gmail.com  Thu Sep  1 02:53:53 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 1 Sep 2011 02:53:53 -0400
Subject: [Bioperl-l] Bioperl query....
In-Reply-To: <CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
References: <CAB2c7yp6p2e_8p7M9wVL2xzU7g+mZ-NVXwLs4PUassRs4PgrTQ@mail.gmail.com>
	<4E5CC8AC.8050800@gmail.com>
	<CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
Message-ID: <CAB2c7yobL=KRW_XWOCfgEwJS17A8Mne4FJhVp88xjJfBqZMHGw@mail.gmail.com>

Thanks For The Reply..
I have already seen this link..But I am confused.

I used to following code and run it...

my $in = Bio::SearchIO->new(-format => 'blast',
                -file => 'seqs.blast');
while( my $result = $in->next_result ) {
  ## $result is a Bio::Search::Result::ResultI compliant object
  while( my $hit = $result->next_hit ) {
    ## $hit is a Bio::Search::Hit::HitI compliant object
    while( my $hsp = $hit->next_hsp ) {
      ## $hsp is a Bio::Search::HSP::HSPI compliant object
      if( $hsp->length('total') > 50 ) {
        if ( $hsp->percent_identity >= 75 ) {
          print "Query=",   $result->query_name,
            " Hit=",        $hit->name,
            " Length=",     $hsp->length('total'),
    " gaps=",            $hsp->gaps,
            " Percent_id=", $hsp->percent_identity, "\n";
        }     } }    }}



and it showing me following output with an error that..


*Erro--*rArgument "" isn't numeric in numeric lt (<) at
/usr/local/share/perl/5.10.1/Bio/SearchIO/SearchResultEventBuilder.pm line
279, <GEN1> line 4113.

Query=NM_181451 Hit=ref|NM_181451.1| Length=1349 gaps=1 Percent_id=100
Query=NM_181451 Hit=ref|XM_002706247.1| Length=1345 gaps=13
Percent_id=93.8289962825279
Query=NM_181451 Hit=ref|NM_001098089.1| Length=1323 gaps=7
Percent_id=91.9123204837491
Query=NM_181451 Hit=ref|NM_001008415.1| Length=1211 gaps=5
Percent_id=94.9628406275805
Query=NM_181451 Hit=ref|XM_001251693.3| Length=1320 gaps=5
Percent_id=91.969696969697
Query=NM_181451 Hit=ref|NM_001097567.1| Length=1338 gaps=4
Percent_id=91.5545590433483
Query=NM_181451 Hit=gb|AY075103.1| Length=1334 gaps=1
Percent_id=91.304347826087
................
..........

Pl Find.whats the error i this code...

Thanks
Manju Rawat.

From locarpau at upvnet.upv.es  Thu Sep  1 10:49:06 2011
From: locarpau at upvnet.upv.es (Lorenzo Carretero Paulet)
Date: Thu,  1 Sep 2011 16:49:06 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
Message-ID: <1314888546.4e5f9b628ecea@webmail.upv.es>

Hi all,
I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:

my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
if ( my $paml_result = $parserF->next_result )
{
say Dumper $paml_result; #Prints Ok
	for ( my $model_result= $paml_result->get_NSSite_results )
	{
        #say Dumper $model_result; #Prints nothing
        $ns_string = "model ".$model_result->model_num."\n
".$model_result->model_description()."\n ".$model_result->time_used."\n";
	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
	#say Dumper $dnds_site_classes;
	for my $sites ( $model_result->get_BEB_pos_selected_sites )
        ...
         ...
          ...

The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
object is not being properly instantiated, as I get the error message:

"Can't call method "model_num" without a package or object reference at ..."

What am I missing?
Best,
Lorenzo



From jason.stajich at gmail.com  Thu Sep  1 16:23:47 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 1 Sep 2011 13:23:47 -0700
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <1314888546.4e5f9b628ecea@webmail.upv.es>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
Message-ID: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>

Lorenzo -

I am sure this is a problem with changes in the output from PAML - this is classic problem with this suite.  This requires some debugging of the parser, not sure if there is anyone out there with time to do the debugging.
I can say all this worked before on an earlier version of PAML but I don't know specifically what is going on with the latest paml4.4 version.

Jason


On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:

> Hi all,
> I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:
> 
> my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> if ( my $paml_result = $parserF->next_result )
> {
> say Dumper $paml_result; #Prints Ok
> 	for ( my $model_result= $paml_result->get_NSSite_results )
> 	{
>        #say Dumper $model_result; #Prints nothing
>        $ns_string = "model ".$model_result->model_num."\n
> ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> 	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> 	#say Dumper $dnds_site_classes;
> 	for my $sites ( $model_result->get_BEB_pos_selected_sites )
>        ...
>         ...
>          ...
> 
> The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
> object is not being properly instantiated, as I get the error message:
> 
> "Can't call method "model_num" without a package or object reference at ..."
> 
> What am I missing?
> Best,
> Lorenzo
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Scott.Markel at accelrys.com  Thu Sep  1 17:22:21 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Thu, 1 Sep 2011 14:22:21 -0700
Subject: [Bioperl-l] file format for alignment plus features for aligned
	sequences
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702F8302A05@EXCH1-COLO.accelrys.net>

A question on behalf of the Discovery Studio group at Accelrys -

They have alignment data with annotations, e.g., visualization settings or alignment properties.  The aligned sequences also have features, e.g., domain boundaries or secondary structure motifs.  They currently use BSML to save sequences and features.

Is there an extension of BSML that can also save the alignment information?

Are there any good file formats that can be used to store an alignment plus features associated with the aligned sequences?

Are there other mailing lists that might be more appropriate for these questions?

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
San Diego, CA 92121                 fax:    +1 858 799 5222
USA                                 web:    http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
    International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics





From ihok at hotmail.com  Thu Sep  1 23:49:50 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Thu, 1 Sep 2011 23:49:50 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
Message-ID: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>

I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty 
quiet codebase these days... Is it dead?

Does anyone have a spec file for building an SRPM for it for RHEL 6?

From cjfields at illinois.edu  Fri Sep  2 00:31:17 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 04:31:17 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
Message-ID: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>

Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.

chris

On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:

> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> 
> Does anyone have a spec file for building an SRPM for it for RHEL 6?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Fri Sep  2 04:44:07 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 10:44:07 +0200
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
Message-ID: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>

As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
http://toolkit.tuebingen.mpg.de/hhpred


He got it working thus:

> Hi Dave,
> thanks a lot. i made it work. The error i got later on was:

 relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making
> a shared object;
> recompile with -fPIC
>


> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared
> --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/<http://forums.fedoraforum.org/showthread.php?t=232607>
> showthread.php?t=232607<http://forums.fedoraforum.org/showthread.php?t=232607>




Dave





On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J
<cjfields at illinois.edu>wrote:

> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone
> who has packaged that up in a while, if ever.
>
> chris
>
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty
> quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From David.Messina at sbc.su.se  Fri Sep  2 05:30:33 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 11:30:33 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com>
	<9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu>
	<4DF56976.8080704@upvnet.upv.es>
	<AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com>
	<9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
	<E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
Message-ID: <CAM3TQQU6YV0+5HEf6_PhNDuh3SK0eYZgHE5kT+F3MbTH8ktsNw@mail.gmail.com>

Looking back at the commit history, back in April and May 2010, I made some
updates for the January 2010 edition of PAML 4.4. All tests passed at that
time, but:

- the tests may be incomplete
- PAML has undoubtedly changed since then, even if it's still called version
4.4


I can't look at this right now myself, but please file a bug report on this,
and hopefully someone else can.


Dave




On Thu, Sep 1, 2011 at 22:23, Jason Stajich <jason.stajich at gmail.com> wrote:

> Lorenzo -
>
> I am sure this is a problem with changes in the output from PAML - this is
> classic problem with this suite.  This requires some debugging of the
> parser, not sure if there is anyone out there with time to do the debugging.
> I can say all this worked before on an earlier version of PAML but I don't
> know specifically what is going on with the latest paml4.4 version.
>
> Jason
>
>
> On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:
>
> > Hi all,
> > I'm trying to parse mlc output files from PAML using
> Bio::Tools::Phylo::PAML as:
> >
> > my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> > my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> > if ( my $paml_result = $parserF->next_result )
> > {
> > say Dumper $paml_result; #Prints Ok
> >       for ( my $model_result= $paml_result->get_NSSite_results )
> >       {
> >        #say Dumper $model_result; #Prints nothing
> >        $ns_string = "model ".$model_result->model_num."\n
> > ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> >       $dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> >       #say Dumper $dnds_site_classes;
> >       for my $sites ( $model_result->get_BEB_pos_selected_sites )
> >        ...
> >         ...
> >          ...
> >
> > The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> > DUmper. In contrast, it seems that the
> Bio::Tools::Phylo::PAML::ModelResult
> > object is not being properly instantiated, as I get the error message:
> >
> > "Can't call method "model_num" without a package or object reference at
> ..."
> >
> > What am I missing?
> > Best,
> > Lorenzo
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From cjfields at illinois.edu  Fri Sep  2 09:00:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 13:00:27 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
Message-ID: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>

I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/

chris

On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:

> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
> http://toolkit.tuebingen.mpg.de/hhpred
> 
> 
> He got it working thus:
> Hi Dave,
> thanks a lot. i made it work. The error i got later on was: 
> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
> recompile with -fPIC 
>  
> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/showthread.php?t=232607
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J <cjfields at illinois.edu> wrote:
> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
> 
> chris
> 
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
> 
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From ihok at hotmail.com  Fri Sep  2 11:20:44 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Fri, 2 Sep 2011 11:20:44 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
	<81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
Message-ID: <BLU0-SMTP2075F7F67ABC5C1860ED380CA180@phx.gbl>

I also see that someone's forked it on Github and made some packaging fixes.

It'd be nice to see it revived.

On 9/2/2011 9:00 AM, Fields, Christopher J wrote:
> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/
>
> chris
>
> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:
>
>> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
>> http://toolkit.tuebingen.mpg.de/hhpred
>>
>>
>> He got it working thus:
>> Hi Dave,
>> thanks a lot. i made it work. The error i got later on was:
>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
>> recompile with -fPIC
>>
>> the solution is:
>> perl Makefile.PL PREFIX=<path to installation>  /fftwsingle --enable-shared --with-pic --enable-single
>> <edit Makefile to add -fPIC to CFLAGS>
>> make
>> make install
>> http://forums.fedoraforum.org/showthread.php?t=232607
>>
>>
>>
>> Dave
>>
>>
>>
>>
>>
>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J<cjfields at illinois.edu>  wrote:
>> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
>>
>> chris
>>
>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>>
>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
>>>
>>> Does anyone have a spec file for building an SRPM for it for RHEL 6?
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>


From manju.rawat2 at gmail.com  Sat Sep  3 01:29:56 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 01:29:56 -0400
Subject: [Bioperl-l] hsps_successfully_gapped: 47
Message-ID: <CAB2c7yr8qHCPO2L6nczPUTWi-L94Bz9kQtyLP-U03=nhWS+66Q@mail.gmail.com>

Hello,


Is There any method in BioPerl through which we can extract
number_of_hsps_successfully_gapped:
from a blast file..
If any one know about the it Pl help me...


Thanks
Manju Rawat

From manju.rawat2 at gmail.com  Sat Sep  3 06:00:22 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 06:00:22 -0400
Subject: [Bioperl-l] blast result not matching.
Message-ID: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


and Output..

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat

From florent.angly at gmail.com  Sun Sep  4 22:14:37 2011
From: florent.angly at gmail.com (Florent Angly)
Date: Mon, 05 Sep 2011 12:14:37 +1000
Subject: [Bioperl-l] Bio::SeqIO can't guess the format of data from a
 pipe
In-Reply-To: <F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
References: <CAFAnT677UmaEsudqoj9UsefdeK9Wx0E_W8iM3zmMAJx8PHzBjA@mail.gmail.com>
	<2E070303-ADDF-472B-835B-6D3959B83E9A@illinois.edu>
	<CAFAnT64JhkP-xzi8TpqHiTJTm3UMgT7SPMWVm+-UhSFwk0G3gQ@mail.gmail.com>
	<E89E20DA-9B27-4D42-ACF8-96A176C85259@illinois.edu>
	<4E58D105.7050805@gmail.com>
	<A249C76A-A0BC-414E-AE78-A2B6CA7B4A9A@drycafe.net>
	<4E5A0590.2010805@gmail.com>
	<8D639B95-0666-4F09-8E9E-88C8CDF76ABC@illinois.edu>
	<4E5AC2B8.9060808@gmail.com>
	<F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
Message-ID: <4E64308D.5060304@gmail.com>


Thanks for your advice Chris. I put a format() and variant() method in 
Bio::Root::IO. All the Bio::*IO methods inherit these methods.

Regarding the module naming, 8 follow the convention Bio::*IO and 8 
follow the Bio::*::IO convention. If we decide to rename some IO modules 
for consistency, I would prefer the Bio::*::IO convention.

Regards,

Florent


On 29/08/11 11:10, Chris Fields wrote:
> On Aug 28, 2011, at 5:35 PM, Florent Angly wrote:
>
>> Hi,
>>
>> I implemented the format() getter method in Bio::SeqIO as discussed, essentially following the way proposed by Hilmar. The variant() method is not needed since Bio::SeqIO::fastq already has a get/set method for that.
> Right, but the method could be used by other modules if it were moved to Bio::SeqIO. for instance.
>
>> I noticed that there are plenty more Bio*IO modules that could benefit from having a format() method, e.g.:
>>     Bio::AlignIO
>>     Bio::ClusterIO
>>     Bio::FeatureIO
>>     Bio::MapIO
>>     Bio::OntologyIO
>>     Bio::SearchIO
>>     Bio::TreeIO
>>     Bio::Assembly::IO *
>> The code could be copy-pasted for each of them but it is not very graceful. Is there a way we could have all these IO modules share the same format() method?
> Move the method to Bio::Root::IO, the common base class for all of the above.
>
>> * Note how the IO class for Bio::Assembly is called Bio::Assembly::IO, and not Bio::AssemblyIO like for other classes. This may be something to change in the future for consistency.
>>
>> Florent
> That's possible; one could take advantage of that for redesign/API issues if it were needed.
>
> chris


From manju.rawat2 at gmail.com  Mon Sep  5 03:53:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 03:53:40 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
Message-ID: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


*and Output..*

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat

From p.j.a.cock at googlemail.com  Mon Sep  5 05:44:06 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 10:44:06 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
Message-ID: <CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>

On Mon, Sep 5, 2011 at 8:53 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
> I doing blast using bioperl...but it not showing me complete result..
>
>
> my program is following...
> ...
>
> this result is not matching with with NCBI result...
> Is there anything wrong..

The NCBI website for BLAST uses different default values
to the BLAST command line tools. Check things like the
gap parameters if you want to use the same settings.

Peter

From p.j.a.cock at googlemail.com  Mon Sep  5 06:25:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 11:25:15 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
Message-ID: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>

Please CC the mailing list.

On Mon, Sep 5, 2011 at 11:19 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
> Thanks for the reply...
> but when i am blasting after getting sequence of any gene (from NCBI using
> bioperl see below)..it showing me same result as shown in NCBI..
>
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq_object = get_sequence('NCBI',"NM_181451");
> $blast_result = blast_sequence($seq);
> write_blast(">roa1.blast",$blast_report);
>
>
> I dnt know why its not working when i am blasting my own sequence..
>

Maybe you need give the sequence as a FASTA entry
rather than a plain string?

Peter

From manju.rawat2 at gmail.com  Mon Sep  5 06:40:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 06:40:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
Message-ID: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>

No..i also tried this..this also dont work..
pls help me..

From cjfields at illinois.edu  Mon Sep  5 15:42:49 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 5 Sep 2011 19:42:49 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
Message-ID: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>

Are you using the latest BioPerl?  I believe there had been some fixes addressing remote blast.

chris

On Sep 5, 2011, at 5:40 AM, Manju Rawat wrote:

> No..i also tried this..this also dont work..
> pls help me..
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From manju.rawat2 at gmail.com  Tue Sep  6 06:59:50 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 6 Sep 2011 06:59:50 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
Message-ID: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>

bioperl 1.6.9 version is installed in my system..
its not the reason bcs blast is working fine when i am blasting with
follwing code..

#!usr/bin/perl -w
use Bio::Perl;
$seq = get_sequence('NCBI',"NM_181451");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


Manju

From sidd.basu at gmail.com  Tue Sep  6 11:51:09 2011
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Tue, 6 Sep 2011 10:51:09 -0500
Subject: [Bioperl-l] Bioinformatics Job Opening at dictyBase in Chicago
Message-ID: <20110906155106.GB1841@Macintosh-388.local>

Hi All, 
We have an open position for a Bioinformatics Software Engineer at dictyBase(Northwestern
University in Chicago). The job involves developing web application and middleware for
a genome database using modern perl(DBIx-Class/Moose/MVC web frameworks etc)
as well as integration of various genomic tools(gbrowse, intermine, apollo,
biomart, pathway tools etc..). 
For full details please see:
 http://www.dictybase.org/dictybase_jobs.html.


thanks, 
-siddhartha

Siddhartha Basu
Software developer,  dictybase
http://www.dictybase.org


From slucky at ibab.ac.in  Wed Sep  7 09:39:03 2011
From: slucky at ibab.ac.in (Lucky Singh)
Date: Wed, 07 Sep 2011 19:09:03 +0530
Subject: [Bioperl-l] Fwd: Re:  Problem using Bio::Tools::Run::RemoteBlast
Message-ID: <4E6773F7.7000703@ibab.ac.in>



-------- Original Message --------
Subject: 	Re: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
Date: 	Sat, 27 Aug 2011 20:36:58 +0530
From: 	Lucky Singh <slucky at ibab.ac.in>
To: 	Carn? Draug <carandraug+dev at gmail.com>



On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>  On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in>   wrote:
>>  Now I
>>  wanted to host it from web server, but This program is not working from it
>>  may be it is not able to create or write on file from web server but in
>>  command line it is working fine. I don't know the possible reason, please
>>  help me to figure it out.
>  Have you looked in the apache logs (look in
>  /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>  content of the error log after trying to run the script?
Dear Carn? Draug,

As per your suggestion, I am attaching blast code file currently it is
not showing any error on error.log.
Thanks a lot for your valuable reply and will be highly grateful if you
can get me out of this problem :)


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From jason.stajich at gmail.com  Wed Sep  7 12:13:46 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 7 Sep 2011 09:13:46 -0700
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
Message-ID: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>

I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.


On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:

> bioperl 1.6.9 version is installed in my system..
> its not the reason bcs blast is working fine when i am blasting with
> follwing code..
> 
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq = get_sequence('NCBI',"NM_181451");
> $blast_result=blast_sequence($seq);
> write_blast(">xyz.blast",$blast_result);
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Wed Sep  7 12:33:52 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 7 Sep 2011 16:33:52 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
Message-ID: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>

I think there was an issue with Bio::Perl BLAST submissions fixed in the 1.6.901 release (1.6.9 != 1.6.901, the latter is newer).  From CPAN:

1.6.901 May 18, 2011

...

    [Bug fixes]

    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
      docs [genehack, cjfields]

chris

On Sep 7, 2011, at 11:13 AM, Jason Stajich wrote:

> I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
> Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.
> 
> 
> On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:
> 
>> bioperl 1.6.9 version is installed in my system..
>> its not the reason bcs blast is working fine when i am blasting with
>> follwing code..
>> 
>> #!usr/bin/perl -w
>> use Bio::Perl;
>> $seq = get_sequence('NCBI',"NM_181451");
>> $blast_result=blast_sequence($seq);
>> write_blast(">xyz.blast",$blast_result);
>> 
>> 
>> Manju
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From carandraug+dev at gmail.com  Wed Sep  7 12:47:16 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 7 Sep 2011 17:47:16 +0100
Subject: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
In-Reply-To: <4E590812.9030006@ibab.ac.in>
References: <37711.192.168.1.254.1313992876.squirrel@webmail.ibab.ac.in>
	<CAPOrs_1TX=+A=hA0bCP56bsW5XdPy5N5mpcnAL=NPugP-4j03Q@mail.gmail.com>
	<4E590812.9030006@ibab.ac.in>
Message-ID: <CAPOrs_2MbWXbtrhj+eOphpDfyaUhdpWvUE8kaMXxKrQe_3m_kw@mail.gmail.com>

2011/8/27 Lucky Singh <slucky at ibab.ac.in>:
> On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>>
>> On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in> ?wrote:
>>>
>>> Now I
>>> wanted to host it from web server, but This program is not working from
>>> it
>>> may be it is not able to create or write on file from web server but in
>>> command line it is working fine. I don't know the possible reason, please
>>> help me to figure it out.
>>
>> Have you looked in the apache logs (look in
>> /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>> content of the error log after trying to run the script?
>
> Dear Carn? Draug,
>
> As per your suggestion, I am attaching blast code file currently it is not
> showing any error on error.log.
> Thanks a lot for your valuable reply and will be highly grateful if you can
> get me out of this problem :)


Hi

sorry for the late reply. Please try to always reply to the mailing
list, maybe someone else can help you too. I don't know about the
script as I never used RemoteBlast from bioperl. But given a quick
look at it, you're not loading the CGI module on the script (
http://perldoc.perl.org/CGI.html ). Here's a simple example using the
CGI module ( http://pastebin.com/miMd70wn ) and a HTML page that will
use it ( http://pastebin.com/kWwwMijd ).

If nothing shows up on error.log, take a look in access.log. Try some
simple CGI script first, such as "hello world!" to see if the problem
lies on your bioperl part of the script, or in the web server, or some
other part.

Carn?


From scott at scottcain.net  Wed Sep  7 13:57:31 2011
From: scott at scottcain.net (Scott Cain)
Date: Wed, 7 Sep 2011 13:57:31 -0400
Subject: [Bioperl-l] October GMOD Meeting in Toronto
Message-ID: <CA+JTaoxxMxNQmOu8wbU=vD+-6eRwPVjpXBAszWn=p6_OOkr9ig@mail.gmail.com>

Hello,

The early registration deadline for the October GMOD meeting in
Toronto, Canada is approaching.  Please register by September 13th to
avoid the late registration fee.  You can register here:

  http://gmod.eventbrite.com/

For information about the GMOD meeting please see the page at:

  http://gmod.org/wiki/October_2011_GMOD_Meeting

In addition to the main meeting, there will be a free BioMart workshop
on the following Friday, which you can also register for at the main
meeting registration page.

Thanks,
Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research


From info at etisalat.com  Wed Sep  7 05:52:00 2011
From: info at etisalat.com (Etisalat Telecommunication Network.)
Date: Wed, 7 Sep 2011 17:52:00 +0800
Subject: [Bioperl-l] Winning No:ETS/G/NG
Message-ID: <20110907092508.M63844@etisalat.com>

Etisalat Telecommunication Network.
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recipients of a cash Grant/Donation.The online cyber draws was conducted
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selection from the web.This promotion is to
celebrate the patronage of our esteem customers and we are giving
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recipients as a way of showing our appreciation.

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NAME:Thompson Thomas
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1.Full Name:
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10.Winning No:

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Etisalat Award Promotion
(c)2011 Online Award Promotion Edition  


From longbow0 at gmail.com  Wed Sep  7 16:19:37 2011
From: longbow0 at gmail.com (longbow leo)
Date: Wed, 7 Sep 2011 15:19:37 -0500
Subject: [Bioperl-l] How to determine strains were evolved independently in
	a phylogenetic tree?
Message-ID: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>

Hi,

I have created a phylogenetic for a virus protein which contained about 200
strains. Next I need to do an analysis to check whether several strains in
this tree were evolved independently. Although it is not too difficult to do
manually, I still have litter idea how to do this in a Perl script since
there are some datasets need to do.

At first I tried to use the method "is_monophyletic" in the module
"Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
work as I have thought. According to the description of "is_monophyletic"
method, it "Will do a test of monophyly for the nodes specified in
comparison to a chosen outgroup". Does here test whether the outgroup strain
is monophyletic to the nodes, or test the nodes only? The description sounds
like the latter but the what the script did seemed to be the first.

Are there any suggestions?

Thank you very much!


Haizhou Liu

From greg at ebi.ac.uk  Thu Sep  8 06:40:30 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Thu, 8 Sep 2011 11:40:30 +0100
Subject: [Bioperl-l] How to determine strains were evolved independently
 in a phylogenetic tree?
In-Reply-To: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
References: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
Message-ID: <CA+08rdT4z5W5OzuuBPsC0icz_LWXCTNWO0uv=w=Bg_0EoU44Gw@mail.gmail.com>

Hi Haizhou,

I'm not sure I understand exactly what you're trying to do. But to clarify
the BioPerl code: the is_monophyletic method (for the actual code, see here
https://github.com/bioperl/bioperl-live/blob/master/Bio/Tree/TreeFunctionsI.pm#L832)
tests
whether the single outgroup node falls *within* or *outside* the last common
ancestor of the group of nodes given. If the outgroup node falls *outside*
the subtree defined by this LCA node, then the group of nodes can be called
monophyletic with respect to that outgroup (at least as far as my
understanding of the word 'monophyletic' goes). If the outgroup node falls
*within* the subtree defined by this LCA node, then the group of nodes is
not monophyletic with respect to that outgroup node.

The term "evolved independently" sounds slightly vague to me -- what is it
exactly about the shape of your tree that allows you to call a strain
independent or not? If you gave an example or two of trees where you
consider the evolution to be independent and non-independent, I (or someone
else on the list) may be able to help you find the right method to do this
automatically.

Cheers,
 Greg

On Wed, Sep 7, 2011 at 9:19 PM, longbow leo <longbow0 at gmail.com> wrote:

> Hi,
>
> I have created a phylogenetic for a virus protein which contained about 200
> strains. Next I need to do an analysis to check whether several strains in
> this tree were evolved independently. Although it is not too difficult to
> do
> manually, I still have litter idea how to do this in a Perl script since
> there are some datasets need to do.
>
> At first I tried to use the method "is_monophyletic" in the module
> "Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
> work as I have thought. According to the description of "is_monophyletic"
> method, it "Will do a test of monophyly for the nodes specified in
> comparison to a chosen outgroup". Does here test whether the outgroup
> strain
> is monophyletic to the nodes, or test the nodes only? The description
> sounds
> like the latter but the what the script did seemed to be the first.
>
> Are there any suggestions?
>
> Thank you very much!
>
>
> Haizhou Liu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From manju.rawat2 at gmail.com  Thu Sep  8 02:11:12 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 8 Sep 2011 02:11:12 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
Message-ID: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>

Toady i installed the latest version of bioperl in my system via CPAN..
But this still not sowing the complete result..


I just want to do nucleotide blast using bioperl..but while i am doing blast
with my sequence it shwowing very samll result..
I dnt know whether it is wrong or right...but while i am blasting the same
sequence in NCBI it showing a diffrent result..

and i have also tried to use the orignl module..but it also dnt work..

Pl see reult of the balst in  attached file of this mail..
#!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO;
$blast_report =blast_sequence('acggctgctgtagatctgatgct');
write_blast(">resl.blast",$blast_report);

Thanks.
Manju Rawat
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From cjfields at illinois.edu  Thu Sep  8 09:05:10 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 13:05:10 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <6D4A142B-9455-4CC3-AFDB-F9B3B991B57F@illinois.edu>

Submissions to NCBI BLAST via their web interface have different parameters than those submitted via their QBLAST interface (what is used in BioPerl).  So the fact there are differing results isn't too surprising, particularly if the results fall close to the e-value cutoff for one or the other.  You will need to set the proper parameters, which I don't believe is possible via the (very simple) Bio::Perl interface, but is possible via Bio::Tools::Run::RemoteBlast.

chris

On Sep 8, 2011, at 1:11 AM, Manju Rawat wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
> 
> 
> I just want to do nucleotide blast using bioperl..but while i am doing blast with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same sequence in NCBI it showing a diffrent result..
> 
> and i have also tried to use the orignl module..but it also dnt work..
> 
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
> 
> Thanks.
> Manju Rawat
> 
> 
> <resl.blast>



From David.Messina at sbc.su.se  Thu Sep  8 09:33:19 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 8 Sep 2011 15:33:19 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>

As I think has been said earlier in this thread, it's almost certainly a
discrepancy in the BLAST parameters between what the blast_sequence function
in the Bio::Perl module is sending, and what the BLAST website is doing.


In this case, you have a very short sequence. If you look in the "Algorithm
parameters" section of the BLAST web form, you'll see that there is an
option that is checked by default, "Automatically adjust parameters for
short input sequences".


If I uncheck that option, I get the same results as you did when you
submitted your BLAST through BioPerl (see http://cl.ly/9ynq).


So to get the same results from a BioPerl-submitted BLAST and a BLAST on
NCBI's website, you need to have the same parameters. You can set the
parameters from BioPerl as described in the documentation:

http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Tools/Run/RemoteBlast.pm


As Jason said earlier, the blast_sequence function in Bio::Perl is intended
as a simple demonstration and uses the default BLAST parameters. That
function is a wrapper around the RemoteBlast module. Since you want to do
something a little different, I believe you'll need to use the RemoteBlast
module directly.




Dave




On Thu, Sep 8, 2011 at 08:11, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
>
>
> I just want to do nucleotide blast using bioperl..but while i am doing
> blast
> with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same
> sequence in NCBI it showing a diffrent result..
>
> and i have also tried to use the orignl module..but it also dnt work..
>
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
>
> Thanks.
> Manju Rawat
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From abualiga2 at gmail.com  Thu Sep  8 10:44:39 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 10:44:39 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
	primary tag
Message-ID: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>

Hi,

I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
multiple tags within a primary tag.  E.g., when there are several 'function'
tag-values within a 'CDS' primary tag, I don't know how to link those
'function' tag-values to a particular 'locus_tag'.  As parsed values are
returned as a list, I tried creating an array of hashes, where the hash-key
is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
miserably.  Pasted below is what I managed so far.  At your convenience,
please advise.

thanks!

galeb

#!/usr/local/bin/perl
# parse_gbk.pl
# gsa 09042011
# script to parse out features from gbk
#
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction

use strict; use warnings;
use Bio::SeqIO;

my @loci;
my @seqs;
my @directions;
my @start_coords;
my @end_coords;
my @genes;
my @products;
my @notes;
my @functions;
my %functions;

my $gb_file = shift;
my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
my $seq_obj = $seqio_obj->next_seq;

for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
    if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
                if ($feat_obj->has_tag( 'locus_tag' ) ) {
                push ( @seqs, $feat_obj->seq->seq ); #collect sequences
                    for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
{
                            push ( @loci, $val ); # locus_tags
            }
        }
                if ( $feat_obj->has_tag( 'gene' ) ) {
                           for my $val ( $feat_obj->get_tag_values( 'gene' )
) {
                            push ( @genes, $val ); # gene names
                        }
                }
                else {
                    push ( @genes, "" ); # if gene names are absent, leave
empty
        }
        if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
coordinates
            for my $location ( $feat_obj->location ) {
                push ( @start_coords, $location->start );
                push ( @end_coords, $location->end );
                if ( $location->strand == -1 ) {
                    push ( @directions, "reverse" );
                }
                else {
                    push ( @directions, "forward" );
                }
            }
        }
    }
    # gene products, notes, functions
    if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
$feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
|| $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
        if ( $feat_obj->has_tag( 'product' ) ) {
            for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
                push ( @products, $product );
            }
        }
        else {
            push ( @products, "" );
        }
        if ( $feat_obj->has_tag( 'note' ) ) {
            for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
                push ( @notes, $note );
            }
        }
        else {
            push ( @notes, "" );
        }
        if ( $feat_obj->has_tag( 'function' ) ) {
            for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
                push ( @functions, $function );
            }
        }
        else {
            push ( @functions, "" );
        }

    }
}

print
"locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
# header

for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
    print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
"\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
$directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
$functions[$elem], "\t", $seqs[$elem], "\n";
}

From p.j.a.cock at googlemail.com  Thu Sep  8 11:27:56 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:27:56 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>

On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> Hi,
>
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag. ?E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.

Do you have GenBank features with multiple locus_tag qualifiers?
That would be very unusual...

Peter


From cjfields at illinois.edu  Thu Sep  8 11:32:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 15:32:21 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
Message-ID: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>

On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:

> On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
>> Hi,
>> 
>> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
>> multiple tags within a primary tag.  E.g., when there are several 'function'
>> tag-values within a 'CDS' primary tag, I don't know how to link those
>> 'function' tag-values to a particular 'locus_tag'.
> 
> Do you have GenBank features with multiple locus_tag qualifiers?
> That would be very unusual...
> 
> Peter

Agreed; in order to clarify what you mean, I think we would need to see the record in question to get a better idea of the problem.

chris

From abualiga2 at gmail.com  Thu Sep  8 11:39:20 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:39:20 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
Message-ID: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>

I guess I was not clear. 'locus_tag' qualifiers are single, but there are
mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

# gbk file
LOCUS       NC_011748            5154862 bp    DNA     circular BCT
15-MAY-2010

# example feature
     gene        complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /db_xref="GeneID:7145846"
     CDS             complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /function="7 : Transport and binding proteins"
                     /function="15.10 : Adaptations to atypical conditions"
                     /function="16.1 : Circulate"
                     /inference="ab initio prediction:AMIGene:2.0"
                     /note="the Vibrio parahaemolyticus gene VP2867 was
found
                     to be a potassium/proton antiporter; can rapidly
extrude
                     potassium against a potassium gradient at alkaline pH
when
                     cloned and expressed in Escherichia coli"
                     /codon_start=1
                     /transl_table=11
                     /product="potassium/proton antiporter"
                     /protein_id="YP_002402372.1"
                     /db_xref="GI:218694705"
                     /db_xref="GeneID:7145846"

/translation="MDATTIISLFILGSILVTSSILLSSFSSRLGIPILVIFLAIGML

AGVDGVGGIPFDNYPFAYMVSNLALAIILLDGGMRTQASSFRVALGPALSLATLGVLI

TSGLTGMMAAWLFNLDLIEGLLIGAIVGSTDAAAVFSLLGGKGLNERVGSTLEIESGS

NDPMAVFLTITLIAMIQQHESSVSWMFVVDILQQFGLGIVIGLGGGYLLLQMINRIAL

PAGLYPLLALSGGILIFALTTALEGSGILAVYLCGFLLGNRPIRNRYGILQNFDGLAW

LAQIAMFLVLGLLVNPSDLLPIAIPALILSAWMIFFARPLSVFAGLLPFRGFNLRERV

FISWVGLRGAVPIILAVFPMMAGLENARLFFNVAFFVVLVSLLLQGTSLSWAAKKAKV

VVPPVGRPVSRVGLDIHPENPWEQFVYQLSADKWCVGAALRDLHMPKETRIAALFRDN

QLLHPTGSTRLREGDVLCVIGRERDLPALGKLFSQSPPVALDQRFFGDFILEASAKYA

DVALIYGLEDGREYRDKQQTLGEIVQQLLGAAPVVGDQVEFAGMIWTVAEKEDNEVLK
                     IGVRVAEEEAES"

On Thu, Sep 8, 2011 at 11:32 AM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:
>
> > On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com>
> wrote:
> >> Hi,
> >>
> >> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> >> multiple tags within a primary tag.  E.g., when there are several
> 'function'
> >> tag-values within a 'CDS' primary tag, I don't know how to link those
> >> 'function' tag-values to a particular 'locus_tag'.
> >
> > Do you have GenBank features with multiple locus_tag qualifiers?
> > That would be very unusual...
> >
> > Peter
>
> Agreed; in order to clarify what you mean, I think we would need to see the
> record in question to get a better idea of the problem.
>
> chris

From p.j.a.cock at googlemail.com  Thu Sep  8 11:46:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:46:28 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
Message-ID: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>

On Thu, Sep 8, 2011 at 4:39 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> I guess I was not clear. 'locus_tag' qualifiers are single, but there are
> mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?

Peter

From abualiga2 at gmail.com  Thu Sep  8 11:55:08 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:55:08 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
	<CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
Message-ID: <CANPzzTsCB8DMzQHMYNOh84hBmu2diwrEA6xb8n3i2RFY9_a4kw@mail.gmail.com>

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?


Precisely!
I want to create a tab delim file with 'locus_tag' as the common identifier
to all the features and gene sequences. So far, I parsed out sequences and
single instance qualifiers, but 'function' and 'db_xref' qualifiers give me
grief.

galeb

From abualiga2 at gmail.com  Thu Sep  8 12:14:07 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:14:07 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.



That's right. Products are not the issue in this particular case, as it's
E.coli and there's no alternate splicing as far as I know so there is a
single product per gene. But there are plenty more 'function' qualifiers,
for example, than loci. And I don't know how to create a data structure that
will link a 'gene' (as primary tag) to all other qualifiers, whether they
belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.

From ss2489 at cornell.edu  Thu Sep  8 12:28:40 2011
From: ss2489 at cornell.edu (Surya Saha)
Date: Thu, 8 Sep 2011 12:28:40 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
Message-ID: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

-Surya

On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:

> I only had a quick look at your code, so maybe I'm missing something but
> you are currently pushing all products of all CDSs into the same array,
> i.e. you do not assign them to a datastructure that links a particular
> CDS to a list of products. You then use the same index to print out a
> locus from the @loci array and a product from @products, but the two
> will not match up because you will have more products than loci.
>
>
>
> That's right. Products are not the issue in this particular case, as it's
> E.coli and there's no alternate splicing as far as I know so there is a
> single product per gene. But there are plenty more 'function' qualifiers,
> for example, than loci. And I don't know how to create a data structure
> that
> will link a 'gene' (as primary tag) to all other qualifiers, whether they
> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From fs5 at sanger.ac.uk  Thu Sep  8 12:04:57 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 08 Sep 2011 17:04:57 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags
	within	primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.

Frank



On Thu, 2011-09-08 at 10:44 -0400, galeb abu-ali wrote:
> Hi,
> 
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag.  E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.  As parsed values are
> returned as a list, I tried creating an array of hashes, where the hash-key
> is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
> miserably.  Pasted below is what I managed so far.  At your convenience,
> please advise.
> 
> thanks!
> 
> galeb
> 
> #!/usr/local/bin/perl
> # parse_gbk.pl
> # gsa 09042011
> # script to parse out features from gbk
> #
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction
> 
> use strict; use warnings;
> use Bio::SeqIO;
> 
> my @loci;
> my @seqs;
> my @directions;
> my @start_coords;
> my @end_coords;
> my @genes;
> my @products;
> my @notes;
> my @functions;
> my %functions;
> 
> my $gb_file = shift;
> my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
> my $seq_obj = $seqio_obj->next_seq;
> 
> for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
>     if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
>                 if ($feat_obj->has_tag( 'locus_tag' ) ) {
>                 push ( @seqs, $feat_obj->seq->seq ); #collect sequences
>                     for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
> {
>                             push ( @loci, $val ); # locus_tags
>             }
>         }
>                 if ( $feat_obj->has_tag( 'gene' ) ) {
>                            for my $val ( $feat_obj->get_tag_values( 'gene' )
> ) {
>                             push ( @genes, $val ); # gene names
>                         }
>                 }
>                 else {
>                     push ( @genes, "" ); # if gene names are absent, leave
> empty
>         }
>         if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
> coordinates
>             for my $location ( $feat_obj->location ) {
>                 push ( @start_coords, $location->start );
>                 push ( @end_coords, $location->end );
>                 if ( $location->strand == -1 ) {
>                     push ( @directions, "reverse" );
>                 }
>                 else {
>                     push ( @directions, "forward" );
>                 }
>             }
>         }
>     }
>     # gene products, notes, functions
>     if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
> 'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
> $feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
> || $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
>         if ( $feat_obj->has_tag( 'product' ) ) {
>             for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
>                 push ( @products, $product );
>             }
>         }
>         else {
>             push ( @products, "" );
>         }
>         if ( $feat_obj->has_tag( 'note' ) ) {
>             for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
>                 push ( @notes, $note );
>             }
>         }
>         else {
>             push ( @notes, "" );
>         }
>         if ( $feat_obj->has_tag( 'function' ) ) {
>             for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
>                 push ( @functions, $function );
>             }
>         }
>         else {
>             push ( @functions, "" );
>         }
> 
>     }
> }
> 
> print
> "locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
> # header
> 
> for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
>     print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
> "\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
> $directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
> $functions[$elem], "\t", $seqs[$elem], "\n";
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From cjfields at illinois.edu  Thu Sep  8 12:51:22 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 16:51:22 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>

There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().

chris

-----------------------------
#!/usr/bin/env perl

use Modern::Perl;
use Bio::SeqIO;

my $in = Bio::SeqIO->new(-format => 'genbank',
                         -file => shift);

while (my $seq = $in->next_seq) {
   for my $feat ($seq->get_SeqFeatures) {
       next unless $feat->primary_tag eq 'CDS';
       my ($locus) = $feat->has_tag('locus_tag') ? 
                     $feat->get_tag_values('locus_tag') : '';
       my @funcs = $feat->has_tag('function') ?
           $feat->get_tag_values('function') : ();
       say join("\t", $locus, join(',', at funcs));
   }
}



On Sep 8, 2011, at 11:28 AM, Surya Saha wrote:

> You might want to explore using a hash of complex records that are very
> similar to structures in C/C++. More info at
> http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS
> 
> -Surya
> 
> On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> 
>> I only had a quick look at your code, so maybe I'm missing something but
>> you are currently pushing all products of all CDSs into the same array,
>> i.e. you do not assign them to a datastructure that links a particular
>> CDS to a list of products. You then use the same index to print out a
>> locus from the @loci array and a product from @products, but the two
>> will not match up because you will have more products than loci.
>> 
>> 
>> 
>> That's right. Products are not the issue in this particular case, as it's
>> E.coli and there's no alternate splicing as far as I know so there is a
>> single product per gene. But there are plenty more 'function' qualifiers,
>> for example, than loci. And I don't know how to create a data structure
>> that
>> will link a 'gene' (as primary tag) to all other qualifiers, whether they
>> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From abualiga2 at gmail.com  Thu Sep  8 12:51:42 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:51:42 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <CANPzzTuAkFy-P9WAVe7bzv=mVEXb-MOLFQrZYv8UX7L2rWcZCA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

alright, thanks!

From jskittrell at unmc.edu  Thu Sep  8 12:40:31 2011
From: jskittrell at unmc.edu (Jeff S Kittrell)
Date: Thu, 8 Sep 2011 11:40:31 -0500
Subject: [Bioperl-l] Error when parsing a blast file
Message-ID: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20110908/486df26d/attachment.html>

From cjfields at illinois.edu  Thu Sep  8 13:28:53 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 17:28:53 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
Message-ID: <1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>

What version of bioperl are you using?  I think this issue was addressed a while ago, but it's possible there has been a regression.

chris

On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:

> Hello Gentlemen,
> 
> I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> When the SearchIO parser encounters this record it dies with the error
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no data for midline Query ------------------------------------------------------------
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> -----------------------------------------------------------
> 
> 
> Has anyone encountered this problem before? Am I doing something wrong?
> 
> Thanks
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> Query= 78065535
> 
> Length=523
> Score E
> Sequences producing significant alignments: (Bits) Value
> 
> gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> 
> 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> receptor 123 (GPR123), mRNA
> Length=4298
> 
> Score = 576 bits (638), Expect = 1e-163
> Identities = 466/583 (80%), Gaps = 82/583 (14%)
> Strand=Plus/Minus
> 
> Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> 
> Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> 
> Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> 
> Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> 
> Query ------------------------------------------------------------ 
> 
> Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> 
> Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> 
> Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> 
> Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> 
> Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> 
> Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> ||||||||||||||||||||||||||||||| ||| || ||||
> Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> 
> 
> 
> Lambda K H
> 0.634 0.408 0.912 
> 
> Gapped
> Lambda K H
> 0.625 0.410 0.780 
> 
> Effective search space used: 47712920310
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From abualiga2 at gmail.com  Thu Sep  8 13:51:34 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 13:51:34 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
Message-ID: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>

thanks, Chris! works perfect.
To make sure I understand what's going on, forcing list context on $locus
allows me to get one value at a time, which is then concatenated with \t to
concatenated functions.

thanks again!

galeb

On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> There is no need to do that if one is using the Bio::SeqFeatureI interface.
>  Note that get_tag_values always returns a list, so to snag a single value
> for a tag in a scalar, force list context on the LHS by enclosing the
> variable in ().
>
> chris
>
> -----------------------------
> #!/usr/bin/env perl
>
> use Modern::Perl;
> use Bio::SeqIO;
>
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
>
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>    }
> }
>
>
>
>

From cjfields at illinois.edu  Thu Sep  8 14:27:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:27:06 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
Message-ID: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>

On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:

> thanks, Chris! works perfect. 
> To make sure I understand what's going on, forcing list context on $locus allows me to get one value at a time,...

You have to be careful in this circumstance; doing this:

   my $foo = @bar;

is scalar context on a list, which returns the number of elements in @bar.  The following

   my ($foo) = @bar;

forces list context and assigns the first value in @bar to $foo but tosses the rest.  If you are sure there is only one value in @bar anyway, the above is fine (and is a common perl idiom).  

> which is then concatenated with \t to concatenated functions. 

I'm just using a simple join() to print off the results.  Note the second element in the join list is an embedded join() with comma-sep values for functions.

chris

> thanks again!
> 
> galeb
> 
> On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().
> 
> chris
> 
> -----------------------------
> #!/usr/bin/env perl
> 
> use Modern::Perl;
> use Bio::SeqIO;
> 
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
> 
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>   }
> }
> 
> 
> 



From cjfields at illinois.edu  Thu Sep  8 14:30:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:30:06 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
	<1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>
	<OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
Message-ID: <C7BC7AE9-FF28-460D-83D1-35F0C8A17832@illinois.edu>

Try updating to the latest CPAN release (1.6.901, which is the pre-1.7 release).

chris

On Sep 8, 2011, at 1:19 PM, Jeff S Kittrell wrote:

> chris,
> 
> I am using version 1.6.1
> 
> Thanks,
> 
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> <graycol.gif>"Fields, Christopher J" ---09/08/2011 12:28:56 PM---What version of bioperl are you using? I think this issue was addressed a while ago, but it's possi
> 
> <ecblank.gif>
> From:
> <ecblank.gif>
> "Fields, Christopher J" <cjfields at illinois.edu>
> <ecblank.gif>
> To:
> <ecblank.gif>
> Jeff S Kittrell <jskittrell at unmc.edu>
> <ecblank.gif>
> Cc:
> <ecblank.gif>
> "<bioperl-l at lists.open-bio.org> " <bioperl-l at lists.open-bio.org>
> <ecblank.gif>
> Date:
> <ecblank.gif>
> 09/08/2011 12:28 PM
> <ecblank.gif>
> Subject:
> <ecblank.gif>
> Re: [Bioperl-l] Error when parsing a blast file
> 
> 
> 
> What version of bioperl are you using? I think this issue was addressed a while ago, but it's possible there has been a regression.
> 
> chris
> 
> On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:
> 
> > Hello Gentlemen,
> > 
> > I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> > When the SearchIO parser encounters this record it dies with the error
> > 
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: no data for midline Query ------------------------------------------------------------
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> > STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> > STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> > -----------------------------------------------------------
> > 
> > 
> > Has anyone encountered this problem before? Am I doing something wrong?
> > 
> > Thanks
> > 
> > Jeff Kittrell
> > Department of Genetics, Cell Biology & Anatomy
> > University of Nebraska Medical Center
> > 985805 Nebraska Medical Center
> > Omaha, NE 68198-5805
> > 
> > Query= 78065535
> > 
> > Length=523
> > Score E
> > Sequences producing significant alignments: (Bits) Value
> > 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> > 
> > 
> > > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> > receptor 123 (GPR123), mRNA
> > Length=4298
> > 
> > Score = 576 bits (638), Expect = 1e-163
> > Identities = 466/583 (80%), Gaps = 82/583 (14%)
> > Strand=Plus/Minus
> > 
> > Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> > ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> > Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> > 
> > Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> > |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> > Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> > 
> > Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> > |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> > Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> > 
> > Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> > ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> > Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> > 
> > Query ------------------------------------------------------------ 
> > 
> > Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> > 
> > Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> > |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> > Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> > 
> > Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> > ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> > Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> > 
> > Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> > |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> > Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> > 
> > Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> > ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> > Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> > 
> > Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> > ||||||||||||||||||||||||||||||| ||| || ||||
> > Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> > 
> > 
> > 
> > Lambda K H
> > 0.634 0.408 0.912 
> > 
> > Gapped
> > Lambda K H
> > 0.625 0.410 0.780 
> > 
> > Effective search space used: 47712920310
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 



From abualiga2 at gmail.com  Thu Sep  8 14:34:41 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 14:34:41 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
	<2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
Message-ID: <CANPzzTvxce3b=-bBUh9xNsda=1HrO9X6tRLhZAN5jhxpkKMLAQ@mail.gmail.com>

many thanks again, Chris! I was reading Programming Perl, but this sums it
up better.

On Thu, Sep 8, 2011 at 2:27 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

> On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:
>
> > thanks, Chris! works perfect.
> > To make sure I understand what's going on, forcing list context on $locus
> allows me to get one value at a time,...
>
> You have to be careful in this circumstance; doing this:
>
>   my $foo = @bar;
>
> is scalar context on a list, which returns the number of elements in @bar.
>  The following
>
>   my ($foo) = @bar;
>
> forces list context and assigns the first value in @bar to $foo but tosses
> the rest.  If you are sure there is only one value in @bar anyway, the above
> is fine (and is a common perl idiom).
>
> > which is then concatenated with \t to concatenated functions.
>
> I'm just using a simple join() to print off the results.  Note the second
> element in the join list is an embedded join() with comma-sep values for
> functions.
>
> chris
>
> > thanks again!
> >
> > galeb
> >
> > On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
> > There is no need to do that if one is using the Bio::SeqFeatureI
> interface.  Note that get_tag_values always returns a list, so to snag a
> single value for a tag in a scalar, force list context on the LHS by
> enclosing the variable in ().
> >
> > chris
> >
> > -----------------------------
> > #!/usr/bin/env perl
> >
> > use Modern::Perl;
> > use Bio::SeqIO;
> >
> > my $in = Bio::SeqIO->new(-format => 'genbank',
> >                         -file => shift);
> >
> > while (my $seq = $in->next_seq) {
> >   for my $feat ($seq->get_SeqFeatures) {
> >       next unless $feat->primary_tag eq 'CDS';
> >       my ($locus) = $feat->has_tag('locus_tag') ?
> >                     $feat->get_tag_values('locus_tag') : '';
> >       my @funcs = $feat->has_tag('function') ?
> >           $feat->get_tag_values('function') : ();
> >       say join("\t", $locus, join(',', at funcs));
> >   }
> > }
> >
> >
> >
>
>

From David.Messina at sbc.su.se  Fri Sep  9 05:40:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 11:40:25 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
Message-ID: <CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>

Hi Manju,


But this is not showing all query coverage as it shows in simple balst.(see
> attached file)
>

I'm not sure what you mean by query coverage here, as blast report you
attached doesn't (as far as I can see) include a calculation of the number
or percentage of query bases covered.

But in any case, everything in that blast report is available in the
Bio::SearchIO object that B::T::R::RemoteBlast returns. Have you taken a
look at http://www.bioperl.org/wiki/HOWTO:SearchIO ? That, along with the
module documentation, should help you find the parts of the BLAST report
you're looking for.



> and i also want to write that result in a blast file..Is there any method
> which can write the remoteblast output
> in a file with blast extension?
>

It is possible to write out the results in a format that closely resembles
the native blast report, but it's not recommended. If you want to just run
BLAST and get back a report, there's no need to use BioPerl to parse the
report first and then recreate the report.

This might also be a good time to mention that, if you're doing more than a
few hundred BLAST searches, you'll find it much more efficient to download
the database and the BLAST program from NCBI and run them on your own
computer. NCBI severely limits the speed and frequency of remote BLASTs, and
furthermore it's much more prone to failure.

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
remotely without BioPerl. Check out the --remote command-line option ? it's
my favorite new feature!


Dave


From David.Messina at sbc.su.se  Fri Sep  9 06:53:01 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 12:53:01 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
Message-ID: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>

If you don't want to learn how to do this in BioPerl, then take my previous
suggestion and just use NCBI's tools:

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
> remotely without BioPerl. Check out the --remote command-line option





On Fri, Sep 9, 2011 at 12:07, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I dont no more about Bioperl....
> and i just want to blast my sequences using bioperl...
> ans see the result in a file...
> pls tell me what should i do???
>

From manju.rawat2 at gmail.com  Fri Sep  9 07:05:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 07:05:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
Message-ID: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>

I want to learn...and i am learing it from starting...
My main query is I want to make a program which gives me that
result(sequence) which have no blast result(no matches in any database/or
particular database).
for this i have to do blast may time....but i am not getting desired result
in blast...this is the main problem which i am facing..
now pls tell me whta procedure i should follow...


Manju

From cjfields at illinois.edu  Fri Sep  9 09:03:26 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 9 Sep 2011 13:03:26 +0000
Subject: [Bioperl-l] blast result not matching.
In-Reply-To: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
	<CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
Message-ID: <AB17FEA3-524D-43EC-8C55-FAF7339FAE4A@illinois.edu>

If you are planning on looking against 'everything' (e.g. nt or nr), and you have many sequences to run, I would follow Dave's suggestion and download BLAST locally.  

chris

On Sep 9, 2011, at 6:05 AM, Manju Rawat wrote:

> I want to learn...and i am learing it from starting...
> My main query is I want to make a program which gives me that
> result(sequence) which have no blast result(no matches in any database/or
> particular database).
> for this i have to do blast may time....but i am not getting desired result
> in blast...this is the main problem which i am facing..
> now pls tell me whta procedure i should follow...
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From manju.rawat2 at gmail.com  Fri Sep  9 05:01:55 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 05:01:55 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
Message-ID: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>

Thanks to all..Its working..
I tried that module...and got the result follwing result in terminal...


waiting......db is All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
hit name is ref|NM_181451.1|
score is 240
hit name is ref|NM_001008415.1|
score is 234
hit name is ref|XM_002706247.1|
score is 212
hit name is ref|XM_002683856.1|
score is 208
hit name is gb|EF197120.1|
score is 208
hit name is ref|XR_083566.1|
score is 198
hit name is ref|NM_001097567.1|
score is 198
hit name is ref|NM_001098089.1|
score is 198
hit name is ref|XM_002699708.1|
score is 192
hit name is ref|XM_592786.5|
score is 192
hit name is ref|XM_001251693.3|
score is 192
hit name is gb|AF490400.1|
score is 190
hit name is gb|AY075103.1|
score is 190
hit name is ref|XR_083457.1|
score is 178


But this is not showing all query coverage as it shows in simple balst.(see
attached file)
and i also want to write that result in a blast file..Is there any method
which can write the remoteblast output
in a file with blast extension?


Thanks
Manju Rawat.
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From ross at cuhk.edu.hk  Sat Sep 10 02:39:23 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 10 Sep 2011 14:39:23 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick file
Message-ID: <048a01cc6f84$60c41090$224c31b0$@edu.hk>

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"

 

What's the problem? 

 

use Bio::TreeIO;

 

($treefh) = @ARGV;

 

my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;

 

$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);

 

my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);

 

my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";

 

 

#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;


From greg at ebi.ac.uk  Sat Sep 10 11:39:52 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Sat, 10 Sep 2011 16:39:52 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
Message-ID: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>

Hi Ross,

Which version of BioPerl are you using?

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
the following script works for me. Do those values look sensible to you? The
code on the new branch is a bit experimental, so I wouldn't be surprised if
all the edge cases for calculations like this aren't covered.

--greg

use Bio::TreeIO;

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");
my $tree = $treeio->next_tree;
my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");
my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");
my $ma = $tree->find("Mycobacterium_abscessus");
my $distance = $mt->distance($ma);
print "MT - MA: ".$mt->distance($ma)."\n";
print "MT - MS: ".$mt->distance($ms)."\n";
print "MS - MA: ".$ms->distance($ma)."\n";
# MT - MA: 0.24326
# MT - MS: 0.18573
# MS - MA: 0.20729

--greg

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From ross at cuhk.edu.hk  Sat Sep 10 19:06:44 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 11 Sep 2011 07:06:44 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
Message-ID: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>

Hi Greg,

 

The values are correct! However, how to install this bioperl-live module? my
bioperl is 1.6.1 but there's an error:

 

Can't locate object method "find" via package "Bio::Tree::Tree" at
TreeCalDist.pl line 32, <GEN0> line 1.

my $mt = $tree->find($keyword);  #line 32

 

 

From: gjuggler at gmail.com [mailto:gjuggler at gmail.com] On Behalf Of Gregory
Jordan
Sent: 2011??9??10?? 23:40
To: bioperl-l List; Ross KK Leung
Subject: Re: [Bioperl-l] fail to obtain node-to-node distance from a newick
file

 

Hi Ross,

 

Which version of BioPerl are you using?

 

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree
/NodeFunctionsI.pm#L406) the following script works for me. Do those values
look sensible to you? The code on the new branch is a bit experimental, so I
wouldn't be surprised if all the edge cases for calculations like this
aren't covered.

 

--greg

 

use Bio::TreeIO;

 

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");

my $tree = $treeio->next_tree;

my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");

my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");

my $ma = $tree->find("Mycobacterium_abscessus");

my $distance = $mt->distance($ma);

print "MT - MA: ".$mt->distance($ma)."\n";

print "MT - MS: ".$mt->distance($ms)."\n";

print "MS - MA: ".$ms->distance($ma)."\n";

# MT - MA: 0.24326

# MT - MS: 0.18573

# MS - MA: 0.20729

 

--greg

 

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"



What's the problem?



use Bio::TreeIO;



($treefh) = @ARGV;



my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;



$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);



my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);



my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";





#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 



From manju.rawat2 at gmail.com  Mon Sep 12 01:37:35 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:37:35 -0400
Subject: [Bioperl-l] no blast result
Message-ID: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>

Hello,
I want to make a program which first generate the random sequence and then
gives me that result(sequence) which have no blast result(no matches in any
database/or particular database).Is there any body who can help me in doing
this.

Pl reply if anybody knows about it..
Thanks
Manju

From zhangchnxp at gmail.com  Mon Sep 12 01:51:59 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 13:51:59 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
Message-ID: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>

Hi,

IMHO, due to the nature of BLAST, it is usually impossible to get no results
from random sequence, but to get a set of matches with lower scores.

What you can do is to focus on the e-value, say, setting a threshold to it.

FYI, http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

On Mon, Sep 12, 2011 at 1:37 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Hello,
> I want to make a program which first generate the random sequence and then
> gives me that result(sequence) which have no blast result(no matches in any
> database/or particular database).Is there any body who can help me in doing
> this.
>
> Pl reply if anybody knows about it..
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From manju.rawat2 at gmail.com  Mon Sep 12 01:58:38 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:58:38 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
Message-ID: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>

Ya i know this....And it is also in my use if i get result with lower
scores.
But how could I do this?


Manju

From zhangchnxp at gmail.com  Mon Sep 12 02:04:17 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 14:04:17 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
Message-ID: <CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>

Please read the documentation for Bio::Tools::Run::StandAloneBlast
and Bio::AlignIO.*
*
On Mon, Sep 12, 2011 at 1:58 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Ya i know this....And it is also in my use if i get result with lower
> scores.
> But how could I do this?
>
>
> Manju
>

From manju.rawat2 at gmail.com  Mon Sep 12 07:12:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 07:12:40 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
Message-ID: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>

I read this..but default program is not runnig fine.it showing many error
that

MSG: cannot find path to blastall..
Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

Am this this is not showing output which i want..

Pl help me..

Manju Rawat

From arguelloj at gmail.com  Sun Sep 11 22:52:42 2011
From: arguelloj at gmail.com (J. Fernando Arguello)
Date: Sun, 11 Sep 2011 19:52:42 -0700
Subject: [Bioperl-l] BioPerl - quick general question
Message-ID: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>

Dear BioPerl,

I'm excited to see a project like this! Basically I have a computer science
background with a few years of development, research and minimal
bioinformatics experience.

Dumb question...where is the best place for a developer to begin on the
BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
BioPerl in the future?

Any input is much appreciated. Thank you all for your time.

Best,
Fernando
jfa

From briano at bioteam.net  Mon Sep 12 09:20:36 2011
From: briano at bioteam.net (Brian Osborne)
Date: Mon, 12 Sep 2011 09:20:36 -0400
Subject: [Bioperl-l] Fwd: cds sequence extract
References: <112c4ef2.641e.1325c4b21cb.Coremail.maliang7121@163.com>
Message-ID: <671CAF11-55A4-462A-BC5B-805C87E1EB0E@bioteam.net>

Liang Ma,

I'm forwarding this to the Bioperl mailing list.

If you're starting out with Bioperl I suggest you read this:

http://www.bioperl.org/wiki/HOWTO:Beginners

Brian O.


Begin forwarded message:

> From: maliang7121 <maliang7121 at 163.com>
> Date: September 12, 2011 2:20:20 AM EDT
> To: briano at bioteam.net
> Subject: cds sequence extract
> 
> Dear Brian:
> 
> I am a student of Chinese Academy of Sience, I begin to love bioperl, but now I have a problem.
> 
> According to the script of the attachment, I could easily dowload sequences from NCBI, now I need extract cds sequence from the genbank format files, and put them all in a single file using fasta format, I can not do it, could you spend a few minite wrinting a script for me?
> 
> Best!
> 
> Liang Ma
> 
> 
> 

Brian O.
--
Brian Osborne, PhD
BioTeam: http://bioteam.net
email: briano at bioteam.net
mobile: 978-317-3101

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From fs5 at sanger.ac.uk  Mon Sep 12 09:54:21 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Mon, 12 Sep 2011 14:54:21 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
Message-ID: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>

looks like BLAST is not install on your system. The BioPerl module only
runs BLAST for you and parses the output but you still need the BLAST
executables installed on your system. Follow the instructions on the
NCBI website to download and install BLAST and try running it on the
commandline with the "blastall" command. If that works then you can run
it also via BioPerl.
Frank


On Mon, 2011-09-12 at 07:12 -0400, Manju Rawat wrote:
> I read this..but default program is not runnig fine.it showing many error
> that
> 
> MSG: cannot find path to blastall..
> Use of uninitialized value $_[0] in join or string at
> /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> Am this this is not showing output which i want..
> 
> Pl help me..
> 
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From p.j.a.cock at googlemail.com  Mon Sep 12 10:00:30 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 12 Sep 2011 15:00:30 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>

On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
> looks like BLAST is not install on your system. The BioPerl module only
> runs BLAST for you and parses the output but you still need the BLAST
> executables installed on your system. Follow the instructions on the
> NCBI website to download and install BLAST and try running it on the
> commandline with the "blastall" command. If that works then you can run
> it also via BioPerl.
> Frank

Hang on - blastall is from the "legacy" BLAST suite, does
BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
blastn and blastp rather then blastall)?

Peter

From cjfields at illinois.edu  Mon Sep 12 13:45:56 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 12 Sep 2011 17:45:56 +0000
Subject: [Bioperl-l] BioPerl - quick general question
In-Reply-To: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
References: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
Message-ID: <62B9B300-96AC-4511-A1B9-CFF36CBE6288@illinois.edu>

On Sep 11, 2011, at 9:52 PM, J. Fernando Arguello wrote:

> Dear BioPerl,
> 
> I'm excited to see a project like this! Basically I have a computer science
> background with a few years of development, research and minimal
> bioinformatics experience.
> 
> Dumb question...where is the best place for a developer to begin on the
> BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
> BioPerl in the future?

The basic starting point: the HOWTOs and the tutorial (not sure how up-to-date some of the latter are, in general they should work):

http://www.bioperl.org/wiki/HOWTOs
http://www.bioperl.org/wiki/Tutorials

> Any input is much appreciated. Thank you all for your time.
> 
> Best,
> Fernando
> jfa

We gladly welcome anyone willing to hack on BioPerl.  The repository is now on github (core is https://github.com/bioperl/bioperl-live), so it's fairly easy to fork the code and make changes.  We are in the middle of splitting up the large codebase into more manageable subdistributions, so it's probably a good idea to ask on list about specific code in case the code is question resides in a separate repository.  

Let us know if you have additional questions!

Cheers!

chris



From shalabh.sharma7 at gmail.com  Mon Sep 12 14:00:16 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Mon, 12 Sep 2011 14:00:16 -0400
Subject: [Bioperl-l] Module for SOCS
Message-ID: <CAA7rn9d37ntxbtMUR3Z41JHTNZypi+2jZQunwGJ5bN8DZ21xtg@mail.gmail.com>

Hi All,
         I am using SOCS for mapping my SOILD data. I was just wondering if
there is any module in bioperl to analyze SOCS output files directly or
mapreads format.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

From greg at ebi.ac.uk  Tue Sep 13 04:30:58 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Tue, 13 Sep 2011 09:30:58 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
Message-ID: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>

Hi Ross,

I don't typically 'install' versions of BioPerl from GitHub. Rather, I check
out the code into a directory that's on my Perl search path (and make sure
any other BioPerl code isn't on the path anymore). I think the following
commands should get you the right set of code:

> git clone git://github.com/bioperl/bioperl-live.git
> git checkout topic/tree_api_refresh

After that, I'm afraid I'll have to leave it to you (or someone else on the
list). I'm no Perl guru, so I don't know the "right" way to direct Perl
towards a developmental BioPerl branch.

Cheers,
 Greg

2011/9/11 Ross KK Leung <ross at cuhk.edu.hk>

> Hi Greg,****
>
> ** **
>
> The values are correct! However, how to install this bioperl-live module?
> my bioperl is 1.6.1 but there's an error:****
>
> ** **
>
> Can't locate object method "find" via package "Bio::Tree::Tree" at
> TreeCalDist.pl line 32, <GEN0> line 1.****
>
> my $mt = $tree->find($keyword);  #line 32****
>
> ** **
>
> ** **
>
> *From:* gjuggler at gmail.com [mailto:gjuggler at gmail.com] *On Behalf Of *Gregory
> Jordan
> *Sent:* 2011?9?10? 23:40
> *To:* bioperl-l List; Ross KK Leung
> *Subject:* Re: [Bioperl-l] fail to obtain node-to-node distance from a
> newick file****
>
> ** **
>
> Hi Ross,****
>
> ** **
>
> Which version of BioPerl are you using?****
>
> ** **
>
> With the refactored tree code (available from the tree_api_refresh branch
> on the BioPerl github repo:
> https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
> the following script works for me. Do those values look sensible to you? The
> code on the new branch is a bit experimental, so I wouldn't be surprised if
> all the edge cases for calculations like this aren't covered.****
>
> ** **
>
> --greg****
>
> ** **
>
> use Bio::TreeIO;****
>
> ** **
>
> my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");**
> **
>
> my $tree = $treeio->next_tree;****
>
> my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");****
>
> my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");****
>
> my $ma = $tree->find("Mycobacterium_abscessus");****
>
> my $distance = $mt->distance($ma);****
>
> print "MT - MA: ".$mt->distance($ma)."\n";****
>
> print "MT - MS: ".$mt->distance($ms)."\n";****
>
> print "MS - MA: ".$ms->distance($ma)."\n";****
>
> # MT - MA: 0.24326****
>
> # MT - MS: 0.18573****
>
> # MS - MA: 0.20729****
>
> ** **
>
> --greg****
>
> ** **
>
> On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:**
> **
>
> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l****
>
> ** **
>


From manju.rawat2 at gmail.com  Tue Sep 13 07:20:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 13 Sep 2011 07:20:07 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>

this is the perl code

 #!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO
use Bio::Tools::Run::StandAloneBlast;
 @params = ('database' => 'swissprot',
        'READMETHOD' => 'Blastn');

 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);


 $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
 $blast_report = $factory->blastall($input);


  write_blast(">rs.blast",$blast_report);


It showing error that


Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

MSG: cannot find path to blastall

From fs5 at sanger.ac.uk  Tue Sep 13 11:09:24 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Tue, 13 Sep 2011 16:09:24 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
Message-ID: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>

Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
StandAloneBlast is still set to "blastall" - I'm not sure if it works
with blast+ too.

Manju: as I said previously, you need to check that you can run BLAST on
the command line, i.e. make sure it is actually installed on your
system. Have you done that?
You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
you can manually set the path to your BLAST executable if it is not in
your path. You have to install BLAST fisrt before you can run this
module.
The other error you get from yuor code refers to something that is
outside of the code fragment you show here, so can't comment on that
one.

Frank


On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> this is the perl code
> 
>  #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO
> use Bio::Tools::Run::StandAloneBlast;
>  @params = ('database' => 'swissprot', 
>         'READMETHOD' => 'Blastn');
> 
>  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> 
> 
>  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
>  $blast_report = $factory->blastall($input);
>  
> 
>   write_blast(">rs.blast",$blast_report);
> 
> 
> It showing error that
> 
> 
> Use of uninitialized value $_[0] in join or string
> at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> MSG: cannot find path to blastall
> 
>  



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From David.Messina at sbc.su.se  Tue Sep 13 11:34:20 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 13 Sep 2011 17:34:20 +0200
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAM3TQQWx_QQK96etWHntvmRRnjJ9ZPCJYMcC0rukNoJD5_et1w@mail.gmail.com>

There's a separate Bio::Tools::Run::BlastPlus module for blast+. And a
related HOWTO:
http://www.bioperl.org/wiki/HOWTO:BlastPlus



On Tue, Sep 13, 2011 at 17:09, Frank Schwach <fs5 at sanger.ac.uk> wrote:

> Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
> StandAloneBlast is still set to "blastall" - I'm not sure if it works
> with blast+ too.
>
> Manju: as I said previously, you need to check that you can run BLAST on
> the command line, i.e. make sure it is actually installed on your
> system. Have you done that?
> You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
> you can manually set the path to your BLAST executable if it is not in
> your path. You have to install BLAST fisrt before you can run this
> module.
> The other error you get from yuor code refers to something that is
> outside of the code fragment you show here, so can't comment on that
> one.
>
> Frank
>
>
> On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> > this is the perl code
> >
> >  #!usr/bin/perl -w
> > use Bio::Perl;
> > use Bio::SearchIO
> > use Bio::Tools::Run::StandAloneBlast;
> >  @params = ('database' => 'swissprot',
> >         'READMETHOD' => 'Blastn');
> >
> >  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> >
> >
> >  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
> >  $blast_report = $factory->blastall($input);
> >
> >
> >   write_blast(">rs.blast",$blast_report);
> >
> >
> > It showing error that
> >
> >
> > Use of uninitialized value $_[0] in join or string
> > at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> >
> > MSG: cannot find path to blastall
> >
> >
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From cjfields at illinois.edu  Tue Sep 13 15:36:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 13 Sep 2011 19:36:21 +0000
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>

On Sep 12, 2011, at 9:00 AM, Peter Cock wrote:

> On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
>> looks like BLAST is not install on your system. The BioPerl module only
>> runs BLAST for you and parses the output but you still need the BLAST
>> executables installed on your system. Follow the instructions on the
>> NCBI website to download and install BLAST and try running it on the
>> commandline with the "blastall" command. If that works then you can run
>> it also via BioPerl.
>> Frank
> 
> Hang on - blastall is from the "legacy" BLAST suite, does
> BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
> blastn and blastp rather then blastall)?
> 
> Peter

(aside: thought I sent this the other day.  never mix grant writing and open source)

Both BLAST and BLAST+ are supported via different modules.  Some users don't want to use BLAST+ for various reasons, though this may soon be out of their control when NCBI eventually stops supporting legacy BLAST entirely.

chris



From manju.rawat2 at gmail.com  Wed Sep 14 07:32:19 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 14 Sep 2011 07:32:19 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>
	<CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
Message-ID: <CAB2c7yqZ0Eb=7=GTiXidD-6_UzF8qB1JBVv+5h6+8xsR84HXuQ@mail.gmail.com>

On Wed, Sep 14, 2011 at 7:31 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I am trying to install Blast+ in my system.(ubuntu) from this link
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html.
> but i am getting error..
>
> first i downloaded the blast(ncbi-blast-2.2.25+-ia32-linux.tar.gz) from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
> .  and then extract it in the home/abc/ folder.
> after that i set the path for configuration in terminal i.e
>
> *PATH=$PATH:/home/abc/blast-2.2.25+/bin*
>
>
> but when i am  running blast -help in terminal it showing me error that
>
> error while loading shared libraries:
>  libbz2.so.1: cannot open shared object file: No such file or directory.
>
>


-- 
Regards
Manju Rawat
Project Assistant(NAIP)
Genomics Lab
ABTC,NDRI Karnal-132001,Haryana

From kumarsaurabh20 at gmail.com  Thu Sep 15 07:20:47 2011
From: kumarsaurabh20 at gmail.com (kumar Saurabh)
Date: Thu, 15 Sep 2011 13:20:47 +0200
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
Message-ID: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>

Hi,

I need to integrate the primer3 module in one of our pipeline. In a process,
I was testing the initial code given on the CPAN website. But whenever I try
to run this program its giving me error...that "Cannot locate the Object
method add_target via the package Bio::Tools:Run::Primer3Redux...."

The line of codes I am using is as follows:

# design some primers.
  # the output will be put into temp.out
  use Bio::Tools::Primer3Redux;
  use Bio::Tools::Run::Primer3Redux;
  use Bio::SeqIO;

  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
  my $seq = $seqio->next_seq;

  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
                                            -path =>
"/home/singh/Downloads/primer3-2.2.3/src/primer3_core");

  # or after the fact you can change the program_name
  $primer3->program_name('my_superfast_primer3');

  unless ($primer3->executable) {
    print STDERR "primer3 can not be found. Is it installed?\n";
    exit(-1)
  }

  # set the maximum and minimum Tm of the primer
  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);

  # Design the primers. This runs primer3 and returns a
  # Bio::Tools::Primer3::result object with the results
  # Primer3 can run in several modes (see explanation for
  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
  # either call it by its PRIMER_TASK name as in these examples:
  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
  $check_results = $primer3->check_primers();

  # Alternatively, explicitly set the PRIMER_TASK parameter and
  # use the generic 'run' method (this is mainly here for backwards
  # compatibility) :
  $primer3->PRIMER_TASK( 'pick_left_only' );
  $result = $primer3->run( $seq );

  # If no task is set and the 'run' method is called, primer3 will default
to
  # pick pcr primers.

  # see the Bio::Tools::Primer3Redux POD for
  # things that you can get from this. For example:

  print "There were ", $results->num_primer_pairs, " primer pairs\n";


Can anyone help me with this???


Best regards,
Kumar

From fs5 at sanger.ac.uk  Thu Sep 15 09:44:03 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 14:44:03 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
Message-ID: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>

Hi Kumar,

We are currently working on this module and you might want to check out
the latest version on Chris Field's github project:

https://github.com/cjfields/Bio-Tools-Primer3Redux

There will probably be some changes again once I get some time again to
work on a few points we discussed lately. You can also check out my repo
here:
https://github.com/fschwach/Bio-Tools-Primer3Redux

but I will certainly have to make changes to that code because I used
AUTOLAD in the last version, which is probably not a good idea.
My recommendation would be to use Chris' repo and see if that works for
you. If not, feedback would be much appreciated.

Cheers,

Frank




On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> Hi,
> 
> I need to integrate the primer3 module in one of our pipeline. In a process,
> I was testing the initial code given on the CPAN website. But whenever I try
> to run this program its giving me error...that "Cannot locate the Object
> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> 
> The line of codes I am using is as follows:
> 
> # design some primers.
>   # the output will be put into temp.out
>   use Bio::Tools::Primer3Redux;
>   use Bio::Tools::Run::Primer3Redux;
>   use Bio::SeqIO;
> 
>   my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>   my $seq = $seqio->next_seq;
> 
>   my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>                                             -path =>
> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> 
>   # or after the fact you can change the program_name
>   $primer3->program_name('my_superfast_primer3');
> 
>   unless ($primer3->executable) {
>     print STDERR "primer3 can not be found. Is it installed?\n";
>     exit(-1)
>   }
> 
>   # set the maximum and minimum Tm of the primer
>   $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> 
>   # Design the primers. This runs primer3 and returns a
>   # Bio::Tools::Primer3::result object with the results
>   # Primer3 can run in several modes (see explanation for
>   # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>   # either call it by its PRIMER_TASK name as in these examples:
>   $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>   $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>   $check_results = $primer3->check_primers();
> 
>   # Alternatively, explicitly set the PRIMER_TASK parameter and
>   # use the generic 'run' method (this is mainly here for backwards
>   # compatibility) :
>   $primer3->PRIMER_TASK( 'pick_left_only' );
>   $result = $primer3->run( $seq );
> 
>   # If no task is set and the 'run' method is called, primer3 will default
> to
>   # pick pcr primers.
> 
>   # see the Bio::Tools::Primer3Redux POD for
>   # things that you can get from this. For example:
> 
>   print "There were ", $results->num_primer_pairs, " primer pairs\n";
> 
> 
> Can anyone help me with this???
> 
> 
> Best regards,
> Kumar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From cjfields at illinois.edu  Thu Sep 15 10:13:38 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 15 Sep 2011 14:13:38 +0000
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>

I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 

chris

On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:

> Hi Kumar,
> 
> We are currently working on this module and you might want to check out
> the latest version on Chris Field's github project:
> 
> https://github.com/cjfields/Bio-Tools-Primer3Redux
> 
> There will probably be some changes again once I get some time again to
> work on a few points we discussed lately. You can also check out my repo
> here:
> https://github.com/fschwach/Bio-Tools-Primer3Redux
> 
> but I will certainly have to make changes to that code because I used
> AUTOLAD in the last version, which is probably not a good idea.
> My recommendation would be to use Chris' repo and see if that works for
> you. If not, feedback would be much appreciated.
> 
> Cheers,
> 
> Frank
> 
> 
> 
> 
> On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
>> Hi,
>> 
>> I need to integrate the primer3 module in one of our pipeline. In a process,
>> I was testing the initial code given on the CPAN website. But whenever I try
>> to run this program its giving me error...that "Cannot locate the Object
>> method add_target via the package Bio::Tools:Run::Primer3Redux...."
>> 
>> The line of codes I am using is as follows:
>> 
>> # design some primers.
>>  # the output will be put into temp.out
>>  use Bio::Tools::Primer3Redux;
>>  use Bio::Tools::Run::Primer3Redux;
>>  use Bio::SeqIO;
>> 
>>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>>  my $seq = $seqio->next_seq;
>> 
>>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>>                                            -path =>
>> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
>> 
>>  # or after the fact you can change the program_name
>>  $primer3->program_name('my_superfast_primer3');
>> 
>>  unless ($primer3->executable) {
>>    print STDERR "primer3 can not be found. Is it installed?\n";
>>    exit(-1)
>>  }
>> 
>>  # set the maximum and minimum Tm of the primer
>>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
>> 
>>  # Design the primers. This runs primer3 and returns a
>>  # Bio::Tools::Primer3::result object with the results
>>  # Primer3 can run in several modes (see explanation for
>>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>>  # either call it by its PRIMER_TASK name as in these examples:
>>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>>  $check_results = $primer3->check_primers();
>> 
>>  # Alternatively, explicitly set the PRIMER_TASK parameter and
>>  # use the generic 'run' method (this is mainly here for backwards
>>  # compatibility) :
>>  $primer3->PRIMER_TASK( 'pick_left_only' );
>>  $result = $primer3->run( $seq );
>> 
>>  # If no task is set and the 'run' method is called, primer3 will default
>> to
>>  # pick pcr primers.
>> 
>>  # see the Bio::Tools::Primer3Redux POD for
>>  # things that you can get from this. For example:
>> 
>>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
>> 
>> 
>> Can anyone help me with this???
>> 
>> 
>> Best regards,
>> Kumar
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From fs5 at sanger.ac.uk  Thu Sep 15 10:43:48 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 15:43:48 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
	<D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
Message-ID: <1316097828.3797.700.camel@deskpro15336.internal.sanger.ac.uk>

I also haven't had the time yet to work on this again but, yes, we need
to make sure we don't loose track of where we are. 


On Thu, 2011-09-15 at 14:13 +0000, Fields, Christopher J wrote:
> I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 
> 
> chris
> 
> On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:
> 
> > Hi Kumar,
> > 
> > We are currently working on this module and you might want to check out
> > the latest version on Chris Field's github project:
> > 
> > https://github.com/cjfields/Bio-Tools-Primer3Redux
> > 
> > There will probably be some changes again once I get some time again to
> > work on a few points we discussed lately. You can also check out my repo
> > here:
> > https://github.com/fschwach/Bio-Tools-Primer3Redux
> > 
> > but I will certainly have to make changes to that code because I used
> > AUTOLAD in the last version, which is probably not a good idea.
> > My recommendation would be to use Chris' repo and see if that works for
> > you. If not, feedback would be much appreciated.
> > 
> > Cheers,
> > 
> > Frank
> > 
> > 
> > 
> > 
> > On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> >> Hi,
> >> 
> >> I need to integrate the primer3 module in one of our pipeline. In a process,
> >> I was testing the initial code given on the CPAN website. But whenever I try
> >> to run this program its giving me error...that "Cannot locate the Object
> >> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> >> 
> >> The line of codes I am using is as follows:
> >> 
> >> # design some primers.
> >>  # the output will be put into temp.out
> >>  use Bio::Tools::Primer3Redux;
> >>  use Bio::Tools::Run::Primer3Redux;
> >>  use Bio::SeqIO;
> >> 
> >>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
> >>  my $seq = $seqio->next_seq;
> >> 
> >>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
> >>                                            -path =>
> >> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> >> 
> >>  # or after the fact you can change the program_name
> >>  $primer3->program_name('my_superfast_primer3');
> >> 
> >>  unless ($primer3->executable) {
> >>    print STDERR "primer3 can not be found. Is it installed?\n";
> >>    exit(-1)
> >>  }
> >> 
> >>  # set the maximum and minimum Tm of the primer
> >>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> >> 
> >>  # Design the primers. This runs primer3 and returns a
> >>  # Bio::Tools::Primer3::result object with the results
> >>  # Primer3 can run in several modes (see explanation for
> >>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
> >>  # either call it by its PRIMER_TASK name as in these examples:
> >>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
> >>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
> >>  $check_results = $primer3->check_primers();
> >> 
> >>  # Alternatively, explicitly set the PRIMER_TASK parameter and
> >>  # use the generic 'run' method (this is mainly here for backwards
> >>  # compatibility) :
> >>  $primer3->PRIMER_TASK( 'pick_left_only' );
> >>  $result = $primer3->run( $seq );
> >> 
> >>  # If no task is set and the 'run' method is called, primer3 will default
> >> to
> >>  # pick pcr primers.
> >> 
> >>  # see the Bio::Tools::Primer3Redux POD for
> >>  # things that you can get from this. For example:
> >> 
> >>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
> >> 
> >> 
> >> Can anyone help me with this???
> >> 
> >> 
> >> Best regards,
> >> Kumar
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > 
> > 
> > -- 
> > The Wellcome Trust Sanger Institute is operated by Genome Research 
> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose registered 
> > office is 215 Euston Road, London, NW1 2BE. 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From manju.rawat2 at gmail.com  Fri Sep 16 01:09:25 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:09:25 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>

Hello Frank,

Yes,u r rite..I tried to run blast in terminal but its not working..
I have installed the latest version of blast and download the database
correctly..

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.
Manju

From manju.rawat2 at gmail.com  Fri Sep 16 01:12:03 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:12:03 -0400
Subject: [Bioperl-l] Command line error in BLAST+
Message-ID: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>

Hi,


I have installed the latest version of blast and download the database
correctly Using this tutorial
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.

Thanks
Manju

From p.j.a.cock at googlemail.com  Fri Sep 16 04:15:46 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:15:46 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <CAKVJ-_4UF=5oBNc-ZRESAXzO-tC2j+nQGn0Qjh4E51Yrvr2o3A@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:12 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
>
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
>
> Thanks
> Manju

You're using the BioPerl wrapper for legacy blast (blastall),
which is not installed. Instead you have the new blast+
suite which includes a wrapper using the perl script
legacy_blast.pl to imitate the old blastall tool (in this
case it calls the new tool blastn).

Fix 1: Edit legacy_blast.pl to use the path to blastn etc
under your home directory

Fix 2: Install BLAST+ at system level

Fix 3: Use the BioPerl wrapper for BLAST+ instead.

I'd go with option 3.

Peter

From p.j.a.cock at googlemail.com  Fri Sep 16 04:17:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:17:58 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
	<CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
Message-ID: <CAKVJ-_5Omy7h9qx++7S-46YrxFTxbGoQZu61GDgM12C2FmQJsQ@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:09 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello Frank,
>
> Yes,u r rite..I tried to run blast in terminal but its not working..
> I have installed the latest version of blast and download the database
> correctly..
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out
> Can't exec "/usr/bin/blastn": No such file or directory at
> /usr/bin/legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
> Manju

For the benefit of anyone reading the archives later,
I tried to answer this in Manju's new thread:
http://lists.open-bio.org/pipermail/bioperl-l/2011-September/035696.html

Peter

From fs5 at sanger.ac.uk  Fri Sep 16 04:36:37 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 16 Sep 2011 09:36:37 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <1316162197.3797.721.camel@deskpro15336.internal.sanger.ac.uk>

Hi Manju,

Are you on Ubuntu? I think I've seen problems with this bzip library on
Ubuntu before. It's not a problem with BLAST in any case. 
Should be possible to install the missing files through your package
manager. I'm sure Google will know what to do :)
Not sure what went wrong with your blast installation. What happens if
you run blastall directly (without the legacy_blast.pl script)? In any
case, it might be better to ask the NCBI people for help with the BLAST
installation as this is not a BioPerl problem.

cheers,

Frank


On Fri, 2011-09-16 at 01:12 -0400, Manju Rawat wrote:
> Hi,
> 
> 
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
> 
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
> 
> 
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
> 
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
> 
> I have checked everything but not able tp fine the error..
> 
> Pl help me.
> 
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From ross at cuhk.edu.hk  Fri Sep 16 04:51:38 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 16 Sep 2011 16:51:38 +0800
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
Message-ID: <085501cc744d$d90b4500$8b21cf00$@edu.hk>

I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!

 



From cjfields at illinois.edu  Fri Sep 16 09:22:07 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 16 Sep 2011 13:22:07 +0000
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <085501cc744d$d90b4500$8b21cf00$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
Message-ID: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>

That seems like a pretty straightforward thing to do; there isn't an all-in-one way of doing this, but that's a good thing (it's a separation of concerns).

1) Run and parse BLAST results and grab seqID and coordinates for each hit (or each HSP for each hit) (Bio::SearchIO)
2) Pull the right subsequence +/- 20bp using above from the indexed flat file of your reference (Bio::DB::Fasta)

You can get revcomped sequence from Bio::DB::Fasta directly by flipping coordinates:
  
  # raw sequence
  my $seq      = $db->seq('CHROMOSOME_I',4_000_000 => 4_100_000);
  my $revseq   = $db->seq('CHROMOSOME_I',4_100_000 => 4_000_000);

chris


On Sep 16, 2011, at 3:51 AM, Ross KK Leung wrote:

> I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From wsavigne at yahoo.com  Fri Sep 16 16:45:12 2011
From: wsavigne at yahoo.com (Willy Savigne)
Date: Fri, 16 Sep 2011 13:45:12 -0700 (PDT)
Subject: [Bioperl-l] question Bioperl installation
Message-ID: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>

my name is william how do download Bioperl i tried other site but NOTHING? i would like to know info in downloading? bioperl .This is my first? time into knowing? bioinformatic i? just got? a book developing bioinformatic and begginning perl bioinformatic. I do alot Dna and RNA sequencing?? and more.
?
Thank u willy

From ross at cuhk.edu.hk  Sun Sep 18 06:51:05 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 18 Sep 2011 18:51:05 +0800
Subject: [Bioperl-l] snp/frameshift identification
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <08a901cc75f0$dd463b30$97d2b190$@edu.hk>

Dear Bioperl-users,

Following Fields, Christopher J's advice on sequence extraction, I manage to
proceed to the last stage of non-synonymous SNP identification. Now what I
have in hand is thousands of reliable multiple sequence alignment files,
e.g.

>seq1
ATGACAGACACGACGTTGCCGTAG
>seq2
ATGACAGACACGACGTAGCCGTAG
>seq3
ATGACAGACACGACGTTGCCGTAG

Seq2 has a T->A mutation and that leads to a stop codon generation. I wonder
if Bioperl has handled this kind of SNP or frameshift or non-sense mutations
that lead to change of amino acid in the translated protein product.

Thanks again to the community that helps me a great deal so I can catch up
progress during this Sat/Sun!!


From rondonbio at yahoo.com.br  Mon Sep 19 09:46:36 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Mon, 19 Sep 2011 06:46:36 -0700 (PDT)
Subject: [Bioperl-l] help-> SearchIO
Message-ID: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>

Hi guys! I need your help in a loop that I have in SearchIO.
I need to check the nucleotide coverage of querys using BLAST. I'm using the script below. It's open the alignment, create arrays for each query with zeros in each nucleotide position but, when I adds values to the coverage of each nucleotide, the script does it once and passes to another query.
Can you hek me?
Thank you very much,

Rondon
a Brazilian friend.


use Bio::SearchIO;
?
my $alignment = new Bio::SearchIO ( -format => 'blastXML',
? ? ? ? ? ? ? ? ? ? ? ? ?? ? -file ? => $alignment_file );

my %positions;
while (my $result = $alignment->next_result) {
while (my $hit = $result->next_hit) {
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
my @pos = $hsp->seq_inds('query','identical');
for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
foreach my $num (@pos) {
${$positions{$query_name}}[$num -1]++; ? ?#This loop is where I believe that is an error.
}
}
}
}

foreach my $key (keys %positions){
print "$key\t@{$positions{$key}}\n";
}

exit;


From roy.chaudhuri at gmail.com  Mon Sep 19 12:29:41 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:29:41 +0100
Subject: [Bioperl-l] help-> SearchIO
In-Reply-To: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
References: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
Message-ID: <4E776DF5.6040504@gmail.com>

Hi Rondon,

The line where you populate your arrayref with 0 (starting "for 
(0..$tam)") is within the HSP loop, so the data from every successive 
HSP will overwrite the previous one in your hash. You will therefore 
only see the data for the last HSP from each query. If you move that 
line to execute once per result (i.e. just after the line starting 
"while (my result ="), then I think it should work as you intended.

Cheers,
Roy.

On 19/09/2011 14:46, Rondon Neto wrote:
> Hi guys! I need your help in a loop that I have in SearchIO. I need
> to check the nucleotide coverage of querys using BLAST. I'm using the
> script below. It's open the alignment, create arrays for each query
> with zeros in each nucleotide position but, when I adds values to the
> coverage of each nucleotide, the script does it once and passes to
> another query. Can you hek me? Thank you very much,
>
> Rondon a Brazilian friend.
>
> use Bio::SearchIO;
>
> my $alignment = new Bio::SearchIO ( -format =>  'blastXML',
>                               -file   =>  $alignment_file );
>
> my %positions;
> while (my $result = $alignment->next_result) {
> while (my $hit = $result->next_hit) {
> while (my $hsp = $hit->next_hsp) {
> my $query_name = $result->query_name();
> my $tam = $result ->  query_length();
> my @pos = $hsp->seq_inds('query','identical');
> for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
> foreach my $num (@pos) {
> ${$positions{$query_name}}[$num -1]++;    #This loop is where I believe that is an error.
> }
> }
> }
> }
>
> foreach my $key (keys %positions){
> print "$key\t@{$positions{$key}}\n";
> }
>
> exit;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From roy.chaudhuri at gmail.com  Mon Sep 19 12:39:40 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:39:40 +0100
Subject: [Bioperl-l] question Bioperl installation
In-Reply-To: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
References: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
Message-ID: <4E77704C.20604@gmail.com>

Hi Willy,

There are instructions for downloading and installing BioPerl on the wiki:
http://www.bioperl.org/wiki/Getting_BioPerl
http://www.bioperl.org/wiki/Installing_BioPerl

These are the first two results when you Google for "bioperl download".

Note that the wiki is a little out of date, the latest BioPerl version 
is 1.6.901:
http://search.cpan.org/~cjfields/BioPerl-1.6.901/

Cheers,
Roy.

On 16/09/2011 21:45, Willy Savigne wrote:
> my name is william how do download Bioperl i tried other site but
> NOTHING  i would like to know info in downloading  bioperl .This is
> my first  time into knowing  bioinformatic i  just got  a book
> developing bioinformatic and begginning perl bioinformatic. I do alot
> Dna and RNA sequencing   and more.
>
> Thank u willy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From bosborne11 at verizon.net  Tue Sep 20 13:01:21 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 13:01:21 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
Message-ID: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>

All,

I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:

..... get the files etc ....

my %alignparams = (
    -seqtype  => 'nucleo',
    -usetree_nowarn => $guidetreefile,
    -in => $tempfile
);
my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);

# $align is a Bio::SimpleAlign object
my $align = $aligner->align($tempfile);

my %treeparams = (
   -data_type => 'nt',
   -model     => 'K80',  # Kimura
   -tree      => 'BIONJ',
   -bootstrap => 1000
);
my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);

#$tree is a Bio::Tree::Tree object
my $tree = $treemaker->run($align);

My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:

$distance = $tree->subtree_length($internal_node)

Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!

Brian O.

From bosborne11 at verizon.net  Tue Sep 20 15:17:13 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 15:17:13 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
In-Reply-To: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
References: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
Message-ID: <A2EDBACB-963C-4E1C-8E7A-5F769BE89476@verizon.net>

Ah, I see:

my $distances = $tree->distance(-nodes => [$node1,$node2]);

Brian O.


On Sep 20, 2011, at 1:01 PM, Brian Osborne wrote:

> All,
> 
> I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:
> 
> ..... get the files etc ....
> 
> my %alignparams = (
>    -seqtype  => 'nucleo',
>    -usetree_nowarn => $guidetreefile,
>    -in => $tempfile
> );
> my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);
> 
> # $align is a Bio::SimpleAlign object
> my $align = $aligner->align($tempfile);
> 
> my %treeparams = (
>   -data_type => 'nt',
>   -model     => 'K80',  # Kimura
>   -tree      => 'BIONJ',
>   -bootstrap => 1000
> );
> my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);
> 
> #$tree is a Bio::Tree::Tree object
> my $tree = $treemaker->run($align);
> 
> My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:
> 
> $distance = $tree->subtree_length($internal_node)
> 
> Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!
> 
> Brian O.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From manju.rawat2 at gmail.com  Thu Sep 22 07:07:39 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 22 Sep 2011 16:37:39 +0530
Subject: [Bioperl-l] database for Bos Touras
Message-ID: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>

Hello To All,

I want to blast my sequence Only in Bos Touras Database Using Local
Blast(Blast+).
But I dnt Know which database I should use for this From this Link.
ftp://ftp.ncbi.nlm.nih.gov/blast/db/

Pl tell me which DB I Should use??

Thanks
Manju

From hrh at fmi.ch  Thu Sep 22 07:44:56 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 13:44:56 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
Message-ID: <4E7B1FB8.8090208@fmi.ch>


assuming you mean 'Bos taurus', it might be easier to get the data from

ucsc:  http://hgdownload.cse.ucsc.edu/downloads.html#cow

or ensembl: ftp://ftp.ensembl.org/pub/release-64/fasta/bos_taurus/dna/



Regards, Hans



On 09/22/2011 01:07 PM, Manju Rawat wrote:
> Hello To All,
>
> I want to blast my sequence Only in Bos Touras Database Using Local
> Blast(Blast+).
> But I dnt Know which database I should use for this From this Link.
> ftp://ftp.ncbi.nlm.nih.gov/blast/db/
>
> Pl tell me which DB I Should use??
>
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From hrh at fmi.ch  Thu Sep 22 08:16:00 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 14:16:00 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
	<4E7B1FB8.8090208@fmi.ch>
	<CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
Message-ID: <4E7B2700.8080904@fmi.ch>


Yes, BLAST uses fasta files. You (may need to concatenate the individual 
chromosomes and the you) need to index them with 'makeblastdb' which is 
also part of the blast+ software package.

see: http://www.ncbi.nlm.nih.gov/books/NBK1762/


Hans

On 09/22/2011 01:49 PM, Manju Rawat wrote:
> It will work on Local Blast or not??????

From bosborne11 at verizon.net  Thu Sep 22 12:16:39 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 22 Sep 2011 12:16:39 -0400
Subject: [Bioperl-l] [bioperl-live] genbank_ref_extractor: new script to
 make search on entrez gene and retrieve related sequences (#23)
In-Reply-To: <bioperl/bioperl-live/pull/23@github.com>
References: <bioperl/bioperl-live/pull/23@github.com>
Message-ID: <245C75D5-61EC-4395-B64F-47D8471568F5@verizon.net>

Carne,

This is impressive looking, it is now in scripts/.

Thanks again,

Brian O.

On Sep 21, 2011, at 11:25 AM, Carn? Draug wrote:

> Hi
> 
> I wrote a script with bioperl that I would like to share back. It takes a list of searches for Entrez Gene and attempts to retrieve the related sequences (genomic, transcripts and proteins). It is also possible to obtain extra upstream and downstream bp for genomic sequences and control the naming of the files. In the end it can save all the results in a CSV file.
> 
> Hope you find it up to your coding standards. Suggestions for improvements are welcome, including for a better name.
> 
> Carn?
> 
> You can merge this Pull Request by running:
> 
>  git pull https://github.com/carandraug/bioperl-live bp_genbank_ref_extractor
> 
> Or you can view, comment on it, or merge it online at:
> 
>  https://github.com/bioperl/bioperl-live/pull/23
> 
> -- Commit Summary --
> 
> * genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences
> 
> -- File Changes --
> 
> A scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl (1064)
> 
> -- Patch Links --
> 
>  https://github.com/bioperl/bioperl-live/pull/23.patch
>  https://github.com/bioperl/bioperl-live/pull/23.diff
> 
> -- 
> Reply to this email directly or view it on GitHub:
> https://github.com/bioperl/bioperl-live/pull/23



From bluecurio at gmail.com  Thu Sep 22 15:32:07 2011
From: bluecurio at gmail.com (Daniel Renfro)
Date: Thu, 22 Sep 2011 14:32:07 -0500
Subject: [Bioperl-l] Download RefSeq revision history programmatically
Message-ID: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>

I am working on a project to find historical differences in GenBank/RefSeq files. I would like to download all the old revisions of a file (for example NC_000913 [http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2?report=girevhist]) using any technology available. I wrote a page-scraper in Perl, but I can't get NCBI to return plaintext, only HTML (which does nobody any good.) 

Does anyone know of a way to get all the "revisions" (not just "versions") of a GenBank/RefSeq file?

-Daniel 
--
http://ecoliwiki.net/User:DanielRenfro
Hu Lab Research Associate
979-862-4055


From ross at cuhk.edu.hk  Tue Sep 27 10:16:14 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 27 Sep 2011 22:16:14 +0800
Subject: [Bioperl-l]  obtain a distance matrix from tree
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>

After using MEGA to generate a newick tree file (phylogram), I wonder if
Bioperl has any convenient functions to derive the (n x n) distance (by NJ,
MP etc) matrix. Thanks for your advice in advance!



From thomas.sharpton at gmail.com  Tue Sep 27 16:02:44 2011
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Tue, 27 Sep 2011 13:02:44 -0700
Subject: [Bioperl-l] obtain a distance matrix from tree
In-Reply-To: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
	<014201cc7d20$03abd4c0$0b037e40$@edu.hk>
Message-ID: <C2ED3ADC-B089-4481-BD63-8D5FDFB51CFA@gmail.com>

Hi Ross,

For very large trees, I found it to be more efficient to do this in R  
using the ape package. I have a script listed in my github repo that  
will convert a tree to a distance matrix via in R at the link below:

https://github.com/sharpton/PhylOTU/blob/master/tree_to_matrix.R

That said, I've also done this in Bioperl using something like the  
following:

use Bio::TreeIO;

my $treein = Bio::TreeIO->new( -fh => "input_tree.nwk", -format =>  
'newick' );
while( my $tree = $treein->next_tree ){
	my %dist_matrix = ();
	my @leaves = $tree->get_leaf_nodes;
	foreach my $leaf1( @leaves ){
		my $id1 = $leaf1->id;	
		foreach my $leaf2( @leaves ){
			my $id2 = $leaf2->id;
			next if $id1 eq $id2;
			next if( defined( $dist_matrix{$id1}->{$id2} ) || defined  
( $dist_matrix{$id2}->{$id1} ) );
			my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] );
			$dist_matrix{$id1}->{$id2} = $distance;
		}
	}
}
#print distance matrix here....

This will put the information you need to create either a full or a  
upper triangle distance matrix into the hash %dist_matrix. I didn't  
test the above, so hopefully there are no bugs....

Someone else may have a more elegant solution.

Best,
Tom

PS: Sorry if you get this twice.

On Sep 27, 2011, at 7:16 AM, Ross KK Leung wrote:

> After using MEGA to generate a newick tree file (phylogram), I  
> wonder if
> Bioperl has any convenient functions to derive the (n x n) distance  
> (by NJ,
> MP etc) matrix. Thanks for your advice in advance!
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From member at linkedin.com  Tue Sep 27 19:45:10 2011
From: member at linkedin.com (Razi Khaja via LinkedIn)
Date: Tue, 27 Sep 2011 23:45:10 +0000 (UTC)
Subject: [Bioperl-l] Invitation to connect on LinkedIn
Message-ID: <1856085440.8574001.1317167110185.JavaMail.app@ela4-bed82.prod>

LinkedIn
------------




    Razi Khaja requested to add you as a connection on LinkedIn:
  
------------------------------------------

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Accept invitation from Razi Khaja
http://www.linkedin.com/e/5drwke-gt3jaequ-6k/uez6TYkHzbaXxXM-lUk23auFwJZodcPlXc2UWC0Ao8h/blk/I3148646357_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPsRcPoQdzwQcjd9bSsPizpOoltTbP0NdPgMd3kTcPgLrCBxbOYWrSlI/EML_comm_afe/?hs=false&tok=2TjQgihXkh-kU1

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------------------------------------------


From ross at cuhk.edu.hk  Tue Sep 27 23:57:52 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 28 Sep 2011 11:57:52 +0800
Subject: [Bioperl-l]  ancestral state derived from Tree
In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
Message-ID: <017701cc7d92$cba88d20$62f9a760$@edu.hk>


By using Tom's advice, I'm able to obtain the distance matrix for the
following tree by Bioperl TreeIO. 

((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000
00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00
000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(
L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0
.00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,
(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000
):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000
00);

For the last few nodes T, U and V, they should be monophyletic but U and V
should be more closely related. Although I can use TreeIO methods like
is_monophyletic or is_paraphyletic to test in this case, the problem becomes
more tricky for nodes A, B, C, D because D actually makes no difference from
the common ancestor of nodes A, B, C and D. Since is_monophyletic does not
take into account for this case, is there any workaround? I have to pay
attention to such a detail in order to make a better guess for the ancestral
state(s) at various points of this tree.

Thanks again for the TreeIO developers for making tree analysis easier for
us biologists!


From manju.rawat2 at gmail.com  Wed Sep 28 05:54:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 28 Sep 2011 15:24:07 +0530
Subject: [Bioperl-l] how to blast a seq against multiple dbase
Message-ID: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>

Hello,

I have downloaded all the chromosome of Bos Taurus and i'd changed them in
blast format using makeblastdb..and now i want to localy blast my sequence
against these all chromosome..
now i have 29 database.Is there any method by which can i blast my sequence
against all 29 database in my program..


whta should i write in database????

@params = ('database' => '????????', 'outfile' => 'blast2.out',
        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');



Thanks
Manju Rawat

From p.j.a.cock at googlemail.com  Wed Sep 28 06:02:07 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 28 Sep 2011 11:02:07 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <CAKVJ-_7HCbvfm=mgcXEmL_9AH6A3rttnLrW86rs1ecNB0L7=XQ@mail.gmail.com>

On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello,
>
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
>
>
> whta should i write in database????
>
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
> ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn');
>

The simple answer is make a combined database. This
works internally with alias files, have a look at the NR
and NT databases for example - they act like singe
databases but are actually a collection of chunks.

Even simpler would be to combine your Bos taurus
sequence files into a single multi-entry FASTA file,
and make that into a single BLAST database.

Peter


From awitney at sgul.ac.uk  Wed Sep 28 06:42:39 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 28 Sep 2011 11:42:39 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <B2F15B1E-24EB-41B5-8BC4-07A2EF4C8286@sgul.ac.uk>


I think if you want to keep the databases separate you would need to create a factory for each database, something like this

foreach my $db ( @databases ) {
	my $factory = Bio::Tools::Run::StandAloneBlastPlus->new( -db_data => $db ,  < ? any other params ? > );

	? do blast stuff?
}

or as Peter says in another email you could combine your databases and run one query then filter them out in the results.

regards

adam

On 28 Sep 2011, at 10:54, Manju Rawat wrote:

> Hello,
> 
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
> 
> 
> whta should i write in database????
> 
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
>        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');
> 
> 
> 
> Thanks
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Wed Sep 28 07:43:02 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 12:43:02 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
Message-ID: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>

Hi everyone,

is there a recommended way to get the version of a script that is part
of bioperl (the ones in the scripts directory)? Rather than hard
coding the version of the script independent of bioperl, I thought on
using the bioperl version itself. How can this be done?

Thanks in advance,
Carn?


From carandraug+dev at gmail.com  Wed Sep 28 11:00:34 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 16:00:34 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
Message-ID: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>

2011/9/28 longbow leo <longbow0 at gmail.com>:
> Hi, Carn?,
>
> Do you mean this:
>
> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>
> In my machine, the output is

Thank you. Yes this is what I was looking for. I looked down how that
variable comes up and so I think I'll use

use Bio::Root::Version;
say $Bio::Root::Version::VERSION;

Carn?


From pcantalupo at gmail.com  Wed Sep 28 12:54:19 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 28 Sep 2011 12:54:19 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
Message-ID: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>

Hello,

I'm using the most recent copy of bioperl-live (pulled yesterday). I
have a BLASTN (from blast+) output file for 3 query sequences
(https://gist.github.com/1248342). I used this script,
https://gist.github.com/1248338, to print the query id, algorithm and
algorithm_version for each result. When I run the script, I get the
following output:

GFAVMM201BADC0 ?BLASTN ?2.2.25+
GFAVMM201A1JOH ?BLASTN
GFAVMM201D933Z ?BLASTN

Algorithm_version outputs the correct version for the first result but
outputs the empty string for the 2nd and 3rd query. Why? This
functionality worked about a month ago. What has changed to cause this
to happen?

Thank you,

Paul


From rondonbio at yahoo.com.br  Wed Sep 28 15:47:45 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Wed, 28 Sep 2011 12:47:45 -0700 (PDT)
Subject: [Bioperl-l] best Hit
Message-ID: <1317239265.98674.YahooMailNeo@web130214.mail.mud.yahoo.com>

Hi guys.?

I have this subroutine that returns a hash with nucleotide's coverage of each query from a blast alignment.
So, I want to compute uniq hits. If a hit has already been aligned with a query, it must be eliminated from my experiment.
Can anyone check if it's right or can fix it to me? Is there a way to do that directly in blast?

Thank you

Rondon Neto


sub nucleotide_coverage{
#Bio::SearchIO dependent
#This subroutine return a Hash and a file with nucleotide coverage?
#for each query in an blast alignment xlm file. The input is the
#alignment file.

my ($alignment_file) = @_;

my $alignment = new Bio::SearchIO ( -format => 'blastXML',
 ? ?-file ? => $alignment_file );my %positions;my @used_reads;
while (my $result = $alignment->next_result) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
for (0..$tam-1){ ${$positions{$query_name}}[$_] = 0 }?
while (my $hit = $result->next_hit) {
my $hit_name = $hit->name;
# Here is my best hit parser. Is it ok?
foreach my $read (@used_reads) {
if ( $read eq $hit_name ) {
next;
}
}
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my @pos = $hsp->seq_inds('query','identical');
foreach my $num (@pos) {
${$positions{$query_name}}[$num-1]++;
}
}
push (@used_reads, $hit_name);
}
}

my $outfile = "nucleotide_coverage.txt";
open OUT, ">$outfile" or die $!;foreach my $key (keys %positions){print OUT "$key\t@{$positions{$key}}\n";
}

close OUT;

return \%positions;

}

From shalabh.sharma7 at gmail.com  Wed Sep 28 15:53:07 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 28 Sep 2011 15:53:07 -0400
Subject: [Bioperl-l] Getting taxa from gi
Message-ID: <CAA7rn9dYGfeCS-qVccDcdwVenj8KFQs4i89EoT8_63gQk5b42g@mail.gmail.com>

Hi All,
        I know this has been discussed before, but this is kind of a new
problem that i am facing.
I want to get taxonomy (full linage) information from the huge list of GI's.
I am using Bio::DB:Genbak for this with perl-5.12.3.
Here is my small script.

#! /usr/local/perl-5.12.3/bin/perl -w
use strict;
use warnings;
use Bio::DB::GenBank;

my @ids = qw( CP000490 );
my $gbh = Bio::DB::GenBank->new();

foreach my $id( @ids ) {
# say "* ID: $id";
 my $seq = $gbh->get_Seq_by_acc( $id );
 my $org = $seq->species;
 #print "$org\n";
 my $class = join'-', $org->classification;
 print "$class\n";
}

The output is: Paracoccus denitrificans
PD1222-Paracoccus-Rhodobacteraceae-Rhodobacterales-Alphaproteobacteria-Proteobacteria-Bacteria
which is fine but i also want to get the taxa id, and if possible taxa ids
for all the linage classification.

ideally i would like to get something like this: 318586 - - - - - - - 1224 -
2

I would really appreciate your help.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

From cjfields at illinois.edu  Wed Sep 28 17:36:37 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:36:37 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
Message-ID: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>

On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:

> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>> Hi, Carn?,
>> 
>> Do you mean this:
>> 
>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>> 
>> In my machine, the output is
> 
> Thank you. Yes this is what I was looking for. I looked down how that
> variable comes up and so I think I'll use
> 
> use Bio::Root::Version;
> say $Bio::Root::Version::VERSION;
> 
> Carn?

Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

chris

From cjfields at illinois.edu  Wed Sep 28 17:40:48 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:40:48 +0000
Subject: [Bioperl-l] algorithm_version not working in multi-result
	blast	output
In-Reply-To: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
Message-ID: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>

Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.  

This should be an easy enough fix, but can you submit it as a bug so we can track it?

chris

On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:

> Hello,
> 
> I'm using the most recent copy of bioperl-live (pulled yesterday). I
> have a BLASTN (from blast+) output file for 3 query sequences
> (https://gist.github.com/1248342). I used this script,
> https://gist.github.com/1248338, to print the query id, algorithm and
> algorithm_version for each result. When I run the script, I get the
> following output:
> 
> GFAVMM201BADC0  BLASTN  2.2.25+
> GFAVMM201A1JOH  BLASTN
> GFAVMM201D933Z  BLASTN
> 
> Algorithm_version outputs the correct version for the first result but
> outputs the empty string for the 2nd and 3rd query. Why? This
> functionality worked about a month ago. What has changed to cause this
> to happen?
> 
> Thank you,
> 
> Paul
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Wed Sep 28 18:07:53 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 23:07:53 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
Message-ID: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>

2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>
>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>> Hi, Carn?,
>>>
>>> Do you mean this:
>>>
>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>
>>> In my machine, the output is
>>
>> Thank you. Yes this is what I was looking for. I looked down how that
>> variable comes up and so I think I'll use
>>
>> use Bio::Root::Version;
>> say $Bio::Root::Version::VERSION;
>>
>> Carn?
>
> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

Where will the scripts end up after this restructuration? What I want
is to create a version of the script (not of bioperl). Since the
script is released with bioperl, they are the same. I actually already
made the commit that makes this, just haven't bothered with the pull
request yet.

Also, will there be a release before this change?

Carn?


From shalabh.sharma7 at gmail.com  Thu Sep 29 10:37:53 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 29 Sep 2011 10:37:53 -0400
Subject: [Bioperl-l] GFF to GTF
Message-ID: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>

Hi,
    Is there any module to convert GFF file to GTF?

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

From cjfields at illinois.edu  Thu Sep 29 11:07:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 29 Sep 2011 15:07:27 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
	<CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
Message-ID: <46733E36-5795-4EB6-9C2B-C978000FFD46@illinois.edu>

On Sep 28, 2011, at 5:07 PM, Carn? Draug wrote:

> 2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
>> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>> 
>>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>>> Hi, Carn?,
>>>> 
>>>> Do you mean this:
>>>> 
>>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>> 
>>>> In my machine, the output is
>>> 
>>> Thank you. Yes this is what I was looking for. I looked down how that
>>> variable comes up and so I think I'll use
>>> 
>>> use Bio::Root::Version;
>>> say $Bio::Root::Version::VERSION;
>>> 
>>> Carn?
>> 
>> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).
> 
> Where will the scripts end up after this restructuration? What I want
> is to create a version of the script (not of bioperl). Since the
> script is released with bioperl, they are the same. I actually already
> made the commit that makes this, just haven't bothered with the pull
> request yet.
> 
> Also, will there be a release before this change?
> 
> Carn?

Scripts will likely go with the distribution that they most closely are tied to, but that's still an area for debate (some may equally fall within one distribution or another, which will be tricky).  

For more on the release aspects see the (currently being revised and thus not complete) wiki page:

http://www.bioperl.org/wiki/BioPerl_Modularization

chris

From pcantalupo at gmail.com  Thu Sep 29 12:13:05 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 29 Sep 2011 12:13:05 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
In-Reply-To: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
	<4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
Message-ID: <CAJqbkv6Cgf8V4x2DDrzJjc7yKyF8j-kMFNz6JGpnhn9QQTZEQg@mail.gmail.com>

Bug submitted: https://redmine.open-bio.org/issues/3298





On Wed, Sep 28, 2011 at 5:40 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.
>
> This should be an easy enough fix, but can you submit it as a bug so we can track it?
>
> chris
>
> On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:
>
>> Hello,
>>
>> I'm using the most recent copy of bioperl-live (pulled yesterday). I
>> have a BLASTN (from blast+) output file for 3 query sequences
>> (https://gist.github.com/1248342). I used this script,
>> https://gist.github.com/1248338, to print the query id, algorithm and
>> algorithm_version for each result. When I run the script, I get the
>> following output:
>>
>> GFAVMM201BADC0 ?BLASTN ?2.2.25+
>> GFAVMM201A1JOH ?BLASTN
>> GFAVMM201D933Z ?BLASTN
>>
>> Algorithm_version outputs the correct version for the first result but
>> outputs the empty string for the 2nd and 3rd query. Why? This
>> functionality worked about a month ago. What has changed to cause this
>> to happen?
>>
>> Thank you,
>>
>> Paul
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


From jluis.lavin at unavarra.es  Fri Sep 30 04:23:19 2011
From: jluis.lavin at unavarra.es (jluis.lavin at unavarra.es)
Date: Fri, 30 Sep 2011 10:23:19 +0200
Subject: [Bioperl-l] Bio-Graphics module
Message-ID: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>


Dear All,

I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
windows machine.

I read about the Bio-Graphics module and it'd be wonderful to install it,
but seems like it is  only available for Perl 5.8...
Is there any other Perl and/or Bioperl module to do the same kind of
genomic and Blast report representation currently available?

Thanks in advance

-- 
Dr. Jos? Luis Lav?n Trueba

Dpto. de Producci?n Agraria
Grupo de Gen?tica y Microbiolog?a
Universidad P?blica de Navarra
31006 Pamplona
Navarra
SPAIN



From cjfields at illinois.edu  Fri Sep 30 08:38:01 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 30 Sep 2011 12:38:01 +0000
Subject: [Bioperl-l] Bio-Graphics module
In-Reply-To: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
Message-ID: <B1F1674B-D8DA-46E2-AAAE-DD9DDBC4C51A@illinois.edu>

It's available for all perl versions from 5.8.8 up.  I have it running with perl 5.14.  Now, I recall there being problems with installation on Mac OS X, though I think that was mainly due to GD.pm and libgd.

chris

On Sep 30, 2011, at 3:23 AM, <jluis.lavin at unavarra.es>
 <jluis.lavin at unavarra.es> wrote:

> 
> Dear All,
> 
> I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
> windows machine.
> 
> I read about the Bio-Graphics module and it'd be wonderful to install it,
> but seems like it is  only available for Perl 5.8...
> Is there any other Perl and/or Bioperl module to do the same kind of
> genomic and Blast report representation currently available?
> 
> Thanks in advance
> 
> -- 
> Dr. Jos? Luis Lav?n Trueba
> 
> Dpto. de Producci?n Agraria
> Grupo de Gen?tica y Microbiolog?a
> Universidad P?blica de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jillianrowe91286 at gmail.com  Wed Sep 28 02:03:32 2011
From: jillianrowe91286 at gmail.com (Jill)
Date: Tue, 27 Sep 2011 23:03:32 -0700 (PDT)
Subject: [Bioperl-l] Gene Type in Entrez gene?
Message-ID: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>

Hi there,

I am using the Bio::DB::Eutilities module to download gene sequences
based on a query.

<code>
while (my $docsum = $summaries->next_DocSum) {
  ## some items in DocSum are also named ChrStart so we pick the
genomic
  ## information item and get the coordinates from it
  my ($genomic_info)  = $docsum->get_Items_by_name('GenomicInfoType');

  ## some entries may have no data on genomic coordinates. This
condition filters then out
  if (!$genomic_info) {
    ## found no genomic coordinates data
    next;
  }

  ## get coordinates of sequence
  ## get_contents_by_name always returns a list
  my ($chr_acc_ver)   = $genomic_info-
>get_contents_by_name("ChrAccVer");
  my ($chr_start)     = $genomic_info-
>get_contents_by_name("ChrStart");
  my ($chr_stop)      = $genomic_info-
>get_contents_by_name("ChrStop");
  my $strand;

  if ($chr_start < $chr_stop) {
    $strand     = 1;
    $chr_start  = $chr_start +1 - $bp5_extra;
    $chr_stop   = $chr_stop  +1 + $bp5_extra;
  } elsif ($chr_start > $chr_stop) {
    $strand     = 2;
    $chr_start  = $chr_start +1 - (-$bp5_extra);
    $chr_stop   = $chr_stop  +1 + (-$bp5_extra);
  } else {
    next;
  }

  while (my $item = $docsum->next_Item('flattened'))  {
	next if ($item->get_name =~ m/NomenclatureName/);
	if($item->get_name =~ m/Description/) {
	  $description = $item->get_content if $item->get_content;
	  $description =~ tr/ /_/;
	  print $description, "\n";}
	if($item->get_name =~ m/Name/) {
	    $name = $item->get_content if $item->get_content;
	    print $name, "\n";
	  }
        printf("%-20s:%s\n",$item->get_name,$item->get_content) if
$item->get_content;
    }
}
</code>

Then I go on to use genbank to download the sequences based on the
chromosome splice. For what I have it works great. But I am trying to
get to the gene type (either protein coding or pseudo) as well. I can
see it in the summary on the Entrez Gene sight, but can't get to it
through bioperl. When I have it print out all the contents of the
summary it doesn't show up there either.

Any help?

Thanks!

From liam.elbourne at mq.edu.au  Thu Sep 29 17:34:04 2011
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Fri, 30 Sep 2011 07:34:04 +1000
Subject: [Bioperl-l] GFF to GTF
In-Reply-To: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
References: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
Message-ID: <8D027281-44E6-467C-8D22-D2D2F87D04B6@mq.edu.au>

Hi Shalabh,

Not sure about bioperl (I looked a while back and either missed it or it's not there) but there is a program associated with the cufflinks suite called gffread that should convert. 

Regards,
Liam Elbourne. 



On 30/09/2011, at 12:37 AM, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:

> Hi,
>    Is there any module to convert GFF file to GTF?
> 
> Thanks
> Shalabh
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From carandraug+dev at gmail.com  Fri Sep 30 09:18:04 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 30 Sep 2011 14:18:04 +0100
Subject: [Bioperl-l] Gene Type in Entrez gene?
In-Reply-To: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
References: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
Message-ID: <CAPOrs_2QOMOyPsZ90iYc3fMd8YE9HGnPcVqELGo+rYRRxJu9NQ@mail.gmail.com>

On 28 September 2011 07:03, Jill <jillianrowe91286 at gmail.com> wrote:
> Hi there,
>
> I am using the Bio::DB::Eutilities module to download gene sequences
> based on a query.
>
> <code>
> [...]
> }
> </code>
>
> Then I go on to use genbank to download the sequences based on the
> chromosome splice. For what I have it works great. But I am trying to
> get to the gene type (either protein coding or pseudo) as well. I can
> see it in the summary on the Entrez Gene sight, but can't get to it
> through bioperl. When I have it print out all the contents of the
> summary it doesn't show up there either.
>
> Any help?

Hi Jill,

there's already a script in bioperl that does what you want, it's just
not part of the current stable release. You can get it here

https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl

You can download the script alone, it will work fine in previous
releases of bioperl, no need to write another one.

Carn? Draug


From manju.rawat2 at gmail.com  Thu Sep  1 02:53:53 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 1 Sep 2011 02:53:53 -0400
Subject: [Bioperl-l] Bioperl query....
In-Reply-To: <CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
References: <CAB2c7yp6p2e_8p7M9wVL2xzU7g+mZ-NVXwLs4PUassRs4PgrTQ@mail.gmail.com>
	<4E5CC8AC.8050800@gmail.com>
	<CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
Message-ID: <CAB2c7yobL=KRW_XWOCfgEwJS17A8Mne4FJhVp88xjJfBqZMHGw@mail.gmail.com>

Thanks For The Reply..
I have already seen this link..But I am confused.

I used to following code and run it...

my $in = Bio::SearchIO->new(-format => 'blast',
                -file => 'seqs.blast');
while( my $result = $in->next_result ) {
  ## $result is a Bio::Search::Result::ResultI compliant object
  while( my $hit = $result->next_hit ) {
    ## $hit is a Bio::Search::Hit::HitI compliant object
    while( my $hsp = $hit->next_hsp ) {
      ## $hsp is a Bio::Search::HSP::HSPI compliant object
      if( $hsp->length('total') > 50 ) {
        if ( $hsp->percent_identity >= 75 ) {
          print "Query=",   $result->query_name,
            " Hit=",        $hit->name,
            " Length=",     $hsp->length('total'),
    " gaps=",            $hsp->gaps,
            " Percent_id=", $hsp->percent_identity, "\n";
        }     } }    }}



and it showing me following output with an error that..


*Erro--*rArgument "" isn't numeric in numeric lt (<) at
/usr/local/share/perl/5.10.1/Bio/SearchIO/SearchResultEventBuilder.pm line
279, <GEN1> line 4113.

Query=NM_181451 Hit=ref|NM_181451.1| Length=1349 gaps=1 Percent_id=100
Query=NM_181451 Hit=ref|XM_002706247.1| Length=1345 gaps=13
Percent_id=93.8289962825279
Query=NM_181451 Hit=ref|NM_001098089.1| Length=1323 gaps=7
Percent_id=91.9123204837491
Query=NM_181451 Hit=ref|NM_001008415.1| Length=1211 gaps=5
Percent_id=94.9628406275805
Query=NM_181451 Hit=ref|XM_001251693.3| Length=1320 gaps=5
Percent_id=91.969696969697
Query=NM_181451 Hit=ref|NM_001097567.1| Length=1338 gaps=4
Percent_id=91.5545590433483
Query=NM_181451 Hit=gb|AY075103.1| Length=1334 gaps=1
Percent_id=91.304347826087
................
..........

Pl Find.whats the error i this code...

Thanks
Manju Rawat.


From locarpau at upvnet.upv.es  Thu Sep  1 10:49:06 2011
From: locarpau at upvnet.upv.es (Lorenzo Carretero Paulet)
Date: Thu,  1 Sep 2011 16:49:06 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
Message-ID: <1314888546.4e5f9b628ecea@webmail.upv.es>

Hi all,
I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:

my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
if ( my $paml_result = $parserF->next_result )
{
say Dumper $paml_result; #Prints Ok
	for ( my $model_result= $paml_result->get_NSSite_results )
	{
        #say Dumper $model_result; #Prints nothing
        $ns_string = "model ".$model_result->model_num."\n
".$model_result->model_description()."\n ".$model_result->time_used."\n";
	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
	#say Dumper $dnds_site_classes;
	for my $sites ( $model_result->get_BEB_pos_selected_sites )
        ...
         ...
          ...

The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
object is not being properly instantiated, as I get the error message:

"Can't call method "model_num" without a package or object reference at ..."

What am I missing?
Best,
Lorenzo




From jason.stajich at gmail.com  Thu Sep  1 16:23:47 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 1 Sep 2011 13:23:47 -0700
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <1314888546.4e5f9b628ecea@webmail.upv.es>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
Message-ID: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>

Lorenzo -

I am sure this is a problem with changes in the output from PAML - this is classic problem with this suite.  This requires some debugging of the parser, not sure if there is anyone out there with time to do the debugging.
I can say all this worked before on an earlier version of PAML but I don't know specifically what is going on with the latest paml4.4 version.

Jason


On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:

> Hi all,
> I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:
> 
> my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> if ( my $paml_result = $parserF->next_result )
> {
> say Dumper $paml_result; #Prints Ok
> 	for ( my $model_result= $paml_result->get_NSSite_results )
> 	{
>        #say Dumper $model_result; #Prints nothing
>        $ns_string = "model ".$model_result->model_num."\n
> ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> 	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> 	#say Dumper $dnds_site_classes;
> 	for my $sites ( $model_result->get_BEB_pos_selected_sites )
>        ...
>         ...
>          ...
> 
> The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
> object is not being properly instantiated, as I get the error message:
> 
> "Can't call method "model_num" without a package or object reference at ..."
> 
> What am I missing?
> Best,
> Lorenzo
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Scott.Markel at accelrys.com  Thu Sep  1 17:22:21 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Thu, 1 Sep 2011 14:22:21 -0700
Subject: [Bioperl-l] file format for alignment plus features for aligned
	sequences
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702F8302A05@EXCH1-COLO.accelrys.net>

A question on behalf of the Discovery Studio group at Accelrys -

They have alignment data with annotations, e.g., visualization settings or alignment properties.  The aligned sequences also have features, e.g., domain boundaries or secondary structure motifs.  They currently use BSML to save sequences and features.

Is there an extension of BSML that can also save the alignment information?

Are there any good file formats that can be used to store an alignment plus features associated with the aligned sequences?

Are there other mailing lists that might be more appropriate for these questions?

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
San Diego, CA 92121                 fax:    +1 858 799 5222
USA                                 web:    http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
    International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics






From ihok at hotmail.com  Thu Sep  1 23:49:50 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Thu, 1 Sep 2011 23:49:50 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
Message-ID: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>

I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty 
quiet codebase these days... Is it dead?

Does anyone have a spec file for building an SRPM for it for RHEL 6?


From cjfields at illinois.edu  Fri Sep  2 00:31:17 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 04:31:17 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
Message-ID: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>

Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.

chris

On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:

> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> 
> Does anyone have a spec file for building an SRPM for it for RHEL 6?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Fri Sep  2 04:44:07 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 10:44:07 +0200
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
Message-ID: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>

As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
http://toolkit.tuebingen.mpg.de/hhpred


He got it working thus:

> Hi Dave,
> thanks a lot. i made it work. The error i got later on was:

 relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making
> a shared object;
> recompile with -fPIC
>


> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared
> --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/<http://forums.fedoraforum.org/showthread.php?t=232607>
> showthread.php?t=232607<http://forums.fedoraforum.org/showthread.php?t=232607>




Dave





On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J
<cjfields at illinois.edu>wrote:

> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone
> who has packaged that up in a while, if ever.
>
> chris
>
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty
> quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From David.Messina at sbc.su.se  Fri Sep  2 05:30:33 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 11:30:33 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com>
	<9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu>
	<4DF56976.8080704@upvnet.upv.es>
	<AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com>
	<9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
	<E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
Message-ID: <CAM3TQQU6YV0+5HEf6_PhNDuh3SK0eYZgHE5kT+F3MbTH8ktsNw@mail.gmail.com>

Looking back at the commit history, back in April and May 2010, I made some
updates for the January 2010 edition of PAML 4.4. All tests passed at that
time, but:

- the tests may be incomplete
- PAML has undoubtedly changed since then, even if it's still called version
4.4


I can't look at this right now myself, but please file a bug report on this,
and hopefully someone else can.


Dave




On Thu, Sep 1, 2011 at 22:23, Jason Stajich <jason.stajich at gmail.com> wrote:

> Lorenzo -
>
> I am sure this is a problem with changes in the output from PAML - this is
> classic problem with this suite.  This requires some debugging of the
> parser, not sure if there is anyone out there with time to do the debugging.
> I can say all this worked before on an earlier version of PAML but I don't
> know specifically what is going on with the latest paml4.4 version.
>
> Jason
>
>
> On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:
>
> > Hi all,
> > I'm trying to parse mlc output files from PAML using
> Bio::Tools::Phylo::PAML as:
> >
> > my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> > my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> > if ( my $paml_result = $parserF->next_result )
> > {
> > say Dumper $paml_result; #Prints Ok
> >       for ( my $model_result= $paml_result->get_NSSite_results )
> >       {
> >        #say Dumper $model_result; #Prints nothing
> >        $ns_string = "model ".$model_result->model_num."\n
> > ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> >       $dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> >       #say Dumper $dnds_site_classes;
> >       for my $sites ( $model_result->get_BEB_pos_selected_sites )
> >        ...
> >         ...
> >          ...
> >
> > The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> > DUmper. In contrast, it seems that the
> Bio::Tools::Phylo::PAML::ModelResult
> > object is not being properly instantiated, as I get the error message:
> >
> > "Can't call method "model_num" without a package or object reference at
> ..."
> >
> > What am I missing?
> > Best,
> > Lorenzo
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Fri Sep  2 09:00:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 13:00:27 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
Message-ID: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>

I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/

chris

On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:

> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
> http://toolkit.tuebingen.mpg.de/hhpred
> 
> 
> He got it working thus:
> Hi Dave,
> thanks a lot. i made it work. The error i got later on was: 
> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
> recompile with -fPIC 
>  
> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/showthread.php?t=232607
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J <cjfields at illinois.edu> wrote:
> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
> 
> chris
> 
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
> 
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From ihok at hotmail.com  Fri Sep  2 11:20:44 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Fri, 2 Sep 2011 11:20:44 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
	<81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
Message-ID: <BLU0-SMTP2075F7F67ABC5C1860ED380CA180@phx.gbl>

I also see that someone's forked it on Github and made some packaging fixes.

It'd be nice to see it revived.

On 9/2/2011 9:00 AM, Fields, Christopher J wrote:
> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/
>
> chris
>
> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:
>
>> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
>> http://toolkit.tuebingen.mpg.de/hhpred
>>
>>
>> He got it working thus:
>> Hi Dave,
>> thanks a lot. i made it work. The error i got later on was:
>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
>> recompile with -fPIC
>>
>> the solution is:
>> perl Makefile.PL PREFIX=<path to installation>  /fftwsingle --enable-shared --with-pic --enable-single
>> <edit Makefile to add -fPIC to CFLAGS>
>> make
>> make install
>> http://forums.fedoraforum.org/showthread.php?t=232607
>>
>>
>>
>> Dave
>>
>>
>>
>>
>>
>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J<cjfields at illinois.edu>  wrote:
>> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
>>
>> chris
>>
>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>>
>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
>>>
>>> Does anyone have a spec file for building an SRPM for it for RHEL 6?
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>



From manju.rawat2 at gmail.com  Sat Sep  3 01:29:56 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 01:29:56 -0400
Subject: [Bioperl-l] hsps_successfully_gapped: 47
Message-ID: <CAB2c7yr8qHCPO2L6nczPUTWi-L94Bz9kQtyLP-U03=nhWS+66Q@mail.gmail.com>

Hello,


Is There any method in BioPerl through which we can extract
number_of_hsps_successfully_gapped:
from a blast file..
If any one know about the it Pl help me...


Thanks
Manju Rawat


From manju.rawat2 at gmail.com  Sat Sep  3 06:00:22 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 06:00:22 -0400
Subject: [Bioperl-l] blast result not matching.
Message-ID: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


and Output..

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat


From florent.angly at gmail.com  Sun Sep  4 22:14:37 2011
From: florent.angly at gmail.com (Florent Angly)
Date: Mon, 05 Sep 2011 12:14:37 +1000
Subject: [Bioperl-l] Bio::SeqIO can't guess the format of data from a
 pipe
In-Reply-To: <F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
References: <CAFAnT677UmaEsudqoj9UsefdeK9Wx0E_W8iM3zmMAJx8PHzBjA@mail.gmail.com>
	<2E070303-ADDF-472B-835B-6D3959B83E9A@illinois.edu>
	<CAFAnT64JhkP-xzi8TpqHiTJTm3UMgT7SPMWVm+-UhSFwk0G3gQ@mail.gmail.com>
	<E89E20DA-9B27-4D42-ACF8-96A176C85259@illinois.edu>
	<4E58D105.7050805@gmail.com>
	<A249C76A-A0BC-414E-AE78-A2B6CA7B4A9A@drycafe.net>
	<4E5A0590.2010805@gmail.com>
	<8D639B95-0666-4F09-8E9E-88C8CDF76ABC@illinois.edu>
	<4E5AC2B8.9060808@gmail.com>
	<F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
Message-ID: <4E64308D.5060304@gmail.com>


Thanks for your advice Chris. I put a format() and variant() method in 
Bio::Root::IO. All the Bio::*IO methods inherit these methods.

Regarding the module naming, 8 follow the convention Bio::*IO and 8 
follow the Bio::*::IO convention. If we decide to rename some IO modules 
for consistency, I would prefer the Bio::*::IO convention.

Regards,

Florent


On 29/08/11 11:10, Chris Fields wrote:
> On Aug 28, 2011, at 5:35 PM, Florent Angly wrote:
>
>> Hi,
>>
>> I implemented the format() getter method in Bio::SeqIO as discussed, essentially following the way proposed by Hilmar. The variant() method is not needed since Bio::SeqIO::fastq already has a get/set method for that.
> Right, but the method could be used by other modules if it were moved to Bio::SeqIO. for instance.
>
>> I noticed that there are plenty more Bio*IO modules that could benefit from having a format() method, e.g.:
>>     Bio::AlignIO
>>     Bio::ClusterIO
>>     Bio::FeatureIO
>>     Bio::MapIO
>>     Bio::OntologyIO
>>     Bio::SearchIO
>>     Bio::TreeIO
>>     Bio::Assembly::IO *
>> The code could be copy-pasted for each of them but it is not very graceful. Is there a way we could have all these IO modules share the same format() method?
> Move the method to Bio::Root::IO, the common base class for all of the above.
>
>> * Note how the IO class for Bio::Assembly is called Bio::Assembly::IO, and not Bio::AssemblyIO like for other classes. This may be something to change in the future for consistency.
>>
>> Florent
> That's possible; one could take advantage of that for redesign/API issues if it were needed.
>
> chris



From manju.rawat2 at gmail.com  Mon Sep  5 03:53:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 03:53:40 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
Message-ID: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


*and Output..*

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat


From p.j.a.cock at googlemail.com  Mon Sep  5 05:44:06 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 10:44:06 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
Message-ID: <CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>

On Mon, Sep 5, 2011 at 8:53 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
> I doing blast using bioperl...but it not showing me complete result..
>
>
> my program is following...
> ...
>
> this result is not matching with with NCBI result...
> Is there anything wrong..

The NCBI website for BLAST uses different default values
to the BLAST command line tools. Check things like the
gap parameters if you want to use the same settings.

Peter


From p.j.a.cock at googlemail.com  Mon Sep  5 06:25:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 11:25:15 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
Message-ID: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>

Please CC the mailing list.

On Mon, Sep 5, 2011 at 11:19 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
> Thanks for the reply...
> but when i am blasting after getting sequence of any gene (from NCBI using
> bioperl see below)..it showing me same result as shown in NCBI..
>
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq_object = get_sequence('NCBI',"NM_181451");
> $blast_result = blast_sequence($seq);
> write_blast(">roa1.blast",$blast_report);
>
>
> I dnt know why its not working when i am blasting my own sequence..
>

Maybe you need give the sequence as a FASTA entry
rather than a plain string?

Peter


From manju.rawat2 at gmail.com  Mon Sep  5 06:40:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 06:40:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
Message-ID: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>

No..i also tried this..this also dont work..
pls help me..


From cjfields at illinois.edu  Mon Sep  5 15:42:49 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 5 Sep 2011 19:42:49 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
Message-ID: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>

Are you using the latest BioPerl?  I believe there had been some fixes addressing remote blast.

chris

On Sep 5, 2011, at 5:40 AM, Manju Rawat wrote:

> No..i also tried this..this also dont work..
> pls help me..
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Tue Sep  6 06:59:50 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 6 Sep 2011 06:59:50 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
Message-ID: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>

bioperl 1.6.9 version is installed in my system..
its not the reason bcs blast is working fine when i am blasting with
follwing code..

#!usr/bin/perl -w
use Bio::Perl;
$seq = get_sequence('NCBI',"NM_181451");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


Manju


From sidd.basu at gmail.com  Tue Sep  6 11:51:09 2011
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Tue, 6 Sep 2011 10:51:09 -0500
Subject: [Bioperl-l] Bioinformatics Job Opening at dictyBase in Chicago
Message-ID: <20110906155106.GB1841@Macintosh-388.local>

Hi All, 
We have an open position for a Bioinformatics Software Engineer at dictyBase(Northwestern
University in Chicago). The job involves developing web application and middleware for
a genome database using modern perl(DBIx-Class/Moose/MVC web frameworks etc)
as well as integration of various genomic tools(gbrowse, intermine, apollo,
biomart, pathway tools etc..). 
For full details please see:
 http://www.dictybase.org/dictybase_jobs.html.


thanks, 
-siddhartha

Siddhartha Basu
Software developer,  dictybase
http://www.dictybase.org



From slucky at ibab.ac.in  Wed Sep  7 09:39:03 2011
From: slucky at ibab.ac.in (Lucky Singh)
Date: Wed, 07 Sep 2011 19:09:03 +0530
Subject: [Bioperl-l] Fwd: Re:  Problem using Bio::Tools::Run::RemoteBlast
Message-ID: <4E6773F7.7000703@ibab.ac.in>



-------- Original Message --------
Subject: 	Re: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
Date: 	Sat, 27 Aug 2011 20:36:58 +0530
From: 	Lucky Singh <slucky at ibab.ac.in>
To: 	Carn? Draug <carandraug+dev at gmail.com>



On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>  On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in>   wrote:
>>  Now I
>>  wanted to host it from web server, but This program is not working from it
>>  may be it is not able to create or write on file from web server but in
>>  command line it is working fine. I don't know the possible reason, please
>>  help me to figure it out.
>  Have you looked in the apache logs (look in
>  /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>  content of the error log after trying to run the script?
Dear Carn? Draug,

As per your suggestion, I am attaching blast code file currently it is
not showing any error on error.log.
Thanks a lot for your valuable reply and will be highly grateful if you
can get me out of this problem :)


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From jason.stajich at gmail.com  Wed Sep  7 12:13:46 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 7 Sep 2011 09:13:46 -0700
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
Message-ID: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>

I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.


On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:

> bioperl 1.6.9 version is installed in my system..
> its not the reason bcs blast is working fine when i am blasting with
> follwing code..
> 
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq = get_sequence('NCBI',"NM_181451");
> $blast_result=blast_sequence($seq);
> write_blast(">xyz.blast",$blast_result);
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Wed Sep  7 12:33:52 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 7 Sep 2011 16:33:52 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
Message-ID: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>

I think there was an issue with Bio::Perl BLAST submissions fixed in the 1.6.901 release (1.6.9 != 1.6.901, the latter is newer).  From CPAN:

1.6.901 May 18, 2011

...

    [Bug fixes]

    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
      docs [genehack, cjfields]

chris

On Sep 7, 2011, at 11:13 AM, Jason Stajich wrote:

> I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
> Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.
> 
> 
> On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:
> 
>> bioperl 1.6.9 version is installed in my system..
>> its not the reason bcs blast is working fine when i am blasting with
>> follwing code..
>> 
>> #!usr/bin/perl -w
>> use Bio::Perl;
>> $seq = get_sequence('NCBI',"NM_181451");
>> $blast_result=blast_sequence($seq);
>> write_blast(">xyz.blast",$blast_result);
>> 
>> 
>> Manju
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From carandraug+dev at gmail.com  Wed Sep  7 12:47:16 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 7 Sep 2011 17:47:16 +0100
Subject: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
In-Reply-To: <4E590812.9030006@ibab.ac.in>
References: <37711.192.168.1.254.1313992876.squirrel@webmail.ibab.ac.in>
	<CAPOrs_1TX=+A=hA0bCP56bsW5XdPy5N5mpcnAL=NPugP-4j03Q@mail.gmail.com>
	<4E590812.9030006@ibab.ac.in>
Message-ID: <CAPOrs_2MbWXbtrhj+eOphpDfyaUhdpWvUE8kaMXxKrQe_3m_kw@mail.gmail.com>

2011/8/27 Lucky Singh <slucky at ibab.ac.in>:
> On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>>
>> On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in> ?wrote:
>>>
>>> Now I
>>> wanted to host it from web server, but This program is not working from
>>> it
>>> may be it is not able to create or write on file from web server but in
>>> command line it is working fine. I don't know the possible reason, please
>>> help me to figure it out.
>>
>> Have you looked in the apache logs (look in
>> /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>> content of the error log after trying to run the script?
>
> Dear Carn? Draug,
>
> As per your suggestion, I am attaching blast code file currently it is not
> showing any error on error.log.
> Thanks a lot for your valuable reply and will be highly grateful if you can
> get me out of this problem :)


Hi

sorry for the late reply. Please try to always reply to the mailing
list, maybe someone else can help you too. I don't know about the
script as I never used RemoteBlast from bioperl. But given a quick
look at it, you're not loading the CGI module on the script (
http://perldoc.perl.org/CGI.html ). Here's a simple example using the
CGI module ( http://pastebin.com/miMd70wn ) and a HTML page that will
use it ( http://pastebin.com/kWwwMijd ).

If nothing shows up on error.log, take a look in access.log. Try some
simple CGI script first, such as "hello world!" to see if the problem
lies on your bioperl part of the script, or in the web server, or some
other part.

Carn?



From scott at scottcain.net  Wed Sep  7 13:57:31 2011
From: scott at scottcain.net (Scott Cain)
Date: Wed, 7 Sep 2011 13:57:31 -0400
Subject: [Bioperl-l] October GMOD Meeting in Toronto
Message-ID: <CA+JTaoxxMxNQmOu8wbU=vD+-6eRwPVjpXBAszWn=p6_OOkr9ig@mail.gmail.com>

Hello,

The early registration deadline for the October GMOD meeting in
Toronto, Canada is approaching.  Please register by September 13th to
avoid the late registration fee.  You can register here:

  http://gmod.eventbrite.com/

For information about the GMOD meeting please see the page at:

  http://gmod.org/wiki/October_2011_GMOD_Meeting

In addition to the main meeting, there will be a free BioMart workshop
on the following Friday, which you can also register for at the main
meeting registration page.

Thanks,
Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From info at etisalat.com  Wed Sep  7 05:52:00 2011
From: info at etisalat.com (Etisalat Telecommunication Network.)
Date: Wed, 7 Sep 2011 17:52:00 +0800
Subject: [Bioperl-l] Winning No:ETS/G/NG
Message-ID: <20110907092508.M63844@etisalat.com>

Etisalat Telecommunication Network.
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recipients as a way of showing our appreciation.

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Etisalat Award Promotion
(c)2011 Online Award Promotion Edition  



From longbow0 at gmail.com  Wed Sep  7 16:19:37 2011
From: longbow0 at gmail.com (longbow leo)
Date: Wed, 7 Sep 2011 15:19:37 -0500
Subject: [Bioperl-l] How to determine strains were evolved independently in
	a phylogenetic tree?
Message-ID: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>

Hi,

I have created a phylogenetic for a virus protein which contained about 200
strains. Next I need to do an analysis to check whether several strains in
this tree were evolved independently. Although it is not too difficult to do
manually, I still have litter idea how to do this in a Perl script since
there are some datasets need to do.

At first I tried to use the method "is_monophyletic" in the module
"Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
work as I have thought. According to the description of "is_monophyletic"
method, it "Will do a test of monophyly for the nodes specified in
comparison to a chosen outgroup". Does here test whether the outgroup strain
is monophyletic to the nodes, or test the nodes only? The description sounds
like the latter but the what the script did seemed to be the first.

Are there any suggestions?

Thank you very much!


Haizhou Liu


From greg at ebi.ac.uk  Thu Sep  8 06:40:30 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Thu, 8 Sep 2011 11:40:30 +0100
Subject: [Bioperl-l] How to determine strains were evolved independently
 in a phylogenetic tree?
In-Reply-To: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
References: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
Message-ID: <CA+08rdT4z5W5OzuuBPsC0icz_LWXCTNWO0uv=w=Bg_0EoU44Gw@mail.gmail.com>

Hi Haizhou,

I'm not sure I understand exactly what you're trying to do. But to clarify
the BioPerl code: the is_monophyletic method (for the actual code, see here
https://github.com/bioperl/bioperl-live/blob/master/Bio/Tree/TreeFunctionsI.pm#L832)
tests
whether the single outgroup node falls *within* or *outside* the last common
ancestor of the group of nodes given. If the outgroup node falls *outside*
the subtree defined by this LCA node, then the group of nodes can be called
monophyletic with respect to that outgroup (at least as far as my
understanding of the word 'monophyletic' goes). If the outgroup node falls
*within* the subtree defined by this LCA node, then the group of nodes is
not monophyletic with respect to that outgroup node.

The term "evolved independently" sounds slightly vague to me -- what is it
exactly about the shape of your tree that allows you to call a strain
independent or not? If you gave an example or two of trees where you
consider the evolution to be independent and non-independent, I (or someone
else on the list) may be able to help you find the right method to do this
automatically.

Cheers,
 Greg

On Wed, Sep 7, 2011 at 9:19 PM, longbow leo <longbow0 at gmail.com> wrote:

> Hi,
>
> I have created a phylogenetic for a virus protein which contained about 200
> strains. Next I need to do an analysis to check whether several strains in
> this tree were evolved independently. Although it is not too difficult to
> do
> manually, I still have litter idea how to do this in a Perl script since
> there are some datasets need to do.
>
> At first I tried to use the method "is_monophyletic" in the module
> "Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
> work as I have thought. According to the description of "is_monophyletic"
> method, it "Will do a test of monophyly for the nodes specified in
> comparison to a chosen outgroup". Does here test whether the outgroup
> strain
> is monophyletic to the nodes, or test the nodes only? The description
> sounds
> like the latter but the what the script did seemed to be the first.
>
> Are there any suggestions?
>
> Thank you very much!
>
>
> Haizhou Liu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From manju.rawat2 at gmail.com  Thu Sep  8 02:11:12 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 8 Sep 2011 02:11:12 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
Message-ID: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>

Toady i installed the latest version of bioperl in my system via CPAN..
But this still not sowing the complete result..


I just want to do nucleotide blast using bioperl..but while i am doing blast
with my sequence it shwowing very samll result..
I dnt know whether it is wrong or right...but while i am blasting the same
sequence in NCBI it showing a diffrent result..

and i have also tried to use the orignl module..but it also dnt work..

Pl see reult of the balst in  attached file of this mail..
#!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO;
$blast_report =blast_sequence('acggctgctgtagatctgatgct');
write_blast(">resl.blast",$blast_report);

Thanks.
Manju Rawat
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From cjfields at illinois.edu  Thu Sep  8 09:05:10 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 13:05:10 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <6D4A142B-9455-4CC3-AFDB-F9B3B991B57F@illinois.edu>

Submissions to NCBI BLAST via their web interface have different parameters than those submitted via their QBLAST interface (what is used in BioPerl).  So the fact there are differing results isn't too surprising, particularly if the results fall close to the e-value cutoff for one or the other.  You will need to set the proper parameters, which I don't believe is possible via the (very simple) Bio::Perl interface, but is possible via Bio::Tools::Run::RemoteBlast.

chris

On Sep 8, 2011, at 1:11 AM, Manju Rawat wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
> 
> 
> I just want to do nucleotide blast using bioperl..but while i am doing blast with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same sequence in NCBI it showing a diffrent result..
> 
> and i have also tried to use the orignl module..but it also dnt work..
> 
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
> 
> Thanks.
> Manju Rawat
> 
> 
> <resl.blast>




From David.Messina at sbc.su.se  Thu Sep  8 09:33:19 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 8 Sep 2011 15:33:19 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>

As I think has been said earlier in this thread, it's almost certainly a
discrepancy in the BLAST parameters between what the blast_sequence function
in the Bio::Perl module is sending, and what the BLAST website is doing.


In this case, you have a very short sequence. If you look in the "Algorithm
parameters" section of the BLAST web form, you'll see that there is an
option that is checked by default, "Automatically adjust parameters for
short input sequences".


If I uncheck that option, I get the same results as you did when you
submitted your BLAST through BioPerl (see http://cl.ly/9ynq).


So to get the same results from a BioPerl-submitted BLAST and a BLAST on
NCBI's website, you need to have the same parameters. You can set the
parameters from BioPerl as described in the documentation:

http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Tools/Run/RemoteBlast.pm


As Jason said earlier, the blast_sequence function in Bio::Perl is intended
as a simple demonstration and uses the default BLAST parameters. That
function is a wrapper around the RemoteBlast module. Since you want to do
something a little different, I believe you'll need to use the RemoteBlast
module directly.




Dave




On Thu, Sep 8, 2011 at 08:11, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
>
>
> I just want to do nucleotide blast using bioperl..but while i am doing
> blast
> with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same
> sequence in NCBI it showing a diffrent result..
>
> and i have also tried to use the orignl module..but it also dnt work..
>
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
>
> Thanks.
> Manju Rawat
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From abualiga2 at gmail.com  Thu Sep  8 10:44:39 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 10:44:39 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
	primary tag
Message-ID: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>

Hi,

I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
multiple tags within a primary tag.  E.g., when there are several 'function'
tag-values within a 'CDS' primary tag, I don't know how to link those
'function' tag-values to a particular 'locus_tag'.  As parsed values are
returned as a list, I tried creating an array of hashes, where the hash-key
is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
miserably.  Pasted below is what I managed so far.  At your convenience,
please advise.

thanks!

galeb

#!/usr/local/bin/perl
# parse_gbk.pl
# gsa 09042011
# script to parse out features from gbk
#
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction

use strict; use warnings;
use Bio::SeqIO;

my @loci;
my @seqs;
my @directions;
my @start_coords;
my @end_coords;
my @genes;
my @products;
my @notes;
my @functions;
my %functions;

my $gb_file = shift;
my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
my $seq_obj = $seqio_obj->next_seq;

for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
    if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
                if ($feat_obj->has_tag( 'locus_tag' ) ) {
                push ( @seqs, $feat_obj->seq->seq ); #collect sequences
                    for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
{
                            push ( @loci, $val ); # locus_tags
            }
        }
                if ( $feat_obj->has_tag( 'gene' ) ) {
                           for my $val ( $feat_obj->get_tag_values( 'gene' )
) {
                            push ( @genes, $val ); # gene names
                        }
                }
                else {
                    push ( @genes, "" ); # if gene names are absent, leave
empty
        }
        if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
coordinates
            for my $location ( $feat_obj->location ) {
                push ( @start_coords, $location->start );
                push ( @end_coords, $location->end );
                if ( $location->strand == -1 ) {
                    push ( @directions, "reverse" );
                }
                else {
                    push ( @directions, "forward" );
                }
            }
        }
    }
    # gene products, notes, functions
    if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
$feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
|| $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
        if ( $feat_obj->has_tag( 'product' ) ) {
            for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
                push ( @products, $product );
            }
        }
        else {
            push ( @products, "" );
        }
        if ( $feat_obj->has_tag( 'note' ) ) {
            for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
                push ( @notes, $note );
            }
        }
        else {
            push ( @notes, "" );
        }
        if ( $feat_obj->has_tag( 'function' ) ) {
            for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
                push ( @functions, $function );
            }
        }
        else {
            push ( @functions, "" );
        }

    }
}

print
"locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
# header

for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
    print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
"\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
$directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
$functions[$elem], "\t", $seqs[$elem], "\n";
}


From p.j.a.cock at googlemail.com  Thu Sep  8 11:27:56 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:27:56 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>

On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> Hi,
>
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag. ?E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.

Do you have GenBank features with multiple locus_tag qualifiers?
That would be very unusual...

Peter



From cjfields at illinois.edu  Thu Sep  8 11:32:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 15:32:21 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
Message-ID: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>

On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:

> On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
>> Hi,
>> 
>> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
>> multiple tags within a primary tag.  E.g., when there are several 'function'
>> tag-values within a 'CDS' primary tag, I don't know how to link those
>> 'function' tag-values to a particular 'locus_tag'.
> 
> Do you have GenBank features with multiple locus_tag qualifiers?
> That would be very unusual...
> 
> Peter

Agreed; in order to clarify what you mean, I think we would need to see the record in question to get a better idea of the problem.

chris


From abualiga2 at gmail.com  Thu Sep  8 11:39:20 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:39:20 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
Message-ID: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>

I guess I was not clear. 'locus_tag' qualifiers are single, but there are
mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

# gbk file
LOCUS       NC_011748            5154862 bp    DNA     circular BCT
15-MAY-2010

# example feature
     gene        complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /db_xref="GeneID:7145846"
     CDS             complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /function="7 : Transport and binding proteins"
                     /function="15.10 : Adaptations to atypical conditions"
                     /function="16.1 : Circulate"
                     /inference="ab initio prediction:AMIGene:2.0"
                     /note="the Vibrio parahaemolyticus gene VP2867 was
found
                     to be a potassium/proton antiporter; can rapidly
extrude
                     potassium against a potassium gradient at alkaline pH
when
                     cloned and expressed in Escherichia coli"
                     /codon_start=1
                     /transl_table=11
                     /product="potassium/proton antiporter"
                     /protein_id="YP_002402372.1"
                     /db_xref="GI:218694705"
                     /db_xref="GeneID:7145846"

/translation="MDATTIISLFILGSILVTSSILLSSFSSRLGIPILVIFLAIGML

AGVDGVGGIPFDNYPFAYMVSNLALAIILLDGGMRTQASSFRVALGPALSLATLGVLI

TSGLTGMMAAWLFNLDLIEGLLIGAIVGSTDAAAVFSLLGGKGLNERVGSTLEIESGS

NDPMAVFLTITLIAMIQQHESSVSWMFVVDILQQFGLGIVIGLGGGYLLLQMINRIAL

PAGLYPLLALSGGILIFALTTALEGSGILAVYLCGFLLGNRPIRNRYGILQNFDGLAW

LAQIAMFLVLGLLVNPSDLLPIAIPALILSAWMIFFARPLSVFAGLLPFRGFNLRERV

FISWVGLRGAVPIILAVFPMMAGLENARLFFNVAFFVVLVSLLLQGTSLSWAAKKAKV

VVPPVGRPVSRVGLDIHPENPWEQFVYQLSADKWCVGAALRDLHMPKETRIAALFRDN

QLLHPTGSTRLREGDVLCVIGRERDLPALGKLFSQSPPVALDQRFFGDFILEASAKYA

DVALIYGLEDGREYRDKQQTLGEIVQQLLGAAPVVGDQVEFAGMIWTVAEKEDNEVLK
                     IGVRVAEEEAES"

On Thu, Sep 8, 2011 at 11:32 AM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:
>
> > On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com>
> wrote:
> >> Hi,
> >>
> >> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> >> multiple tags within a primary tag.  E.g., when there are several
> 'function'
> >> tag-values within a 'CDS' primary tag, I don't know how to link those
> >> 'function' tag-values to a particular 'locus_tag'.
> >
> > Do you have GenBank features with multiple locus_tag qualifiers?
> > That would be very unusual...
> >
> > Peter
>
> Agreed; in order to clarify what you mean, I think we would need to see the
> record in question to get a better idea of the problem.
>
> chris


From p.j.a.cock at googlemail.com  Thu Sep  8 11:46:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:46:28 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
Message-ID: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>

On Thu, Sep 8, 2011 at 4:39 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> I guess I was not clear. 'locus_tag' qualifiers are single, but there are
> mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?

Peter


From abualiga2 at gmail.com  Thu Sep  8 11:55:08 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:55:08 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
	<CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
Message-ID: <CANPzzTsCB8DMzQHMYNOh84hBmu2diwrEA6xb8n3i2RFY9_a4kw@mail.gmail.com>

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?


Precisely!
I want to create a tab delim file with 'locus_tag' as the common identifier
to all the features and gene sequences. So far, I parsed out sequences and
single instance qualifiers, but 'function' and 'db_xref' qualifiers give me
grief.

galeb


From abualiga2 at gmail.com  Thu Sep  8 12:14:07 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:14:07 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.



That's right. Products are not the issue in this particular case, as it's
E.coli and there's no alternate splicing as far as I know so there is a
single product per gene. But there are plenty more 'function' qualifiers,
for example, than loci. And I don't know how to create a data structure that
will link a 'gene' (as primary tag) to all other qualifiers, whether they
belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.


From ss2489 at cornell.edu  Thu Sep  8 12:28:40 2011
From: ss2489 at cornell.edu (Surya Saha)
Date: Thu, 8 Sep 2011 12:28:40 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
Message-ID: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

-Surya

On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:

> I only had a quick look at your code, so maybe I'm missing something but
> you are currently pushing all products of all CDSs into the same array,
> i.e. you do not assign them to a datastructure that links a particular
> CDS to a list of products. You then use the same index to print out a
> locus from the @loci array and a product from @products, but the two
> will not match up because you will have more products than loci.
>
>
>
> That's right. Products are not the issue in this particular case, as it's
> E.coli and there's no alternate splicing as far as I know so there is a
> single product per gene. But there are plenty more 'function' qualifiers,
> for example, than loci. And I don't know how to create a data structure
> that
> will link a 'gene' (as primary tag) to all other qualifiers, whether they
> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From fs5 at sanger.ac.uk  Thu Sep  8 12:04:57 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 08 Sep 2011 17:04:57 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags
	within	primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.

Frank



On Thu, 2011-09-08 at 10:44 -0400, galeb abu-ali wrote:
> Hi,
> 
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag.  E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.  As parsed values are
> returned as a list, I tried creating an array of hashes, where the hash-key
> is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
> miserably.  Pasted below is what I managed so far.  At your convenience,
> please advise.
> 
> thanks!
> 
> galeb
> 
> #!/usr/local/bin/perl
> # parse_gbk.pl
> # gsa 09042011
> # script to parse out features from gbk
> #
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction
> 
> use strict; use warnings;
> use Bio::SeqIO;
> 
> my @loci;
> my @seqs;
> my @directions;
> my @start_coords;
> my @end_coords;
> my @genes;
> my @products;
> my @notes;
> my @functions;
> my %functions;
> 
> my $gb_file = shift;
> my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
> my $seq_obj = $seqio_obj->next_seq;
> 
> for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
>     if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
>                 if ($feat_obj->has_tag( 'locus_tag' ) ) {
>                 push ( @seqs, $feat_obj->seq->seq ); #collect sequences
>                     for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
> {
>                             push ( @loci, $val ); # locus_tags
>             }
>         }
>                 if ( $feat_obj->has_tag( 'gene' ) ) {
>                            for my $val ( $feat_obj->get_tag_values( 'gene' )
> ) {
>                             push ( @genes, $val ); # gene names
>                         }
>                 }
>                 else {
>                     push ( @genes, "" ); # if gene names are absent, leave
> empty
>         }
>         if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
> coordinates
>             for my $location ( $feat_obj->location ) {
>                 push ( @start_coords, $location->start );
>                 push ( @end_coords, $location->end );
>                 if ( $location->strand == -1 ) {
>                     push ( @directions, "reverse" );
>                 }
>                 else {
>                     push ( @directions, "forward" );
>                 }
>             }
>         }
>     }
>     # gene products, notes, functions
>     if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
> 'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
> $feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
> || $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
>         if ( $feat_obj->has_tag( 'product' ) ) {
>             for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
>                 push ( @products, $product );
>             }
>         }
>         else {
>             push ( @products, "" );
>         }
>         if ( $feat_obj->has_tag( 'note' ) ) {
>             for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
>                 push ( @notes, $note );
>             }
>         }
>         else {
>             push ( @notes, "" );
>         }
>         if ( $feat_obj->has_tag( 'function' ) ) {
>             for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
>                 push ( @functions, $function );
>             }
>         }
>         else {
>             push ( @functions, "" );
>         }
> 
>     }
> }
> 
> print
> "locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
> # header
> 
> for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
>     print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
> "\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
> $directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
> $functions[$elem], "\t", $seqs[$elem], "\n";
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From cjfields at illinois.edu  Thu Sep  8 12:51:22 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 16:51:22 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>

There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().

chris

-----------------------------
#!/usr/bin/env perl

use Modern::Perl;
use Bio::SeqIO;

my $in = Bio::SeqIO->new(-format => 'genbank',
                         -file => shift);

while (my $seq = $in->next_seq) {
   for my $feat ($seq->get_SeqFeatures) {
       next unless $feat->primary_tag eq 'CDS';
       my ($locus) = $feat->has_tag('locus_tag') ? 
                     $feat->get_tag_values('locus_tag') : '';
       my @funcs = $feat->has_tag('function') ?
           $feat->get_tag_values('function') : ();
       say join("\t", $locus, join(',', at funcs));
   }
}



On Sep 8, 2011, at 11:28 AM, Surya Saha wrote:

> You might want to explore using a hash of complex records that are very
> similar to structures in C/C++. More info at
> http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS
> 
> -Surya
> 
> On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> 
>> I only had a quick look at your code, so maybe I'm missing something but
>> you are currently pushing all products of all CDSs into the same array,
>> i.e. you do not assign them to a datastructure that links a particular
>> CDS to a list of products. You then use the same index to print out a
>> locus from the @loci array and a product from @products, but the two
>> will not match up because you will have more products than loci.
>> 
>> 
>> 
>> That's right. Products are not the issue in this particular case, as it's
>> E.coli and there's no alternate splicing as far as I know so there is a
>> single product per gene. But there are plenty more 'function' qualifiers,
>> for example, than loci. And I don't know how to create a data structure
>> that
>> will link a 'gene' (as primary tag) to all other qualifiers, whether they
>> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From abualiga2 at gmail.com  Thu Sep  8 12:51:42 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:51:42 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <CANPzzTuAkFy-P9WAVe7bzv=mVEXb-MOLFQrZYv8UX7L2rWcZCA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

alright, thanks!


From jskittrell at unmc.edu  Thu Sep  8 12:40:31 2011
From: jskittrell at unmc.edu (Jeff S Kittrell)
Date: Thu, 8 Sep 2011 11:40:31 -0500
Subject: [Bioperl-l] Error when parsing a blast file
Message-ID: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>

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From cjfields at illinois.edu  Thu Sep  8 13:28:53 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 17:28:53 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
Message-ID: <1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>

What version of bioperl are you using?  I think this issue was addressed a while ago, but it's possible there has been a regression.

chris

On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:

> Hello Gentlemen,
> 
> I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> When the SearchIO parser encounters this record it dies with the error
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no data for midline Query ------------------------------------------------------------
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> -----------------------------------------------------------
> 
> 
> Has anyone encountered this problem before? Am I doing something wrong?
> 
> Thanks
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> Query= 78065535
> 
> Length=523
> Score E
> Sequences producing significant alignments: (Bits) Value
> 
> gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> 
> 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> receptor 123 (GPR123), mRNA
> Length=4298
> 
> Score = 576 bits (638), Expect = 1e-163
> Identities = 466/583 (80%), Gaps = 82/583 (14%)
> Strand=Plus/Minus
> 
> Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> 
> Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> 
> Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> 
> Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> 
> Query ------------------------------------------------------------ 
> 
> Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> 
> Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> 
> Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> 
> Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> 
> Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> 
> Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> ||||||||||||||||||||||||||||||| ||| || ||||
> Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> 
> 
> 
> Lambda K H
> 0.634 0.408 0.912 
> 
> Gapped
> Lambda K H
> 0.625 0.410 0.780 
> 
> Effective search space used: 47712920310
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From abualiga2 at gmail.com  Thu Sep  8 13:51:34 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 13:51:34 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
Message-ID: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>

thanks, Chris! works perfect.
To make sure I understand what's going on, forcing list context on $locus
allows me to get one value at a time, which is then concatenated with \t to
concatenated functions.

thanks again!

galeb

On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> There is no need to do that if one is using the Bio::SeqFeatureI interface.
>  Note that get_tag_values always returns a list, so to snag a single value
> for a tag in a scalar, force list context on the LHS by enclosing the
> variable in ().
>
> chris
>
> -----------------------------
> #!/usr/bin/env perl
>
> use Modern::Perl;
> use Bio::SeqIO;
>
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
>
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>    }
> }
>
>
>
>


From cjfields at illinois.edu  Thu Sep  8 14:27:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:27:06 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
Message-ID: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>

On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:

> thanks, Chris! works perfect. 
> To make sure I understand what's going on, forcing list context on $locus allows me to get one value at a time,...

You have to be careful in this circumstance; doing this:

   my $foo = @bar;

is scalar context on a list, which returns the number of elements in @bar.  The following

   my ($foo) = @bar;

forces list context and assigns the first value in @bar to $foo but tosses the rest.  If you are sure there is only one value in @bar anyway, the above is fine (and is a common perl idiom).  

> which is then concatenated with \t to concatenated functions. 

I'm just using a simple join() to print off the results.  Note the second element in the join list is an embedded join() with comma-sep values for functions.

chris

> thanks again!
> 
> galeb
> 
> On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().
> 
> chris
> 
> -----------------------------
> #!/usr/bin/env perl
> 
> use Modern::Perl;
> use Bio::SeqIO;
> 
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
> 
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>   }
> }
> 
> 
> 




From cjfields at illinois.edu  Thu Sep  8 14:30:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:30:06 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
	<1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>
	<OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
Message-ID: <C7BC7AE9-FF28-460D-83D1-35F0C8A17832@illinois.edu>

Try updating to the latest CPAN release (1.6.901, which is the pre-1.7 release).

chris

On Sep 8, 2011, at 1:19 PM, Jeff S Kittrell wrote:

> chris,
> 
> I am using version 1.6.1
> 
> Thanks,
> 
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> <graycol.gif>"Fields, Christopher J" ---09/08/2011 12:28:56 PM---What version of bioperl are you using? I think this issue was addressed a while ago, but it's possi
> 
> <ecblank.gif>
> From:
> <ecblank.gif>
> "Fields, Christopher J" <cjfields at illinois.edu>
> <ecblank.gif>
> To:
> <ecblank.gif>
> Jeff S Kittrell <jskittrell at unmc.edu>
> <ecblank.gif>
> Cc:
> <ecblank.gif>
> "<bioperl-l at lists.open-bio.org> " <bioperl-l at lists.open-bio.org>
> <ecblank.gif>
> Date:
> <ecblank.gif>
> 09/08/2011 12:28 PM
> <ecblank.gif>
> Subject:
> <ecblank.gif>
> Re: [Bioperl-l] Error when parsing a blast file
> 
> 
> 
> What version of bioperl are you using? I think this issue was addressed a while ago, but it's possible there has been a regression.
> 
> chris
> 
> On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:
> 
> > Hello Gentlemen,
> > 
> > I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> > When the SearchIO parser encounters this record it dies with the error
> > 
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: no data for midline Query ------------------------------------------------------------
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> > STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> > STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> > -----------------------------------------------------------
> > 
> > 
> > Has anyone encountered this problem before? Am I doing something wrong?
> > 
> > Thanks
> > 
> > Jeff Kittrell
> > Department of Genetics, Cell Biology & Anatomy
> > University of Nebraska Medical Center
> > 985805 Nebraska Medical Center
> > Omaha, NE 68198-5805
> > 
> > Query= 78065535
> > 
> > Length=523
> > Score E
> > Sequences producing significant alignments: (Bits) Value
> > 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> > 
> > 
> > > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> > receptor 123 (GPR123), mRNA
> > Length=4298
> > 
> > Score = 576 bits (638), Expect = 1e-163
> > Identities = 466/583 (80%), Gaps = 82/583 (14%)
> > Strand=Plus/Minus
> > 
> > Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> > ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> > Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> > 
> > Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> > |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> > Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> > 
> > Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> > |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> > Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> > 
> > Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> > ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> > Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> > 
> > Query ------------------------------------------------------------ 
> > 
> > Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> > 
> > Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> > |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> > Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> > 
> > Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> > ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> > Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> > 
> > Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> > |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> > Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> > 
> > Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> > ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> > Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> > 
> > Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> > ||||||||||||||||||||||||||||||| ||| || ||||
> > Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> > 
> > 
> > 
> > Lambda K H
> > 0.634 0.408 0.912 
> > 
> > Gapped
> > Lambda K H
> > 0.625 0.410 0.780 
> > 
> > Effective search space used: 47712920310
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 




From abualiga2 at gmail.com  Thu Sep  8 14:34:41 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 14:34:41 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
	<2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
Message-ID: <CANPzzTvxce3b=-bBUh9xNsda=1HrO9X6tRLhZAN5jhxpkKMLAQ@mail.gmail.com>

many thanks again, Chris! I was reading Programming Perl, but this sums it
up better.

On Thu, Sep 8, 2011 at 2:27 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

> On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:
>
> > thanks, Chris! works perfect.
> > To make sure I understand what's going on, forcing list context on $locus
> allows me to get one value at a time,...
>
> You have to be careful in this circumstance; doing this:
>
>   my $foo = @bar;
>
> is scalar context on a list, which returns the number of elements in @bar.
>  The following
>
>   my ($foo) = @bar;
>
> forces list context and assigns the first value in @bar to $foo but tosses
> the rest.  If you are sure there is only one value in @bar anyway, the above
> is fine (and is a common perl idiom).
>
> > which is then concatenated with \t to concatenated functions.
>
> I'm just using a simple join() to print off the results.  Note the second
> element in the join list is an embedded join() with comma-sep values for
> functions.
>
> chris
>
> > thanks again!
> >
> > galeb
> >
> > On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
> > There is no need to do that if one is using the Bio::SeqFeatureI
> interface.  Note that get_tag_values always returns a list, so to snag a
> single value for a tag in a scalar, force list context on the LHS by
> enclosing the variable in ().
> >
> > chris
> >
> > -----------------------------
> > #!/usr/bin/env perl
> >
> > use Modern::Perl;
> > use Bio::SeqIO;
> >
> > my $in = Bio::SeqIO->new(-format => 'genbank',
> >                         -file => shift);
> >
> > while (my $seq = $in->next_seq) {
> >   for my $feat ($seq->get_SeqFeatures) {
> >       next unless $feat->primary_tag eq 'CDS';
> >       my ($locus) = $feat->has_tag('locus_tag') ?
> >                     $feat->get_tag_values('locus_tag') : '';
> >       my @funcs = $feat->has_tag('function') ?
> >           $feat->get_tag_values('function') : ();
> >       say join("\t", $locus, join(',', at funcs));
> >   }
> > }
> >
> >
> >
>
>


From David.Messina at sbc.su.se  Fri Sep  9 05:40:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 11:40:25 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
Message-ID: <CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>

Hi Manju,


But this is not showing all query coverage as it shows in simple balst.(see
> attached file)
>

I'm not sure what you mean by query coverage here, as blast report you
attached doesn't (as far as I can see) include a calculation of the number
or percentage of query bases covered.

But in any case, everything in that blast report is available in the
Bio::SearchIO object that B::T::R::RemoteBlast returns. Have you taken a
look at http://www.bioperl.org/wiki/HOWTO:SearchIO ? That, along with the
module documentation, should help you find the parts of the BLAST report
you're looking for.



> and i also want to write that result in a blast file..Is there any method
> which can write the remoteblast output
> in a file with blast extension?
>

It is possible to write out the results in a format that closely resembles
the native blast report, but it's not recommended. If you want to just run
BLAST and get back a report, there's no need to use BioPerl to parse the
report first and then recreate the report.

This might also be a good time to mention that, if you're doing more than a
few hundred BLAST searches, you'll find it much more efficient to download
the database and the BLAST program from NCBI and run them on your own
computer. NCBI severely limits the speed and frequency of remote BLASTs, and
furthermore it's much more prone to failure.

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
remotely without BioPerl. Check out the --remote command-line option ? it's
my favorite new feature!


Dave



From David.Messina at sbc.su.se  Fri Sep  9 06:53:01 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 12:53:01 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
Message-ID: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>

If you don't want to learn how to do this in BioPerl, then take my previous
suggestion and just use NCBI's tools:

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
> remotely without BioPerl. Check out the --remote command-line option





On Fri, Sep 9, 2011 at 12:07, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I dont no more about Bioperl....
> and i just want to blast my sequences using bioperl...
> ans see the result in a file...
> pls tell me what should i do???
>


From manju.rawat2 at gmail.com  Fri Sep  9 07:05:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 07:05:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
Message-ID: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>

I want to learn...and i am learing it from starting...
My main query is I want to make a program which gives me that
result(sequence) which have no blast result(no matches in any database/or
particular database).
for this i have to do blast may time....but i am not getting desired result
in blast...this is the main problem which i am facing..
now pls tell me whta procedure i should follow...


Manju


From cjfields at illinois.edu  Fri Sep  9 09:03:26 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 9 Sep 2011 13:03:26 +0000
Subject: [Bioperl-l] blast result not matching.
In-Reply-To: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
	<CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
Message-ID: <AB17FEA3-524D-43EC-8C55-FAF7339FAE4A@illinois.edu>

If you are planning on looking against 'everything' (e.g. nt or nr), and you have many sequences to run, I would follow Dave's suggestion and download BLAST locally.  

chris

On Sep 9, 2011, at 6:05 AM, Manju Rawat wrote:

> I want to learn...and i am learing it from starting...
> My main query is I want to make a program which gives me that
> result(sequence) which have no blast result(no matches in any database/or
> particular database).
> for this i have to do blast may time....but i am not getting desired result
> in blast...this is the main problem which i am facing..
> now pls tell me whta procedure i should follow...
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Fri Sep  9 05:01:55 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 05:01:55 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
Message-ID: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>

Thanks to all..Its working..
I tried that module...and got the result follwing result in terminal...


waiting......db is All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
hit name is ref|NM_181451.1|
score is 240
hit name is ref|NM_001008415.1|
score is 234
hit name is ref|XM_002706247.1|
score is 212
hit name is ref|XM_002683856.1|
score is 208
hit name is gb|EF197120.1|
score is 208
hit name is ref|XR_083566.1|
score is 198
hit name is ref|NM_001097567.1|
score is 198
hit name is ref|NM_001098089.1|
score is 198
hit name is ref|XM_002699708.1|
score is 192
hit name is ref|XM_592786.5|
score is 192
hit name is ref|XM_001251693.3|
score is 192
hit name is gb|AF490400.1|
score is 190
hit name is gb|AY075103.1|
score is 190
hit name is ref|XR_083457.1|
score is 178


But this is not showing all query coverage as it shows in simple balst.(see
attached file)
and i also want to write that result in a blast file..Is there any method
which can write the remoteblast output
in a file with blast extension?


Thanks
Manju Rawat.
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From ross at cuhk.edu.hk  Sat Sep 10 02:39:23 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 10 Sep 2011 14:39:23 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick file
Message-ID: <048a01cc6f84$60c41090$224c31b0$@edu.hk>

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"

 

What's the problem? 

 

use Bio::TreeIO;

 

($treefh) = @ARGV;

 

my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;

 

$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);

 

my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);

 

my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";

 

 

#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;



From greg at ebi.ac.uk  Sat Sep 10 11:39:52 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Sat, 10 Sep 2011 16:39:52 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
Message-ID: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>

Hi Ross,

Which version of BioPerl are you using?

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
the following script works for me. Do those values look sensible to you? The
code on the new branch is a bit experimental, so I wouldn't be surprised if
all the edge cases for calculations like this aren't covered.

--greg

use Bio::TreeIO;

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");
my $tree = $treeio->next_tree;
my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");
my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");
my $ma = $tree->find("Mycobacterium_abscessus");
my $distance = $mt->distance($ma);
print "MT - MA: ".$mt->distance($ma)."\n";
print "MT - MS: ".$mt->distance($ms)."\n";
print "MS - MA: ".$ms->distance($ma)."\n";
# MT - MA: 0.24326
# MT - MS: 0.18573
# MS - MA: 0.20729

--greg

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ross at cuhk.edu.hk  Sat Sep 10 19:06:44 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 11 Sep 2011 07:06:44 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
Message-ID: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>

Hi Greg,

 

The values are correct! However, how to install this bioperl-live module? my
bioperl is 1.6.1 but there's an error:

 

Can't locate object method "find" via package "Bio::Tree::Tree" at
TreeCalDist.pl line 32, <GEN0> line 1.

my $mt = $tree->find($keyword);  #line 32

 

 

From: gjuggler at gmail.com [mailto:gjuggler at gmail.com] On Behalf Of Gregory
Jordan
Sent: 2011??9??10?? 23:40
To: bioperl-l List; Ross KK Leung
Subject: Re: [Bioperl-l] fail to obtain node-to-node distance from a newick
file

 

Hi Ross,

 

Which version of BioPerl are you using?

 

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree
/NodeFunctionsI.pm#L406) the following script works for me. Do those values
look sensible to you? The code on the new branch is a bit experimental, so I
wouldn't be surprised if all the edge cases for calculations like this
aren't covered.

 

--greg

 

use Bio::TreeIO;

 

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");

my $tree = $treeio->next_tree;

my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");

my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");

my $ma = $tree->find("Mycobacterium_abscessus");

my $distance = $mt->distance($ma);

print "MT - MA: ".$mt->distance($ma)."\n";

print "MT - MS: ".$mt->distance($ms)."\n";

print "MS - MA: ".$ms->distance($ma)."\n";

# MT - MA: 0.24326

# MT - MS: 0.18573

# MS - MA: 0.20729

 

--greg

 

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"



What's the problem?



use Bio::TreeIO;



($treefh) = @ARGV;



my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;



$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);



my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);



my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";





#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 




From manju.rawat2 at gmail.com  Mon Sep 12 01:37:35 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:37:35 -0400
Subject: [Bioperl-l] no blast result
Message-ID: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>

Hello,
I want to make a program which first generate the random sequence and then
gives me that result(sequence) which have no blast result(no matches in any
database/or particular database).Is there any body who can help me in doing
this.

Pl reply if anybody knows about it..
Thanks
Manju


From zhangchnxp at gmail.com  Mon Sep 12 01:51:59 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 13:51:59 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
Message-ID: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>

Hi,

IMHO, due to the nature of BLAST, it is usually impossible to get no results
from random sequence, but to get a set of matches with lower scores.

What you can do is to focus on the e-value, say, setting a threshold to it.

FYI, http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

On Mon, Sep 12, 2011 at 1:37 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Hello,
> I want to make a program which first generate the random sequence and then
> gives me that result(sequence) which have no blast result(no matches in any
> database/or particular database).Is there any body who can help me in doing
> this.
>
> Pl reply if anybody knows about it..
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From manju.rawat2 at gmail.com  Mon Sep 12 01:58:38 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:58:38 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
Message-ID: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>

Ya i know this....And it is also in my use if i get result with lower
scores.
But how could I do this?


Manju


From zhangchnxp at gmail.com  Mon Sep 12 02:04:17 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 14:04:17 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
Message-ID: <CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>

Please read the documentation for Bio::Tools::Run::StandAloneBlast
and Bio::AlignIO.*
*
On Mon, Sep 12, 2011 at 1:58 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Ya i know this....And it is also in my use if i get result with lower
> scores.
> But how could I do this?
>
>
> Manju
>


From manju.rawat2 at gmail.com  Mon Sep 12 07:12:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 07:12:40 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
Message-ID: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>

I read this..but default program is not runnig fine.it showing many error
that

MSG: cannot find path to blastall..
Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

Am this this is not showing output which i want..

Pl help me..

Manju Rawat


From arguelloj at gmail.com  Sun Sep 11 22:52:42 2011
From: arguelloj at gmail.com (J. Fernando Arguello)
Date: Sun, 11 Sep 2011 19:52:42 -0700
Subject: [Bioperl-l] BioPerl - quick general question
Message-ID: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>

Dear BioPerl,

I'm excited to see a project like this! Basically I have a computer science
background with a few years of development, research and minimal
bioinformatics experience.

Dumb question...where is the best place for a developer to begin on the
BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
BioPerl in the future?

Any input is much appreciated. Thank you all for your time.

Best,
Fernando
jfa


From briano at bioteam.net  Mon Sep 12 09:20:36 2011
From: briano at bioteam.net (Brian Osborne)
Date: Mon, 12 Sep 2011 09:20:36 -0400
Subject: [Bioperl-l] Fwd: cds sequence extract
References: <112c4ef2.641e.1325c4b21cb.Coremail.maliang7121@163.com>
Message-ID: <671CAF11-55A4-462A-BC5B-805C87E1EB0E@bioteam.net>

Liang Ma,

I'm forwarding this to the Bioperl mailing list.

If you're starting out with Bioperl I suggest you read this:

http://www.bioperl.org/wiki/HOWTO:Beginners

Brian O.


Begin forwarded message:

> From: maliang7121 <maliang7121 at 163.com>
> Date: September 12, 2011 2:20:20 AM EDT
> To: briano at bioteam.net
> Subject: cds sequence extract
> 
> Dear Brian:
> 
> I am a student of Chinese Academy of Sience, I begin to love bioperl, but now I have a problem.
> 
> According to the script of the attachment, I could easily dowload sequences from NCBI, now I need extract cds sequence from the genbank format files, and put them all in a single file using fasta format, I can not do it, could you spend a few minite wrinting a script for me?
> 
> Best!
> 
> Liang Ma
> 
> 
> 

Brian O.
--
Brian Osborne, PhD
BioTeam: http://bioteam.net
email: briano at bioteam.net
mobile: 978-317-3101

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From fs5 at sanger.ac.uk  Mon Sep 12 09:54:21 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Mon, 12 Sep 2011 14:54:21 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
Message-ID: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>

looks like BLAST is not install on your system. The BioPerl module only
runs BLAST for you and parses the output but you still need the BLAST
executables installed on your system. Follow the instructions on the
NCBI website to download and install BLAST and try running it on the
commandline with the "blastall" command. If that works then you can run
it also via BioPerl.
Frank


On Mon, 2011-09-12 at 07:12 -0400, Manju Rawat wrote:
> I read this..but default program is not runnig fine.it showing many error
> that
> 
> MSG: cannot find path to blastall..
> Use of uninitialized value $_[0] in join or string at
> /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> Am this this is not showing output which i want..
> 
> Pl help me..
> 
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From p.j.a.cock at googlemail.com  Mon Sep 12 10:00:30 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 12 Sep 2011 15:00:30 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>

On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
> looks like BLAST is not install on your system. The BioPerl module only
> runs BLAST for you and parses the output but you still need the BLAST
> executables installed on your system. Follow the instructions on the
> NCBI website to download and install BLAST and try running it on the
> commandline with the "blastall" command. If that works then you can run
> it also via BioPerl.
> Frank

Hang on - blastall is from the "legacy" BLAST suite, does
BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
blastn and blastp rather then blastall)?

Peter


From cjfields at illinois.edu  Mon Sep 12 13:45:56 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 12 Sep 2011 17:45:56 +0000
Subject: [Bioperl-l] BioPerl - quick general question
In-Reply-To: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
References: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
Message-ID: <62B9B300-96AC-4511-A1B9-CFF36CBE6288@illinois.edu>

On Sep 11, 2011, at 9:52 PM, J. Fernando Arguello wrote:

> Dear BioPerl,
> 
> I'm excited to see a project like this! Basically I have a computer science
> background with a few years of development, research and minimal
> bioinformatics experience.
> 
> Dumb question...where is the best place for a developer to begin on the
> BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
> BioPerl in the future?

The basic starting point: the HOWTOs and the tutorial (not sure how up-to-date some of the latter are, in general they should work):

http://www.bioperl.org/wiki/HOWTOs
http://www.bioperl.org/wiki/Tutorials

> Any input is much appreciated. Thank you all for your time.
> 
> Best,
> Fernando
> jfa

We gladly welcome anyone willing to hack on BioPerl.  The repository is now on github (core is https://github.com/bioperl/bioperl-live), so it's fairly easy to fork the code and make changes.  We are in the middle of splitting up the large codebase into more manageable subdistributions, so it's probably a good idea to ask on list about specific code in case the code is question resides in a separate repository.  

Let us know if you have additional questions!

Cheers!

chris




From shalabh.sharma7 at gmail.com  Mon Sep 12 14:00:16 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Mon, 12 Sep 2011 14:00:16 -0400
Subject: [Bioperl-l] Module for SOCS
Message-ID: <CAA7rn9d37ntxbtMUR3Z41JHTNZypi+2jZQunwGJ5bN8DZ21xtg@mail.gmail.com>

Hi All,
         I am using SOCS for mapping my SOILD data. I was just wondering if
there is any module in bioperl to analyze SOCS output files directly or
mapreads format.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From greg at ebi.ac.uk  Tue Sep 13 04:30:58 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Tue, 13 Sep 2011 09:30:58 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
Message-ID: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>

Hi Ross,

I don't typically 'install' versions of BioPerl from GitHub. Rather, I check
out the code into a directory that's on my Perl search path (and make sure
any other BioPerl code isn't on the path anymore). I think the following
commands should get you the right set of code:

> git clone git://github.com/bioperl/bioperl-live.git
> git checkout topic/tree_api_refresh

After that, I'm afraid I'll have to leave it to you (or someone else on the
list). I'm no Perl guru, so I don't know the "right" way to direct Perl
towards a developmental BioPerl branch.

Cheers,
 Greg

2011/9/11 Ross KK Leung <ross at cuhk.edu.hk>

> Hi Greg,****
>
> ** **
>
> The values are correct! However, how to install this bioperl-live module?
> my bioperl is 1.6.1 but there's an error:****
>
> ** **
>
> Can't locate object method "find" via package "Bio::Tree::Tree" at
> TreeCalDist.pl line 32, <GEN0> line 1.****
>
> my $mt = $tree->find($keyword);  #line 32****
>
> ** **
>
> ** **
>
> *From:* gjuggler at gmail.com [mailto:gjuggler at gmail.com] *On Behalf Of *Gregory
> Jordan
> *Sent:* 2011?9?10? 23:40
> *To:* bioperl-l List; Ross KK Leung
> *Subject:* Re: [Bioperl-l] fail to obtain node-to-node distance from a
> newick file****
>
> ** **
>
> Hi Ross,****
>
> ** **
>
> Which version of BioPerl are you using?****
>
> ** **
>
> With the refactored tree code (available from the tree_api_refresh branch
> on the BioPerl github repo:
> https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
> the following script works for me. Do those values look sensible to you? The
> code on the new branch is a bit experimental, so I wouldn't be surprised if
> all the edge cases for calculations like this aren't covered.****
>
> ** **
>
> --greg****
>
> ** **
>
> use Bio::TreeIO;****
>
> ** **
>
> my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");**
> **
>
> my $tree = $treeio->next_tree;****
>
> my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");****
>
> my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");****
>
> my $ma = $tree->find("Mycobacterium_abscessus");****
>
> my $distance = $mt->distance($ma);****
>
> print "MT - MA: ".$mt->distance($ma)."\n";****
>
> print "MT - MS: ".$mt->distance($ms)."\n";****
>
> print "MS - MA: ".$ms->distance($ma)."\n";****
>
> # MT - MA: 0.24326****
>
> # MT - MS: 0.18573****
>
> # MS - MA: 0.20729****
>
> ** **
>
> --greg****
>
> ** **
>
> On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:**
> **
>
> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l****
>
> ** **
>



From manju.rawat2 at gmail.com  Tue Sep 13 07:20:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 13 Sep 2011 07:20:07 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>

this is the perl code

 #!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO
use Bio::Tools::Run::StandAloneBlast;
 @params = ('database' => 'swissprot',
        'READMETHOD' => 'Blastn');

 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);


 $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
 $blast_report = $factory->blastall($input);


  write_blast(">rs.blast",$blast_report);


It showing error that


Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

MSG: cannot find path to blastall


From fs5 at sanger.ac.uk  Tue Sep 13 11:09:24 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Tue, 13 Sep 2011 16:09:24 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
Message-ID: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>

Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
StandAloneBlast is still set to "blastall" - I'm not sure if it works
with blast+ too.

Manju: as I said previously, you need to check that you can run BLAST on
the command line, i.e. make sure it is actually installed on your
system. Have you done that?
You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
you can manually set the path to your BLAST executable if it is not in
your path. You have to install BLAST fisrt before you can run this
module.
The other error you get from yuor code refers to something that is
outside of the code fragment you show here, so can't comment on that
one.

Frank


On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> this is the perl code
> 
>  #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO
> use Bio::Tools::Run::StandAloneBlast;
>  @params = ('database' => 'swissprot', 
>         'READMETHOD' => 'Blastn');
> 
>  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> 
> 
>  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
>  $blast_report = $factory->blastall($input);
>  
> 
>   write_blast(">rs.blast",$blast_report);
> 
> 
> It showing error that
> 
> 
> Use of uninitialized value $_[0] in join or string
> at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> MSG: cannot find path to blastall
> 
>  



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From David.Messina at sbc.su.se  Tue Sep 13 11:34:20 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 13 Sep 2011 17:34:20 +0200
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAM3TQQWx_QQK96etWHntvmRRnjJ9ZPCJYMcC0rukNoJD5_et1w@mail.gmail.com>

There's a separate Bio::Tools::Run::BlastPlus module for blast+. And a
related HOWTO:
http://www.bioperl.org/wiki/HOWTO:BlastPlus



On Tue, Sep 13, 2011 at 17:09, Frank Schwach <fs5 at sanger.ac.uk> wrote:

> Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
> StandAloneBlast is still set to "blastall" - I'm not sure if it works
> with blast+ too.
>
> Manju: as I said previously, you need to check that you can run BLAST on
> the command line, i.e. make sure it is actually installed on your
> system. Have you done that?
> You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
> you can manually set the path to your BLAST executable if it is not in
> your path. You have to install BLAST fisrt before you can run this
> module.
> The other error you get from yuor code refers to something that is
> outside of the code fragment you show here, so can't comment on that
> one.
>
> Frank
>
>
> On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> > this is the perl code
> >
> >  #!usr/bin/perl -w
> > use Bio::Perl;
> > use Bio::SearchIO
> > use Bio::Tools::Run::StandAloneBlast;
> >  @params = ('database' => 'swissprot',
> >         'READMETHOD' => 'Blastn');
> >
> >  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> >
> >
> >  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
> >  $blast_report = $factory->blastall($input);
> >
> >
> >   write_blast(">rs.blast",$blast_report);
> >
> >
> > It showing error that
> >
> >
> > Use of uninitialized value $_[0] in join or string
> > at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> >
> > MSG: cannot find path to blastall
> >
> >
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Tue Sep 13 15:36:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 13 Sep 2011 19:36:21 +0000
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>

On Sep 12, 2011, at 9:00 AM, Peter Cock wrote:

> On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
>> looks like BLAST is not install on your system. The BioPerl module only
>> runs BLAST for you and parses the output but you still need the BLAST
>> executables installed on your system. Follow the instructions on the
>> NCBI website to download and install BLAST and try running it on the
>> commandline with the "blastall" command. If that works then you can run
>> it also via BioPerl.
>> Frank
> 
> Hang on - blastall is from the "legacy" BLAST suite, does
> BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
> blastn and blastp rather then blastall)?
> 
> Peter

(aside: thought I sent this the other day.  never mix grant writing and open source)

Both BLAST and BLAST+ are supported via different modules.  Some users don't want to use BLAST+ for various reasons, though this may soon be out of their control when NCBI eventually stops supporting legacy BLAST entirely.

chris




From manju.rawat2 at gmail.com  Wed Sep 14 07:32:19 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 14 Sep 2011 07:32:19 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>
	<CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
Message-ID: <CAB2c7yqZ0Eb=7=GTiXidD-6_UzF8qB1JBVv+5h6+8xsR84HXuQ@mail.gmail.com>

On Wed, Sep 14, 2011 at 7:31 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I am trying to install Blast+ in my system.(ubuntu) from this link
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html.
> but i am getting error..
>
> first i downloaded the blast(ncbi-blast-2.2.25+-ia32-linux.tar.gz) from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
> .  and then extract it in the home/abc/ folder.
> after that i set the path for configuration in terminal i.e
>
> *PATH=$PATH:/home/abc/blast-2.2.25+/bin*
>
>
> but when i am  running blast -help in terminal it showing me error that
>
> error while loading shared libraries:
>  libbz2.so.1: cannot open shared object file: No such file or directory.
>
>


-- 
Regards
Manju Rawat
Project Assistant(NAIP)
Genomics Lab
ABTC,NDRI Karnal-132001,Haryana


From kumarsaurabh20 at gmail.com  Thu Sep 15 07:20:47 2011
From: kumarsaurabh20 at gmail.com (kumar Saurabh)
Date: Thu, 15 Sep 2011 13:20:47 +0200
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
Message-ID: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>

Hi,

I need to integrate the primer3 module in one of our pipeline. In a process,
I was testing the initial code given on the CPAN website. But whenever I try
to run this program its giving me error...that "Cannot locate the Object
method add_target via the package Bio::Tools:Run::Primer3Redux...."

The line of codes I am using is as follows:

# design some primers.
  # the output will be put into temp.out
  use Bio::Tools::Primer3Redux;
  use Bio::Tools::Run::Primer3Redux;
  use Bio::SeqIO;

  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
  my $seq = $seqio->next_seq;

  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
                                            -path =>
"/home/singh/Downloads/primer3-2.2.3/src/primer3_core");

  # or after the fact you can change the program_name
  $primer3->program_name('my_superfast_primer3');

  unless ($primer3->executable) {
    print STDERR "primer3 can not be found. Is it installed?\n";
    exit(-1)
  }

  # set the maximum and minimum Tm of the primer
  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);

  # Design the primers. This runs primer3 and returns a
  # Bio::Tools::Primer3::result object with the results
  # Primer3 can run in several modes (see explanation for
  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
  # either call it by its PRIMER_TASK name as in these examples:
  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
  $check_results = $primer3->check_primers();

  # Alternatively, explicitly set the PRIMER_TASK parameter and
  # use the generic 'run' method (this is mainly here for backwards
  # compatibility) :
  $primer3->PRIMER_TASK( 'pick_left_only' );
  $result = $primer3->run( $seq );

  # If no task is set and the 'run' method is called, primer3 will default
to
  # pick pcr primers.

  # see the Bio::Tools::Primer3Redux POD for
  # things that you can get from this. For example:

  print "There were ", $results->num_primer_pairs, " primer pairs\n";


Can anyone help me with this???


Best regards,
Kumar


From fs5 at sanger.ac.uk  Thu Sep 15 09:44:03 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 14:44:03 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
Message-ID: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>

Hi Kumar,

We are currently working on this module and you might want to check out
the latest version on Chris Field's github project:

https://github.com/cjfields/Bio-Tools-Primer3Redux

There will probably be some changes again once I get some time again to
work on a few points we discussed lately. You can also check out my repo
here:
https://github.com/fschwach/Bio-Tools-Primer3Redux

but I will certainly have to make changes to that code because I used
AUTOLAD in the last version, which is probably not a good idea.
My recommendation would be to use Chris' repo and see if that works for
you. If not, feedback would be much appreciated.

Cheers,

Frank




On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> Hi,
> 
> I need to integrate the primer3 module in one of our pipeline. In a process,
> I was testing the initial code given on the CPAN website. But whenever I try
> to run this program its giving me error...that "Cannot locate the Object
> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> 
> The line of codes I am using is as follows:
> 
> # design some primers.
>   # the output will be put into temp.out
>   use Bio::Tools::Primer3Redux;
>   use Bio::Tools::Run::Primer3Redux;
>   use Bio::SeqIO;
> 
>   my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>   my $seq = $seqio->next_seq;
> 
>   my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>                                             -path =>
> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> 
>   # or after the fact you can change the program_name
>   $primer3->program_name('my_superfast_primer3');
> 
>   unless ($primer3->executable) {
>     print STDERR "primer3 can not be found. Is it installed?\n";
>     exit(-1)
>   }
> 
>   # set the maximum and minimum Tm of the primer
>   $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> 
>   # Design the primers. This runs primer3 and returns a
>   # Bio::Tools::Primer3::result object with the results
>   # Primer3 can run in several modes (see explanation for
>   # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>   # either call it by its PRIMER_TASK name as in these examples:
>   $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>   $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>   $check_results = $primer3->check_primers();
> 
>   # Alternatively, explicitly set the PRIMER_TASK parameter and
>   # use the generic 'run' method (this is mainly here for backwards
>   # compatibility) :
>   $primer3->PRIMER_TASK( 'pick_left_only' );
>   $result = $primer3->run( $seq );
> 
>   # If no task is set and the 'run' method is called, primer3 will default
> to
>   # pick pcr primers.
> 
>   # see the Bio::Tools::Primer3Redux POD for
>   # things that you can get from this. For example:
> 
>   print "There were ", $results->num_primer_pairs, " primer pairs\n";
> 
> 
> Can anyone help me with this???
> 
> 
> Best regards,
> Kumar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From cjfields at illinois.edu  Thu Sep 15 10:13:38 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 15 Sep 2011 14:13:38 +0000
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>

I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 

chris

On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:

> Hi Kumar,
> 
> We are currently working on this module and you might want to check out
> the latest version on Chris Field's github project:
> 
> https://github.com/cjfields/Bio-Tools-Primer3Redux
> 
> There will probably be some changes again once I get some time again to
> work on a few points we discussed lately. You can also check out my repo
> here:
> https://github.com/fschwach/Bio-Tools-Primer3Redux
> 
> but I will certainly have to make changes to that code because I used
> AUTOLAD in the last version, which is probably not a good idea.
> My recommendation would be to use Chris' repo and see if that works for
> you. If not, feedback would be much appreciated.
> 
> Cheers,
> 
> Frank
> 
> 
> 
> 
> On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
>> Hi,
>> 
>> I need to integrate the primer3 module in one of our pipeline. In a process,
>> I was testing the initial code given on the CPAN website. But whenever I try
>> to run this program its giving me error...that "Cannot locate the Object
>> method add_target via the package Bio::Tools:Run::Primer3Redux...."
>> 
>> The line of codes I am using is as follows:
>> 
>> # design some primers.
>>  # the output will be put into temp.out
>>  use Bio::Tools::Primer3Redux;
>>  use Bio::Tools::Run::Primer3Redux;
>>  use Bio::SeqIO;
>> 
>>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>>  my $seq = $seqio->next_seq;
>> 
>>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>>                                            -path =>
>> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
>> 
>>  # or after the fact you can change the program_name
>>  $primer3->program_name('my_superfast_primer3');
>> 
>>  unless ($primer3->executable) {
>>    print STDERR "primer3 can not be found. Is it installed?\n";
>>    exit(-1)
>>  }
>> 
>>  # set the maximum and minimum Tm of the primer
>>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
>> 
>>  # Design the primers. This runs primer3 and returns a
>>  # Bio::Tools::Primer3::result object with the results
>>  # Primer3 can run in several modes (see explanation for
>>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>>  # either call it by its PRIMER_TASK name as in these examples:
>>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>>  $check_results = $primer3->check_primers();
>> 
>>  # Alternatively, explicitly set the PRIMER_TASK parameter and
>>  # use the generic 'run' method (this is mainly here for backwards
>>  # compatibility) :
>>  $primer3->PRIMER_TASK( 'pick_left_only' );
>>  $result = $primer3->run( $seq );
>> 
>>  # If no task is set and the 'run' method is called, primer3 will default
>> to
>>  # pick pcr primers.
>> 
>>  # see the Bio::Tools::Primer3Redux POD for
>>  # things that you can get from this. For example:
>> 
>>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
>> 
>> 
>> Can anyone help me with this???
>> 
>> 
>> Best regards,
>> Kumar
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From fs5 at sanger.ac.uk  Thu Sep 15 10:43:48 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 15:43:48 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
	<D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
Message-ID: <1316097828.3797.700.camel@deskpro15336.internal.sanger.ac.uk>

I also haven't had the time yet to work on this again but, yes, we need
to make sure we don't loose track of where we are. 


On Thu, 2011-09-15 at 14:13 +0000, Fields, Christopher J wrote:
> I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 
> 
> chris
> 
> On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:
> 
> > Hi Kumar,
> > 
> > We are currently working on this module and you might want to check out
> > the latest version on Chris Field's github project:
> > 
> > https://github.com/cjfields/Bio-Tools-Primer3Redux
> > 
> > There will probably be some changes again once I get some time again to
> > work on a few points we discussed lately. You can also check out my repo
> > here:
> > https://github.com/fschwach/Bio-Tools-Primer3Redux
> > 
> > but I will certainly have to make changes to that code because I used
> > AUTOLAD in the last version, which is probably not a good idea.
> > My recommendation would be to use Chris' repo and see if that works for
> > you. If not, feedback would be much appreciated.
> > 
> > Cheers,
> > 
> > Frank
> > 
> > 
> > 
> > 
> > On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> >> Hi,
> >> 
> >> I need to integrate the primer3 module in one of our pipeline. In a process,
> >> I was testing the initial code given on the CPAN website. But whenever I try
> >> to run this program its giving me error...that "Cannot locate the Object
> >> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> >> 
> >> The line of codes I am using is as follows:
> >> 
> >> # design some primers.
> >>  # the output will be put into temp.out
> >>  use Bio::Tools::Primer3Redux;
> >>  use Bio::Tools::Run::Primer3Redux;
> >>  use Bio::SeqIO;
> >> 
> >>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
> >>  my $seq = $seqio->next_seq;
> >> 
> >>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
> >>                                            -path =>
> >> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> >> 
> >>  # or after the fact you can change the program_name
> >>  $primer3->program_name('my_superfast_primer3');
> >> 
> >>  unless ($primer3->executable) {
> >>    print STDERR "primer3 can not be found. Is it installed?\n";
> >>    exit(-1)
> >>  }
> >> 
> >>  # set the maximum and minimum Tm of the primer
> >>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> >> 
> >>  # Design the primers. This runs primer3 and returns a
> >>  # Bio::Tools::Primer3::result object with the results
> >>  # Primer3 can run in several modes (see explanation for
> >>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
> >>  # either call it by its PRIMER_TASK name as in these examples:
> >>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
> >>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
> >>  $check_results = $primer3->check_primers();
> >> 
> >>  # Alternatively, explicitly set the PRIMER_TASK parameter and
> >>  # use the generic 'run' method (this is mainly here for backwards
> >>  # compatibility) :
> >>  $primer3->PRIMER_TASK( 'pick_left_only' );
> >>  $result = $primer3->run( $seq );
> >> 
> >>  # If no task is set and the 'run' method is called, primer3 will default
> >> to
> >>  # pick pcr primers.
> >> 
> >>  # see the Bio::Tools::Primer3Redux POD for
> >>  # things that you can get from this. For example:
> >> 
> >>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
> >> 
> >> 
> >> Can anyone help me with this???
> >> 
> >> 
> >> Best regards,
> >> Kumar
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > 
> > 
> > -- 
> > The Wellcome Trust Sanger Institute is operated by Genome Research 
> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose registered 
> > office is 215 Euston Road, London, NW1 2BE. 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From manju.rawat2 at gmail.com  Fri Sep 16 01:09:25 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:09:25 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>

Hello Frank,

Yes,u r rite..I tried to run blast in terminal but its not working..
I have installed the latest version of blast and download the database
correctly..

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.
Manju


From manju.rawat2 at gmail.com  Fri Sep 16 01:12:03 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:12:03 -0400
Subject: [Bioperl-l] Command line error in BLAST+
Message-ID: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>

Hi,


I have installed the latest version of blast and download the database
correctly Using this tutorial
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.

Thanks
Manju


From p.j.a.cock at googlemail.com  Fri Sep 16 04:15:46 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:15:46 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <CAKVJ-_4UF=5oBNc-ZRESAXzO-tC2j+nQGn0Qjh4E51Yrvr2o3A@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:12 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
>
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
>
> Thanks
> Manju

You're using the BioPerl wrapper for legacy blast (blastall),
which is not installed. Instead you have the new blast+
suite which includes a wrapper using the perl script
legacy_blast.pl to imitate the old blastall tool (in this
case it calls the new tool blastn).

Fix 1: Edit legacy_blast.pl to use the path to blastn etc
under your home directory

Fix 2: Install BLAST+ at system level

Fix 3: Use the BioPerl wrapper for BLAST+ instead.

I'd go with option 3.

Peter


From p.j.a.cock at googlemail.com  Fri Sep 16 04:17:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:17:58 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
	<CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
Message-ID: <CAKVJ-_5Omy7h9qx++7S-46YrxFTxbGoQZu61GDgM12C2FmQJsQ@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:09 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello Frank,
>
> Yes,u r rite..I tried to run blast in terminal but its not working..
> I have installed the latest version of blast and download the database
> correctly..
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out
> Can't exec "/usr/bin/blastn": No such file or directory at
> /usr/bin/legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
> Manju

For the benefit of anyone reading the archives later,
I tried to answer this in Manju's new thread:
http://lists.open-bio.org/pipermail/bioperl-l/2011-September/035696.html

Peter


From fs5 at sanger.ac.uk  Fri Sep 16 04:36:37 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 16 Sep 2011 09:36:37 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <1316162197.3797.721.camel@deskpro15336.internal.sanger.ac.uk>

Hi Manju,

Are you on Ubuntu? I think I've seen problems with this bzip library on
Ubuntu before. It's not a problem with BLAST in any case. 
Should be possible to install the missing files through your package
manager. I'm sure Google will know what to do :)
Not sure what went wrong with your blast installation. What happens if
you run blastall directly (without the legacy_blast.pl script)? In any
case, it might be better to ask the NCBI people for help with the BLAST
installation as this is not a BioPerl problem.

cheers,

Frank


On Fri, 2011-09-16 at 01:12 -0400, Manju Rawat wrote:
> Hi,
> 
> 
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
> 
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
> 
> 
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
> 
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
> 
> I have checked everything but not able tp fine the error..
> 
> Pl help me.
> 
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From ross at cuhk.edu.hk  Fri Sep 16 04:51:38 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 16 Sep 2011 16:51:38 +0800
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
Message-ID: <085501cc744d$d90b4500$8b21cf00$@edu.hk>

I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!

 




From cjfields at illinois.edu  Fri Sep 16 09:22:07 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 16 Sep 2011 13:22:07 +0000
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <085501cc744d$d90b4500$8b21cf00$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
Message-ID: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>

That seems like a pretty straightforward thing to do; there isn't an all-in-one way of doing this, but that's a good thing (it's a separation of concerns).

1) Run and parse BLAST results and grab seqID and coordinates for each hit (or each HSP for each hit) (Bio::SearchIO)
2) Pull the right subsequence +/- 20bp using above from the indexed flat file of your reference (Bio::DB::Fasta)

You can get revcomped sequence from Bio::DB::Fasta directly by flipping coordinates:
  
  # raw sequence
  my $seq      = $db->seq('CHROMOSOME_I',4_000_000 => 4_100_000);
  my $revseq   = $db->seq('CHROMOSOME_I',4_100_000 => 4_000_000);

chris


On Sep 16, 2011, at 3:51 AM, Ross KK Leung wrote:

> I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From wsavigne at yahoo.com  Fri Sep 16 16:45:12 2011
From: wsavigne at yahoo.com (Willy Savigne)
Date: Fri, 16 Sep 2011 13:45:12 -0700 (PDT)
Subject: [Bioperl-l] question Bioperl installation
Message-ID: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>

my name is william how do download Bioperl i tried other site but NOTHING? i would like to know info in downloading? bioperl .This is my first? time into knowing? bioinformatic i? just got? a book developing bioinformatic and begginning perl bioinformatic. I do alot Dna and RNA sequencing?? and more.
?
Thank u willy


From ross at cuhk.edu.hk  Sun Sep 18 06:51:05 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 18 Sep 2011 18:51:05 +0800
Subject: [Bioperl-l] snp/frameshift identification
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <08a901cc75f0$dd463b30$97d2b190$@edu.hk>

Dear Bioperl-users,

Following Fields, Christopher J's advice on sequence extraction, I manage to
proceed to the last stage of non-synonymous SNP identification. Now what I
have in hand is thousands of reliable multiple sequence alignment files,
e.g.

>seq1
ATGACAGACACGACGTTGCCGTAG
>seq2
ATGACAGACACGACGTAGCCGTAG
>seq3
ATGACAGACACGACGTTGCCGTAG

Seq2 has a T->A mutation and that leads to a stop codon generation. I wonder
if Bioperl has handled this kind of SNP or frameshift or non-sense mutations
that lead to change of amino acid in the translated protein product.

Thanks again to the community that helps me a great deal so I can catch up
progress during this Sat/Sun!!



From rondonbio at yahoo.com.br  Mon Sep 19 09:46:36 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Mon, 19 Sep 2011 06:46:36 -0700 (PDT)
Subject: [Bioperl-l] help-> SearchIO
Message-ID: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>

Hi guys! I need your help in a loop that I have in SearchIO.
I need to check the nucleotide coverage of querys using BLAST. I'm using the script below. It's open the alignment, create arrays for each query with zeros in each nucleotide position but, when I adds values to the coverage of each nucleotide, the script does it once and passes to another query.
Can you hek me?
Thank you very much,

Rondon
a Brazilian friend.


use Bio::SearchIO;
?
my $alignment = new Bio::SearchIO ( -format => 'blastXML',
? ? ? ? ? ? ? ? ? ? ? ? ?? ? -file ? => $alignment_file );

my %positions;
while (my $result = $alignment->next_result) {
while (my $hit = $result->next_hit) {
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
my @pos = $hsp->seq_inds('query','identical');
for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
foreach my $num (@pos) {
${$positions{$query_name}}[$num -1]++; ? ?#This loop is where I believe that is an error.
}
}
}
}

foreach my $key (keys %positions){
print "$key\t@{$positions{$key}}\n";
}

exit;



From roy.chaudhuri at gmail.com  Mon Sep 19 12:29:41 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:29:41 +0100
Subject: [Bioperl-l] help-> SearchIO
In-Reply-To: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
References: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
Message-ID: <4E776DF5.6040504@gmail.com>

Hi Rondon,

The line where you populate your arrayref with 0 (starting "for 
(0..$tam)") is within the HSP loop, so the data from every successive 
HSP will overwrite the previous one in your hash. You will therefore 
only see the data for the last HSP from each query. If you move that 
line to execute once per result (i.e. just after the line starting 
"while (my result ="), then I think it should work as you intended.

Cheers,
Roy.

On 19/09/2011 14:46, Rondon Neto wrote:
> Hi guys! I need your help in a loop that I have in SearchIO. I need
> to check the nucleotide coverage of querys using BLAST. I'm using the
> script below. It's open the alignment, create arrays for each query
> with zeros in each nucleotide position but, when I adds values to the
> coverage of each nucleotide, the script does it once and passes to
> another query. Can you hek me? Thank you very much,
>
> Rondon a Brazilian friend.
>
> use Bio::SearchIO;
>
> my $alignment = new Bio::SearchIO ( -format =>  'blastXML',
>                               -file   =>  $alignment_file );
>
> my %positions;
> while (my $result = $alignment->next_result) {
> while (my $hit = $result->next_hit) {
> while (my $hsp = $hit->next_hsp) {
> my $query_name = $result->query_name();
> my $tam = $result ->  query_length();
> my @pos = $hsp->seq_inds('query','identical');
> for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
> foreach my $num (@pos) {
> ${$positions{$query_name}}[$num -1]++;    #This loop is where I believe that is an error.
> }
> }
> }
> }
>
> foreach my $key (keys %positions){
> print "$key\t@{$positions{$key}}\n";
> }
>
> exit;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From roy.chaudhuri at gmail.com  Mon Sep 19 12:39:40 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:39:40 +0100
Subject: [Bioperl-l] question Bioperl installation
In-Reply-To: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
References: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
Message-ID: <4E77704C.20604@gmail.com>

Hi Willy,

There are instructions for downloading and installing BioPerl on the wiki:
http://www.bioperl.org/wiki/Getting_BioPerl
http://www.bioperl.org/wiki/Installing_BioPerl

These are the first two results when you Google for "bioperl download".

Note that the wiki is a little out of date, the latest BioPerl version 
is 1.6.901:
http://search.cpan.org/~cjfields/BioPerl-1.6.901/

Cheers,
Roy.

On 16/09/2011 21:45, Willy Savigne wrote:
> my name is william how do download Bioperl i tried other site but
> NOTHING  i would like to know info in downloading  bioperl .This is
> my first  time into knowing  bioinformatic i  just got  a book
> developing bioinformatic and begginning perl bioinformatic. I do alot
> Dna and RNA sequencing   and more.
>
> Thank u willy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From bosborne11 at verizon.net  Tue Sep 20 13:01:21 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 13:01:21 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
Message-ID: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>

All,

I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:

..... get the files etc ....

my %alignparams = (
    -seqtype  => 'nucleo',
    -usetree_nowarn => $guidetreefile,
    -in => $tempfile
);
my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);

# $align is a Bio::SimpleAlign object
my $align = $aligner->align($tempfile);

my %treeparams = (
   -data_type => 'nt',
   -model     => 'K80',  # Kimura
   -tree      => 'BIONJ',
   -bootstrap => 1000
);
my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);

#$tree is a Bio::Tree::Tree object
my $tree = $treemaker->run($align);

My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:

$distance = $tree->subtree_length($internal_node)

Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!

Brian O.


From bosborne11 at verizon.net  Tue Sep 20 15:17:13 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 15:17:13 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
In-Reply-To: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
References: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
Message-ID: <A2EDBACB-963C-4E1C-8E7A-5F769BE89476@verizon.net>

Ah, I see:

my $distances = $tree->distance(-nodes => [$node1,$node2]);

Brian O.


On Sep 20, 2011, at 1:01 PM, Brian Osborne wrote:

> All,
> 
> I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:
> 
> ..... get the files etc ....
> 
> my %alignparams = (
>    -seqtype  => 'nucleo',
>    -usetree_nowarn => $guidetreefile,
>    -in => $tempfile
> );
> my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);
> 
> # $align is a Bio::SimpleAlign object
> my $align = $aligner->align($tempfile);
> 
> my %treeparams = (
>   -data_type => 'nt',
>   -model     => 'K80',  # Kimura
>   -tree      => 'BIONJ',
>   -bootstrap => 1000
> );
> my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);
> 
> #$tree is a Bio::Tree::Tree object
> my $tree = $treemaker->run($align);
> 
> My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:
> 
> $distance = $tree->subtree_length($internal_node)
> 
> Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!
> 
> Brian O.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Thu Sep 22 07:07:39 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 22 Sep 2011 16:37:39 +0530
Subject: [Bioperl-l] database for Bos Touras
Message-ID: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>

Hello To All,

I want to blast my sequence Only in Bos Touras Database Using Local
Blast(Blast+).
But I dnt Know which database I should use for this From this Link.
ftp://ftp.ncbi.nlm.nih.gov/blast/db/

Pl tell me which DB I Should use??

Thanks
Manju


From hrh at fmi.ch  Thu Sep 22 07:44:56 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 13:44:56 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
Message-ID: <4E7B1FB8.8090208@fmi.ch>


assuming you mean 'Bos taurus', it might be easier to get the data from

ucsc:  http://hgdownload.cse.ucsc.edu/downloads.html#cow

or ensembl: ftp://ftp.ensembl.org/pub/release-64/fasta/bos_taurus/dna/



Regards, Hans



On 09/22/2011 01:07 PM, Manju Rawat wrote:
> Hello To All,
>
> I want to blast my sequence Only in Bos Touras Database Using Local
> Blast(Blast+).
> But I dnt Know which database I should use for this From this Link.
> ftp://ftp.ncbi.nlm.nih.gov/blast/db/
>
> Pl tell me which DB I Should use??
>
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From hrh at fmi.ch  Thu Sep 22 08:16:00 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 14:16:00 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
	<4E7B1FB8.8090208@fmi.ch>
	<CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
Message-ID: <4E7B2700.8080904@fmi.ch>


Yes, BLAST uses fasta files. You (may need to concatenate the individual 
chromosomes and the you) need to index them with 'makeblastdb' which is 
also part of the blast+ software package.

see: http://www.ncbi.nlm.nih.gov/books/NBK1762/


Hans

On 09/22/2011 01:49 PM, Manju Rawat wrote:
> It will work on Local Blast or not??????


From bosborne11 at verizon.net  Thu Sep 22 12:16:39 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 22 Sep 2011 12:16:39 -0400
Subject: [Bioperl-l] [bioperl-live] genbank_ref_extractor: new script to
 make search on entrez gene and retrieve related sequences (#23)
In-Reply-To: <bioperl/bioperl-live/pull/23@github.com>
References: <bioperl/bioperl-live/pull/23@github.com>
Message-ID: <245C75D5-61EC-4395-B64F-47D8471568F5@verizon.net>

Carne,

This is impressive looking, it is now in scripts/.

Thanks again,

Brian O.

On Sep 21, 2011, at 11:25 AM, Carn? Draug wrote:

> Hi
> 
> I wrote a script with bioperl that I would like to share back. It takes a list of searches for Entrez Gene and attempts to retrieve the related sequences (genomic, transcripts and proteins). It is also possible to obtain extra upstream and downstream bp for genomic sequences and control the naming of the files. In the end it can save all the results in a CSV file.
> 
> Hope you find it up to your coding standards. Suggestions for improvements are welcome, including for a better name.
> 
> Carn?
> 
> You can merge this Pull Request by running:
> 
>  git pull https://github.com/carandraug/bioperl-live bp_genbank_ref_extractor
> 
> Or you can view, comment on it, or merge it online at:
> 
>  https://github.com/bioperl/bioperl-live/pull/23
> 
> -- Commit Summary --
> 
> * genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences
> 
> -- File Changes --
> 
> A scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl (1064)
> 
> -- Patch Links --
> 
>  https://github.com/bioperl/bioperl-live/pull/23.patch
>  https://github.com/bioperl/bioperl-live/pull/23.diff
> 
> -- 
> Reply to this email directly or view it on GitHub:
> https://github.com/bioperl/bioperl-live/pull/23




From bluecurio at gmail.com  Thu Sep 22 15:32:07 2011
From: bluecurio at gmail.com (Daniel Renfro)
Date: Thu, 22 Sep 2011 14:32:07 -0500
Subject: [Bioperl-l] Download RefSeq revision history programmatically
Message-ID: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>

I am working on a project to find historical differences in GenBank/RefSeq files. I would like to download all the old revisions of a file (for example NC_000913 [http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2?report=girevhist]) using any technology available. I wrote a page-scraper in Perl, but I can't get NCBI to return plaintext, only HTML (which does nobody any good.) 

Does anyone know of a way to get all the "revisions" (not just "versions") of a GenBank/RefSeq file?

-Daniel 
--
http://ecoliwiki.net/User:DanielRenfro
Hu Lab Research Associate
979-862-4055



From ross at cuhk.edu.hk  Tue Sep 27 10:16:14 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 27 Sep 2011 22:16:14 +0800
Subject: [Bioperl-l]  obtain a distance matrix from tree
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>

After using MEGA to generate a newick tree file (phylogram), I wonder if
Bioperl has any convenient functions to derive the (n x n) distance (by NJ,
MP etc) matrix. Thanks for your advice in advance!




From thomas.sharpton at gmail.com  Tue Sep 27 16:02:44 2011
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Tue, 27 Sep 2011 13:02:44 -0700
Subject: [Bioperl-l] obtain a distance matrix from tree
In-Reply-To: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
	<014201cc7d20$03abd4c0$0b037e40$@edu.hk>
Message-ID: <C2ED3ADC-B089-4481-BD63-8D5FDFB51CFA@gmail.com>

Hi Ross,

For very large trees, I found it to be more efficient to do this in R  
using the ape package. I have a script listed in my github repo that  
will convert a tree to a distance matrix via in R at the link below:

https://github.com/sharpton/PhylOTU/blob/master/tree_to_matrix.R

That said, I've also done this in Bioperl using something like the  
following:

use Bio::TreeIO;

my $treein = Bio::TreeIO->new( -fh => "input_tree.nwk", -format =>  
'newick' );
while( my $tree = $treein->next_tree ){
	my %dist_matrix = ();
	my @leaves = $tree->get_leaf_nodes;
	foreach my $leaf1( @leaves ){
		my $id1 = $leaf1->id;	
		foreach my $leaf2( @leaves ){
			my $id2 = $leaf2->id;
			next if $id1 eq $id2;
			next if( defined( $dist_matrix{$id1}->{$id2} ) || defined  
( $dist_matrix{$id2}->{$id1} ) );
			my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] );
			$dist_matrix{$id1}->{$id2} = $distance;
		}
	}
}
#print distance matrix here....

This will put the information you need to create either a full or a  
upper triangle distance matrix into the hash %dist_matrix. I didn't  
test the above, so hopefully there are no bugs....

Someone else may have a more elegant solution.

Best,
Tom

PS: Sorry if you get this twice.

On Sep 27, 2011, at 7:16 AM, Ross KK Leung wrote:

> After using MEGA to generate a newick tree file (phylogram), I  
> wonder if
> Bioperl has any convenient functions to derive the (n x n) distance  
> (by NJ,
> MP etc) matrix. Thanks for your advice in advance!
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From member at linkedin.com  Tue Sep 27 19:45:10 2011
From: member at linkedin.com (Razi Khaja via LinkedIn)
Date: Tue, 27 Sep 2011 23:45:10 +0000 (UTC)
Subject: [Bioperl-l] Invitation to connect on LinkedIn
Message-ID: <1856085440.8574001.1317167110185.JavaMail.app@ela4-bed82.prod>

LinkedIn
------------




    Razi Khaja requested to add you as a connection on LinkedIn:
  
------------------------------------------

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Accept invitation from Razi Khaja
http://www.linkedin.com/e/5drwke-gt3jaequ-6k/uez6TYkHzbaXxXM-lUk23auFwJZodcPlXc2UWC0Ao8h/blk/I3148646357_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPsRcPoQdzwQcjd9bSsPizpOoltTbP0NdPgMd3kTcPgLrCBxbOYWrSlI/EML_comm_afe/?hs=false&tok=2TjQgihXkh-kU1

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------------------------------------------



From ross at cuhk.edu.hk  Tue Sep 27 23:57:52 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 28 Sep 2011 11:57:52 +0800
Subject: [Bioperl-l]  ancestral state derived from Tree
In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
Message-ID: <017701cc7d92$cba88d20$62f9a760$@edu.hk>


By using Tom's advice, I'm able to obtain the distance matrix for the
following tree by Bioperl TreeIO. 

((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000
00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00
000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(
L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0
.00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,
(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000
):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000
00);

For the last few nodes T, U and V, they should be monophyletic but U and V
should be more closely related. Although I can use TreeIO methods like
is_monophyletic or is_paraphyletic to test in this case, the problem becomes
more tricky for nodes A, B, C, D because D actually makes no difference from
the common ancestor of nodes A, B, C and D. Since is_monophyletic does not
take into account for this case, is there any workaround? I have to pay
attention to such a detail in order to make a better guess for the ancestral
state(s) at various points of this tree.

Thanks again for the TreeIO developers for making tree analysis easier for
us biologists!



From manju.rawat2 at gmail.com  Wed Sep 28 05:54:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 28 Sep 2011 15:24:07 +0530
Subject: [Bioperl-l] how to blast a seq against multiple dbase
Message-ID: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>

Hello,

I have downloaded all the chromosome of Bos Taurus and i'd changed them in
blast format using makeblastdb..and now i want to localy blast my sequence
against these all chromosome..
now i have 29 database.Is there any method by which can i blast my sequence
against all 29 database in my program..


whta should i write in database????

@params = ('database' => '????????', 'outfile' => 'blast2.out',
        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');



Thanks
Manju Rawat


From p.j.a.cock at googlemail.com  Wed Sep 28 06:02:07 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 28 Sep 2011 11:02:07 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <CAKVJ-_7HCbvfm=mgcXEmL_9AH6A3rttnLrW86rs1ecNB0L7=XQ@mail.gmail.com>

On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello,
>
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
>
>
> whta should i write in database????
>
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
> ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn');
>

The simple answer is make a combined database. This
works internally with alias files, have a look at the NR
and NT databases for example - they act like singe
databases but are actually a collection of chunks.

Even simpler would be to combine your Bos taurus
sequence files into a single multi-entry FASTA file,
and make that into a single BLAST database.

Peter



From awitney at sgul.ac.uk  Wed Sep 28 06:42:39 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 28 Sep 2011 11:42:39 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <B2F15B1E-24EB-41B5-8BC4-07A2EF4C8286@sgul.ac.uk>


I think if you want to keep the databases separate you would need to create a factory for each database, something like this

foreach my $db ( @databases ) {
	my $factory = Bio::Tools::Run::StandAloneBlastPlus->new( -db_data => $db ,  < ? any other params ? > );

	? do blast stuff?
}

or as Peter says in another email you could combine your databases and run one query then filter them out in the results.

regards

adam

On 28 Sep 2011, at 10:54, Manju Rawat wrote:

> Hello,
> 
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
> 
> 
> whta should i write in database????
> 
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
>        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');
> 
> 
> 
> Thanks
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Wed Sep 28 07:43:02 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 12:43:02 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
Message-ID: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>

Hi everyone,

is there a recommended way to get the version of a script that is part
of bioperl (the ones in the scripts directory)? Rather than hard
coding the version of the script independent of bioperl, I thought on
using the bioperl version itself. How can this be done?

Thanks in advance,
Carn?



From carandraug+dev at gmail.com  Wed Sep 28 11:00:34 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 16:00:34 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
Message-ID: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>

2011/9/28 longbow leo <longbow0 at gmail.com>:
> Hi, Carn?,
>
> Do you mean this:
>
> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>
> In my machine, the output is

Thank you. Yes this is what I was looking for. I looked down how that
variable comes up and so I think I'll use

use Bio::Root::Version;
say $Bio::Root::Version::VERSION;

Carn?



From pcantalupo at gmail.com  Wed Sep 28 12:54:19 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 28 Sep 2011 12:54:19 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
Message-ID: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>

Hello,

I'm using the most recent copy of bioperl-live (pulled yesterday). I
have a BLASTN (from blast+) output file for 3 query sequences
(https://gist.github.com/1248342). I used this script,
https://gist.github.com/1248338, to print the query id, algorithm and
algorithm_version for each result. When I run the script, I get the
following output:

GFAVMM201BADC0 ?BLASTN ?2.2.25+
GFAVMM201A1JOH ?BLASTN
GFAVMM201D933Z ?BLASTN

Algorithm_version outputs the correct version for the first result but
outputs the empty string for the 2nd and 3rd query. Why? This
functionality worked about a month ago. What has changed to cause this
to happen?

Thank you,

Paul



From rondonbio at yahoo.com.br  Wed Sep 28 15:47:45 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Wed, 28 Sep 2011 12:47:45 -0700 (PDT)
Subject: [Bioperl-l] best Hit
Message-ID: <1317239265.98674.YahooMailNeo@web130214.mail.mud.yahoo.com>

Hi guys.?

I have this subroutine that returns a hash with nucleotide's coverage of each query from a blast alignment.
So, I want to compute uniq hits. If a hit has already been aligned with a query, it must be eliminated from my experiment.
Can anyone check if it's right or can fix it to me? Is there a way to do that directly in blast?

Thank you

Rondon Neto


sub nucleotide_coverage{
#Bio::SearchIO dependent
#This subroutine return a Hash and a file with nucleotide coverage?
#for each query in an blast alignment xlm file. The input is the
#alignment file.

my ($alignment_file) = @_;

my $alignment = new Bio::SearchIO ( -format => 'blastXML',
 ? ?-file ? => $alignment_file );my %positions;my @used_reads;
while (my $result = $alignment->next_result) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
for (0..$tam-1){ ${$positions{$query_name}}[$_] = 0 }?
while (my $hit = $result->next_hit) {
my $hit_name = $hit->name;
# Here is my best hit parser. Is it ok?
foreach my $read (@used_reads) {
if ( $read eq $hit_name ) {
next;
}
}
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my @pos = $hsp->seq_inds('query','identical');
foreach my $num (@pos) {
${$positions{$query_name}}[$num-1]++;
}
}
push (@used_reads, $hit_name);
}
}

my $outfile = "nucleotide_coverage.txt";
open OUT, ">$outfile" or die $!;foreach my $key (keys %positions){print OUT "$key\t@{$positions{$key}}\n";
}

close OUT;

return \%positions;

}


From shalabh.sharma7 at gmail.com  Wed Sep 28 15:53:07 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 28 Sep 2011 15:53:07 -0400
Subject: [Bioperl-l] Getting taxa from gi
Message-ID: <CAA7rn9dYGfeCS-qVccDcdwVenj8KFQs4i89EoT8_63gQk5b42g@mail.gmail.com>

Hi All,
        I know this has been discussed before, but this is kind of a new
problem that i am facing.
I want to get taxonomy (full linage) information from the huge list of GI's.
I am using Bio::DB:Genbak for this with perl-5.12.3.
Here is my small script.

#! /usr/local/perl-5.12.3/bin/perl -w
use strict;
use warnings;
use Bio::DB::GenBank;

my @ids = qw( CP000490 );
my $gbh = Bio::DB::GenBank->new();

foreach my $id( @ids ) {
# say "* ID: $id";
 my $seq = $gbh->get_Seq_by_acc( $id );
 my $org = $seq->species;
 #print "$org\n";
 my $class = join'-', $org->classification;
 print "$class\n";
}

The output is: Paracoccus denitrificans
PD1222-Paracoccus-Rhodobacteraceae-Rhodobacterales-Alphaproteobacteria-Proteobacteria-Bacteria
which is fine but i also want to get the taxa id, and if possible taxa ids
for all the linage classification.

ideally i would like to get something like this: 318586 - - - - - - - 1224 -
2

I would really appreciate your help.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Wed Sep 28 17:36:37 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:36:37 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
Message-ID: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>

On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:

> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>> Hi, Carn?,
>> 
>> Do you mean this:
>> 
>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>> 
>> In my machine, the output is
> 
> Thank you. Yes this is what I was looking for. I looked down how that
> variable comes up and so I think I'll use
> 
> use Bio::Root::Version;
> say $Bio::Root::Version::VERSION;
> 
> Carn?

Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

chris


From cjfields at illinois.edu  Wed Sep 28 17:40:48 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:40:48 +0000
Subject: [Bioperl-l] algorithm_version not working in multi-result
	blast	output
In-Reply-To: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
Message-ID: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>

Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.  

This should be an easy enough fix, but can you submit it as a bug so we can track it?

chris

On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:

> Hello,
> 
> I'm using the most recent copy of bioperl-live (pulled yesterday). I
> have a BLASTN (from blast+) output file for 3 query sequences
> (https://gist.github.com/1248342). I used this script,
> https://gist.github.com/1248338, to print the query id, algorithm and
> algorithm_version for each result. When I run the script, I get the
> following output:
> 
> GFAVMM201BADC0  BLASTN  2.2.25+
> GFAVMM201A1JOH  BLASTN
> GFAVMM201D933Z  BLASTN
> 
> Algorithm_version outputs the correct version for the first result but
> outputs the empty string for the 2nd and 3rd query. Why? This
> functionality worked about a month ago. What has changed to cause this
> to happen?
> 
> Thank you,
> 
> Paul
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Wed Sep 28 18:07:53 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 23:07:53 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
Message-ID: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>

2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>
>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>> Hi, Carn?,
>>>
>>> Do you mean this:
>>>
>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>
>>> In my machine, the output is
>>
>> Thank you. Yes this is what I was looking for. I looked down how that
>> variable comes up and so I think I'll use
>>
>> use Bio::Root::Version;
>> say $Bio::Root::Version::VERSION;
>>
>> Carn?
>
> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

Where will the scripts end up after this restructuration? What I want
is to create a version of the script (not of bioperl). Since the
script is released with bioperl, they are the same. I actually already
made the commit that makes this, just haven't bothered with the pull
request yet.

Also, will there be a release before this change?

Carn?



From shalabh.sharma7 at gmail.com  Thu Sep 29 10:37:53 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 29 Sep 2011 10:37:53 -0400
Subject: [Bioperl-l] GFF to GTF
Message-ID: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>

Hi,
    Is there any module to convert GFF file to GTF?

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Thu Sep 29 11:07:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 29 Sep 2011 15:07:27 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
	<CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
Message-ID: <46733E36-5795-4EB6-9C2B-C978000FFD46@illinois.edu>

On Sep 28, 2011, at 5:07 PM, Carn? Draug wrote:

> 2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
>> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>> 
>>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>>> Hi, Carn?,
>>>> 
>>>> Do you mean this:
>>>> 
>>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>> 
>>>> In my machine, the output is
>>> 
>>> Thank you. Yes this is what I was looking for. I looked down how that
>>> variable comes up and so I think I'll use
>>> 
>>> use Bio::Root::Version;
>>> say $Bio::Root::Version::VERSION;
>>> 
>>> Carn?
>> 
>> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).
> 
> Where will the scripts end up after this restructuration? What I want
> is to create a version of the script (not of bioperl). Since the
> script is released with bioperl, they are the same. I actually already
> made the commit that makes this, just haven't bothered with the pull
> request yet.
> 
> Also, will there be a release before this change?
> 
> Carn?

Scripts will likely go with the distribution that they most closely are tied to, but that's still an area for debate (some may equally fall within one distribution or another, which will be tricky).  

For more on the release aspects see the (currently being revised and thus not complete) wiki page:

http://www.bioperl.org/wiki/BioPerl_Modularization

chris


From pcantalupo at gmail.com  Thu Sep 29 12:13:05 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 29 Sep 2011 12:13:05 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
In-Reply-To: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
	<4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
Message-ID: <CAJqbkv6Cgf8V4x2DDrzJjc7yKyF8j-kMFNz6JGpnhn9QQTZEQg@mail.gmail.com>

Bug submitted: https://redmine.open-bio.org/issues/3298





On Wed, Sep 28, 2011 at 5:40 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.
>
> This should be an easy enough fix, but can you submit it as a bug so we can track it?
>
> chris
>
> On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:
>
>> Hello,
>>
>> I'm using the most recent copy of bioperl-live (pulled yesterday). I
>> have a BLASTN (from blast+) output file for 3 query sequences
>> (https://gist.github.com/1248342). I used this script,
>> https://gist.github.com/1248338, to print the query id, algorithm and
>> algorithm_version for each result. When I run the script, I get the
>> following output:
>>
>> GFAVMM201BADC0 ?BLASTN ?2.2.25+
>> GFAVMM201A1JOH ?BLASTN
>> GFAVMM201D933Z ?BLASTN
>>
>> Algorithm_version outputs the correct version for the first result but
>> outputs the empty string for the 2nd and 3rd query. Why? This
>> functionality worked about a month ago. What has changed to cause this
>> to happen?
>>
>> Thank you,
>>
>> Paul
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



From jluis.lavin at unavarra.es  Fri Sep 30 04:23:19 2011
From: jluis.lavin at unavarra.es (jluis.lavin at unavarra.es)
Date: Fri, 30 Sep 2011 10:23:19 +0200
Subject: [Bioperl-l] Bio-Graphics module
Message-ID: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>


Dear All,

I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
windows machine.

I read about the Bio-Graphics module and it'd be wonderful to install it,
but seems like it is  only available for Perl 5.8...
Is there any other Perl and/or Bioperl module to do the same kind of
genomic and Blast report representation currently available?

Thanks in advance

-- 
Dr. Jos? Luis Lav?n Trueba

Dpto. de Producci?n Agraria
Grupo de Gen?tica y Microbiolog?a
Universidad P?blica de Navarra
31006 Pamplona
Navarra
SPAIN




From cjfields at illinois.edu  Fri Sep 30 08:38:01 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 30 Sep 2011 12:38:01 +0000
Subject: [Bioperl-l] Bio-Graphics module
In-Reply-To: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
Message-ID: <B1F1674B-D8DA-46E2-AAAE-DD9DDBC4C51A@illinois.edu>

It's available for all perl versions from 5.8.8 up.  I have it running with perl 5.14.  Now, I recall there being problems with installation on Mac OS X, though I think that was mainly due to GD.pm and libgd.

chris

On Sep 30, 2011, at 3:23 AM, <jluis.lavin at unavarra.es>
 <jluis.lavin at unavarra.es> wrote:

> 
> Dear All,
> 
> I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
> windows machine.
> 
> I read about the Bio-Graphics module and it'd be wonderful to install it,
> but seems like it is  only available for Perl 5.8...
> Is there any other Perl and/or Bioperl module to do the same kind of
> genomic and Blast report representation currently available?
> 
> Thanks in advance
> 
> -- 
> Dr. Jos? Luis Lav?n Trueba
> 
> Dpto. de Producci?n Agraria
> Grupo de Gen?tica y Microbiolog?a
> Universidad P?blica de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jillianrowe91286 at gmail.com  Wed Sep 28 02:03:32 2011
From: jillianrowe91286 at gmail.com (Jill)
Date: Tue, 27 Sep 2011 23:03:32 -0700 (PDT)
Subject: [Bioperl-l] Gene Type in Entrez gene?
Message-ID: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>

Hi there,

I am using the Bio::DB::Eutilities module to download gene sequences
based on a query.

<code>
while (my $docsum = $summaries->next_DocSum) {
  ## some items in DocSum are also named ChrStart so we pick the
genomic
  ## information item and get the coordinates from it
  my ($genomic_info)  = $docsum->get_Items_by_name('GenomicInfoType');

  ## some entries may have no data on genomic coordinates. This
condition filters then out
  if (!$genomic_info) {
    ## found no genomic coordinates data
    next;
  }

  ## get coordinates of sequence
  ## get_contents_by_name always returns a list
  my ($chr_acc_ver)   = $genomic_info-
>get_contents_by_name("ChrAccVer");
  my ($chr_start)     = $genomic_info-
>get_contents_by_name("ChrStart");
  my ($chr_stop)      = $genomic_info-
>get_contents_by_name("ChrStop");
  my $strand;

  if ($chr_start < $chr_stop) {
    $strand     = 1;
    $chr_start  = $chr_start +1 - $bp5_extra;
    $chr_stop   = $chr_stop  +1 + $bp5_extra;
  } elsif ($chr_start > $chr_stop) {
    $strand     = 2;
    $chr_start  = $chr_start +1 - (-$bp5_extra);
    $chr_stop   = $chr_stop  +1 + (-$bp5_extra);
  } else {
    next;
  }

  while (my $item = $docsum->next_Item('flattened'))  {
	next if ($item->get_name =~ m/NomenclatureName/);
	if($item->get_name =~ m/Description/) {
	  $description = $item->get_content if $item->get_content;
	  $description =~ tr/ /_/;
	  print $description, "\n";}
	if($item->get_name =~ m/Name/) {
	    $name = $item->get_content if $item->get_content;
	    print $name, "\n";
	  }
        printf("%-20s:%s\n",$item->get_name,$item->get_content) if
$item->get_content;
    }
}
</code>

Then I go on to use genbank to download the sequences based on the
chromosome splice. For what I have it works great. But I am trying to
get to the gene type (either protein coding or pseudo) as well. I can
see it in the summary on the Entrez Gene sight, but can't get to it
through bioperl. When I have it print out all the contents of the
summary it doesn't show up there either.

Any help?

Thanks!


From liam.elbourne at mq.edu.au  Thu Sep 29 17:34:04 2011
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Fri, 30 Sep 2011 07:34:04 +1000
Subject: [Bioperl-l] GFF to GTF
In-Reply-To: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
References: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
Message-ID: <8D027281-44E6-467C-8D22-D2D2F87D04B6@mq.edu.au>

Hi Shalabh,

Not sure about bioperl (I looked a while back and either missed it or it's not there) but there is a program associated with the cufflinks suite called gffread that should convert. 

Regards,
Liam Elbourne. 



On 30/09/2011, at 12:37 AM, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:

> Hi,
>    Is there any module to convert GFF file to GTF?
> 
> Thanks
> Shalabh
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Fri Sep 30 09:18:04 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 30 Sep 2011 14:18:04 +0100
Subject: [Bioperl-l] Gene Type in Entrez gene?
In-Reply-To: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
References: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
Message-ID: <CAPOrs_2QOMOyPsZ90iYc3fMd8YE9HGnPcVqELGo+rYRRxJu9NQ@mail.gmail.com>

On 28 September 2011 07:03, Jill <jillianrowe91286 at gmail.com> wrote:
> Hi there,
>
> I am using the Bio::DB::Eutilities module to download gene sequences
> based on a query.
>
> <code>
> [...]
> }
> </code>
>
> Then I go on to use genbank to download the sequences based on the
> chromosome splice. For what I have it works great. But I am trying to
> get to the gene type (either protein coding or pseudo) as well. I can
> see it in the summary on the Entrez Gene sight, but can't get to it
> through bioperl. When I have it print out all the contents of the
> summary it doesn't show up there either.
>
> Any help?

Hi Jill,

there's already a script in bioperl that does what you want, it's just
not part of the current stable release. You can get it here

https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl

You can download the script alone, it will work fine in previous
releases of bioperl, no need to write another one.

Carn? Draug



From manju.rawat2 at gmail.com  Thu Sep  1 02:53:53 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 1 Sep 2011 02:53:53 -0400
Subject: [Bioperl-l] Bioperl query....
In-Reply-To: <CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
References: <CAB2c7yp6p2e_8p7M9wVL2xzU7g+mZ-NVXwLs4PUassRs4PgrTQ@mail.gmail.com>
	<4E5CC8AC.8050800@gmail.com>
	<CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
Message-ID: <CAB2c7yobL=KRW_XWOCfgEwJS17A8Mne4FJhVp88xjJfBqZMHGw@mail.gmail.com>

Thanks For The Reply..
I have already seen this link..But I am confused.

I used to following code and run it...

my $in = Bio::SearchIO->new(-format => 'blast',
                -file => 'seqs.blast');
while( my $result = $in->next_result ) {
  ## $result is a Bio::Search::Result::ResultI compliant object
  while( my $hit = $result->next_hit ) {
    ## $hit is a Bio::Search::Hit::HitI compliant object
    while( my $hsp = $hit->next_hsp ) {
      ## $hsp is a Bio::Search::HSP::HSPI compliant object
      if( $hsp->length('total') > 50 ) {
        if ( $hsp->percent_identity >= 75 ) {
          print "Query=",   $result->query_name,
            " Hit=",        $hit->name,
            " Length=",     $hsp->length('total'),
    " gaps=",            $hsp->gaps,
            " Percent_id=", $hsp->percent_identity, "\n";
        }     } }    }}



and it showing me following output with an error that..


*Erro--*rArgument "" isn't numeric in numeric lt (<) at
/usr/local/share/perl/5.10.1/Bio/SearchIO/SearchResultEventBuilder.pm line
279, <GEN1> line 4113.

Query=NM_181451 Hit=ref|NM_181451.1| Length=1349 gaps=1 Percent_id=100
Query=NM_181451 Hit=ref|XM_002706247.1| Length=1345 gaps=13
Percent_id=93.8289962825279
Query=NM_181451 Hit=ref|NM_001098089.1| Length=1323 gaps=7
Percent_id=91.9123204837491
Query=NM_181451 Hit=ref|NM_001008415.1| Length=1211 gaps=5
Percent_id=94.9628406275805
Query=NM_181451 Hit=ref|XM_001251693.3| Length=1320 gaps=5
Percent_id=91.969696969697
Query=NM_181451 Hit=ref|NM_001097567.1| Length=1338 gaps=4
Percent_id=91.5545590433483
Query=NM_181451 Hit=gb|AY075103.1| Length=1334 gaps=1
Percent_id=91.304347826087
................
..........

Pl Find.whats the error i this code...

Thanks
Manju Rawat.


From locarpau at upvnet.upv.es  Thu Sep  1 10:49:06 2011
From: locarpau at upvnet.upv.es (Lorenzo Carretero Paulet)
Date: Thu,  1 Sep 2011 16:49:06 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
Message-ID: <1314888546.4e5f9b628ecea@webmail.upv.es>

Hi all,
I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:

my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
if ( my $paml_result = $parserF->next_result )
{
say Dumper $paml_result; #Prints Ok
	for ( my $model_result= $paml_result->get_NSSite_results )
	{
        #say Dumper $model_result; #Prints nothing
        $ns_string = "model ".$model_result->model_num."\n
".$model_result->model_description()."\n ".$model_result->time_used."\n";
	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
	#say Dumper $dnds_site_classes;
	for my $sites ( $model_result->get_BEB_pos_selected_sites )
        ...
         ...
          ...

The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
object is not being properly instantiated, as I get the error message:

"Can't call method "model_num" without a package or object reference at ..."

What am I missing?
Best,
Lorenzo




From jason.stajich at gmail.com  Thu Sep  1 16:23:47 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 1 Sep 2011 13:23:47 -0700
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <1314888546.4e5f9b628ecea@webmail.upv.es>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
Message-ID: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>

Lorenzo -

I am sure this is a problem with changes in the output from PAML - this is classic problem with this suite.  This requires some debugging of the parser, not sure if there is anyone out there with time to do the debugging.
I can say all this worked before on an earlier version of PAML but I don't know specifically what is going on with the latest paml4.4 version.

Jason


On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:

> Hi all,
> I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:
> 
> my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> if ( my $paml_result = $parserF->next_result )
> {
> say Dumper $paml_result; #Prints Ok
> 	for ( my $model_result= $paml_result->get_NSSite_results )
> 	{
>        #say Dumper $model_result; #Prints nothing
>        $ns_string = "model ".$model_result->model_num."\n
> ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> 	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> 	#say Dumper $dnds_site_classes;
> 	for my $sites ( $model_result->get_BEB_pos_selected_sites )
>        ...
>         ...
>          ...
> 
> The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
> object is not being properly instantiated, as I get the error message:
> 
> "Can't call method "model_num" without a package or object reference at ..."
> 
> What am I missing?
> Best,
> Lorenzo
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Scott.Markel at accelrys.com  Thu Sep  1 17:22:21 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Thu, 1 Sep 2011 14:22:21 -0700
Subject: [Bioperl-l] file format for alignment plus features for aligned
	sequences
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702F8302A05@EXCH1-COLO.accelrys.net>

A question on behalf of the Discovery Studio group at Accelrys -

They have alignment data with annotations, e.g., visualization settings or alignment properties.  The aligned sequences also have features, e.g., domain boundaries or secondary structure motifs.  They currently use BSML to save sequences and features.

Is there an extension of BSML that can also save the alignment information?

Are there any good file formats that can be used to store an alignment plus features associated with the aligned sequences?

Are there other mailing lists that might be more appropriate for these questions?

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
San Diego, CA 92121                 fax:    +1 858 799 5222
USA                                 web:    http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
    International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics






From ihok at hotmail.com  Thu Sep  1 23:49:50 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Thu, 1 Sep 2011 23:49:50 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
Message-ID: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>

I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty 
quiet codebase these days... Is it dead?

Does anyone have a spec file for building an SRPM for it for RHEL 6?


From cjfields at illinois.edu  Fri Sep  2 00:31:17 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 04:31:17 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
Message-ID: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>

Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.

chris

On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:

> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> 
> Does anyone have a spec file for building an SRPM for it for RHEL 6?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Fri Sep  2 04:44:07 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 10:44:07 +0200
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
Message-ID: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>

As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
http://toolkit.tuebingen.mpg.de/hhpred


He got it working thus:

> Hi Dave,
> thanks a lot. i made it work. The error i got later on was:

 relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making
> a shared object;
> recompile with -fPIC
>


> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared
> --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/<http://forums.fedoraforum.org/showthread.php?t=232607>
> showthread.php?t=232607<http://forums.fedoraforum.org/showthread.php?t=232607>




Dave





On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J
<cjfields at illinois.edu>wrote:

> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone
> who has packaged that up in a while, if ever.
>
> chris
>
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty
> quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From David.Messina at sbc.su.se  Fri Sep  2 05:30:33 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 11:30:33 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com>
	<9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu>
	<4DF56976.8080704@upvnet.upv.es>
	<AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com>
	<9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
	<E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
Message-ID: <CAM3TQQU6YV0+5HEf6_PhNDuh3SK0eYZgHE5kT+F3MbTH8ktsNw@mail.gmail.com>

Looking back at the commit history, back in April and May 2010, I made some
updates for the January 2010 edition of PAML 4.4. All tests passed at that
time, but:

- the tests may be incomplete
- PAML has undoubtedly changed since then, even if it's still called version
4.4


I can't look at this right now myself, but please file a bug report on this,
and hopefully someone else can.


Dave




On Thu, Sep 1, 2011 at 22:23, Jason Stajich <jason.stajich at gmail.com> wrote:

> Lorenzo -
>
> I am sure this is a problem with changes in the output from PAML - this is
> classic problem with this suite.  This requires some debugging of the
> parser, not sure if there is anyone out there with time to do the debugging.
> I can say all this worked before on an earlier version of PAML but I don't
> know specifically what is going on with the latest paml4.4 version.
>
> Jason
>
>
> On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:
>
> > Hi all,
> > I'm trying to parse mlc output files from PAML using
> Bio::Tools::Phylo::PAML as:
> >
> > my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> > my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> > if ( my $paml_result = $parserF->next_result )
> > {
> > say Dumper $paml_result; #Prints Ok
> >       for ( my $model_result= $paml_result->get_NSSite_results )
> >       {
> >        #say Dumper $model_result; #Prints nothing
> >        $ns_string = "model ".$model_result->model_num."\n
> > ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> >       $dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> >       #say Dumper $dnds_site_classes;
> >       for my $sites ( $model_result->get_BEB_pos_selected_sites )
> >        ...
> >         ...
> >          ...
> >
> > The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> > DUmper. In contrast, it seems that the
> Bio::Tools::Phylo::PAML::ModelResult
> > object is not being properly instantiated, as I get the error message:
> >
> > "Can't call method "model_num" without a package or object reference at
> ..."
> >
> > What am I missing?
> > Best,
> > Lorenzo
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Fri Sep  2 09:00:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 13:00:27 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
Message-ID: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>

I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/

chris

On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:

> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
> http://toolkit.tuebingen.mpg.de/hhpred
> 
> 
> He got it working thus:
> Hi Dave,
> thanks a lot. i made it work. The error i got later on was: 
> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
> recompile with -fPIC 
>  
> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/showthread.php?t=232607
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J <cjfields at illinois.edu> wrote:
> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
> 
> chris
> 
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
> 
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From ihok at hotmail.com  Fri Sep  2 11:20:44 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Fri, 2 Sep 2011 11:20:44 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
	<81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
Message-ID: <BLU0-SMTP2075F7F67ABC5C1860ED380CA180@phx.gbl>

I also see that someone's forked it on Github and made some packaging fixes.

It'd be nice to see it revived.

On 9/2/2011 9:00 AM, Fields, Christopher J wrote:
> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/
>
> chris
>
> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:
>
>> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
>> http://toolkit.tuebingen.mpg.de/hhpred
>>
>>
>> He got it working thus:
>> Hi Dave,
>> thanks a lot. i made it work. The error i got later on was:
>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
>> recompile with -fPIC
>>
>> the solution is:
>> perl Makefile.PL PREFIX=<path to installation>  /fftwsingle --enable-shared --with-pic --enable-single
>> <edit Makefile to add -fPIC to CFLAGS>
>> make
>> make install
>> http://forums.fedoraforum.org/showthread.php?t=232607
>>
>>
>>
>> Dave
>>
>>
>>
>>
>>
>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J<cjfields at illinois.edu>  wrote:
>> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
>>
>> chris
>>
>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>>
>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
>>>
>>> Does anyone have a spec file for building an SRPM for it for RHEL 6?
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>



From manju.rawat2 at gmail.com  Sat Sep  3 01:29:56 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 01:29:56 -0400
Subject: [Bioperl-l] hsps_successfully_gapped: 47
Message-ID: <CAB2c7yr8qHCPO2L6nczPUTWi-L94Bz9kQtyLP-U03=nhWS+66Q@mail.gmail.com>

Hello,


Is There any method in BioPerl through which we can extract
number_of_hsps_successfully_gapped:
from a blast file..
If any one know about the it Pl help me...


Thanks
Manju Rawat


From manju.rawat2 at gmail.com  Sat Sep  3 06:00:22 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 06:00:22 -0400
Subject: [Bioperl-l] blast result not matching.
Message-ID: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


and Output..

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat


From florent.angly at gmail.com  Sun Sep  4 22:14:37 2011
From: florent.angly at gmail.com (Florent Angly)
Date: Mon, 05 Sep 2011 12:14:37 +1000
Subject: [Bioperl-l] Bio::SeqIO can't guess the format of data from a
 pipe
In-Reply-To: <F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
References: <CAFAnT677UmaEsudqoj9UsefdeK9Wx0E_W8iM3zmMAJx8PHzBjA@mail.gmail.com>
	<2E070303-ADDF-472B-835B-6D3959B83E9A@illinois.edu>
	<CAFAnT64JhkP-xzi8TpqHiTJTm3UMgT7SPMWVm+-UhSFwk0G3gQ@mail.gmail.com>
	<E89E20DA-9B27-4D42-ACF8-96A176C85259@illinois.edu>
	<4E58D105.7050805@gmail.com>
	<A249C76A-A0BC-414E-AE78-A2B6CA7B4A9A@drycafe.net>
	<4E5A0590.2010805@gmail.com>
	<8D639B95-0666-4F09-8E9E-88C8CDF76ABC@illinois.edu>
	<4E5AC2B8.9060808@gmail.com>
	<F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
Message-ID: <4E64308D.5060304@gmail.com>


Thanks for your advice Chris. I put a format() and variant() method in 
Bio::Root::IO. All the Bio::*IO methods inherit these methods.

Regarding the module naming, 8 follow the convention Bio::*IO and 8 
follow the Bio::*::IO convention. If we decide to rename some IO modules 
for consistency, I would prefer the Bio::*::IO convention.

Regards,

Florent


On 29/08/11 11:10, Chris Fields wrote:
> On Aug 28, 2011, at 5:35 PM, Florent Angly wrote:
>
>> Hi,
>>
>> I implemented the format() getter method in Bio::SeqIO as discussed, essentially following the way proposed by Hilmar. The variant() method is not needed since Bio::SeqIO::fastq already has a get/set method for that.
> Right, but the method could be used by other modules if it were moved to Bio::SeqIO. for instance.
>
>> I noticed that there are plenty more Bio*IO modules that could benefit from having a format() method, e.g.:
>>     Bio::AlignIO
>>     Bio::ClusterIO
>>     Bio::FeatureIO
>>     Bio::MapIO
>>     Bio::OntologyIO
>>     Bio::SearchIO
>>     Bio::TreeIO
>>     Bio::Assembly::IO *
>> The code could be copy-pasted for each of them but it is not very graceful. Is there a way we could have all these IO modules share the same format() method?
> Move the method to Bio::Root::IO, the common base class for all of the above.
>
>> * Note how the IO class for Bio::Assembly is called Bio::Assembly::IO, and not Bio::AssemblyIO like for other classes. This may be something to change in the future for consistency.
>>
>> Florent
> That's possible; one could take advantage of that for redesign/API issues if it were needed.
>
> chris



From manju.rawat2 at gmail.com  Mon Sep  5 03:53:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 03:53:40 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
Message-ID: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


*and Output..*

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat


From p.j.a.cock at googlemail.com  Mon Sep  5 05:44:06 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 10:44:06 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
Message-ID: <CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>

On Mon, Sep 5, 2011 at 8:53 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
> I doing blast using bioperl...but it not showing me complete result..
>
>
> my program is following...
> ...
>
> this result is not matching with with NCBI result...
> Is there anything wrong..

The NCBI website for BLAST uses different default values
to the BLAST command line tools. Check things like the
gap parameters if you want to use the same settings.

Peter


From p.j.a.cock at googlemail.com  Mon Sep  5 06:25:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 11:25:15 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
Message-ID: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>

Please CC the mailing list.

On Mon, Sep 5, 2011 at 11:19 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
> Thanks for the reply...
> but when i am blasting after getting sequence of any gene (from NCBI using
> bioperl see below)..it showing me same result as shown in NCBI..
>
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq_object = get_sequence('NCBI',"NM_181451");
> $blast_result = blast_sequence($seq);
> write_blast(">roa1.blast",$blast_report);
>
>
> I dnt know why its not working when i am blasting my own sequence..
>

Maybe you need give the sequence as a FASTA entry
rather than a plain string?

Peter


From manju.rawat2 at gmail.com  Mon Sep  5 06:40:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 06:40:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
Message-ID: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>

No..i also tried this..this also dont work..
pls help me..


From cjfields at illinois.edu  Mon Sep  5 15:42:49 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 5 Sep 2011 19:42:49 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
Message-ID: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>

Are you using the latest BioPerl?  I believe there had been some fixes addressing remote blast.

chris

On Sep 5, 2011, at 5:40 AM, Manju Rawat wrote:

> No..i also tried this..this also dont work..
> pls help me..
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Tue Sep  6 06:59:50 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 6 Sep 2011 06:59:50 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
Message-ID: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>

bioperl 1.6.9 version is installed in my system..
its not the reason bcs blast is working fine when i am blasting with
follwing code..

#!usr/bin/perl -w
use Bio::Perl;
$seq = get_sequence('NCBI',"NM_181451");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


Manju


From sidd.basu at gmail.com  Tue Sep  6 11:51:09 2011
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Tue, 6 Sep 2011 10:51:09 -0500
Subject: [Bioperl-l] Bioinformatics Job Opening at dictyBase in Chicago
Message-ID: <20110906155106.GB1841@Macintosh-388.local>

Hi All, 
We have an open position for a Bioinformatics Software Engineer at dictyBase(Northwestern
University in Chicago). The job involves developing web application and middleware for
a genome database using modern perl(DBIx-Class/Moose/MVC web frameworks etc)
as well as integration of various genomic tools(gbrowse, intermine, apollo,
biomart, pathway tools etc..). 
For full details please see:
 http://www.dictybase.org/dictybase_jobs.html.


thanks, 
-siddhartha

Siddhartha Basu
Software developer,  dictybase
http://www.dictybase.org



From slucky at ibab.ac.in  Wed Sep  7 09:39:03 2011
From: slucky at ibab.ac.in (Lucky Singh)
Date: Wed, 07 Sep 2011 19:09:03 +0530
Subject: [Bioperl-l] Fwd: Re:  Problem using Bio::Tools::Run::RemoteBlast
Message-ID: <4E6773F7.7000703@ibab.ac.in>



-------- Original Message --------
Subject: 	Re: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
Date: 	Sat, 27 Aug 2011 20:36:58 +0530
From: 	Lucky Singh <slucky at ibab.ac.in>
To: 	Carn? Draug <carandraug+dev at gmail.com>



On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>  On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in>   wrote:
>>  Now I
>>  wanted to host it from web server, but This program is not working from it
>>  may be it is not able to create or write on file from web server but in
>>  command line it is working fine. I don't know the possible reason, please
>>  help me to figure it out.
>  Have you looked in the apache logs (look in
>  /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>  content of the error log after trying to run the script?
Dear Carn? Draug,

As per your suggestion, I am attaching blast code file currently it is
not showing any error on error.log.
Thanks a lot for your valuable reply and will be highly grateful if you
can get me out of this problem :)


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From jason.stajich at gmail.com  Wed Sep  7 12:13:46 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 7 Sep 2011 09:13:46 -0700
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
Message-ID: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>

I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.


On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:

> bioperl 1.6.9 version is installed in my system..
> its not the reason bcs blast is working fine when i am blasting with
> follwing code..
> 
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq = get_sequence('NCBI',"NM_181451");
> $blast_result=blast_sequence($seq);
> write_blast(">xyz.blast",$blast_result);
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Wed Sep  7 12:33:52 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 7 Sep 2011 16:33:52 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
Message-ID: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>

I think there was an issue with Bio::Perl BLAST submissions fixed in the 1.6.901 release (1.6.9 != 1.6.901, the latter is newer).  From CPAN:

1.6.901 May 18, 2011

...

    [Bug fixes]

    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
      docs [genehack, cjfields]

chris

On Sep 7, 2011, at 11:13 AM, Jason Stajich wrote:

> I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
> Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.
> 
> 
> On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:
> 
>> bioperl 1.6.9 version is installed in my system..
>> its not the reason bcs blast is working fine when i am blasting with
>> follwing code..
>> 
>> #!usr/bin/perl -w
>> use Bio::Perl;
>> $seq = get_sequence('NCBI',"NM_181451");
>> $blast_result=blast_sequence($seq);
>> write_blast(">xyz.blast",$blast_result);
>> 
>> 
>> Manju
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From carandraug+dev at gmail.com  Wed Sep  7 12:47:16 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 7 Sep 2011 17:47:16 +0100
Subject: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
In-Reply-To: <4E590812.9030006@ibab.ac.in>
References: <37711.192.168.1.254.1313992876.squirrel@webmail.ibab.ac.in>
	<CAPOrs_1TX=+A=hA0bCP56bsW5XdPy5N5mpcnAL=NPugP-4j03Q@mail.gmail.com>
	<4E590812.9030006@ibab.ac.in>
Message-ID: <CAPOrs_2MbWXbtrhj+eOphpDfyaUhdpWvUE8kaMXxKrQe_3m_kw@mail.gmail.com>

2011/8/27 Lucky Singh <slucky at ibab.ac.in>:
> On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>>
>> On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in> ?wrote:
>>>
>>> Now I
>>> wanted to host it from web server, but This program is not working from
>>> it
>>> may be it is not able to create or write on file from web server but in
>>> command line it is working fine. I don't know the possible reason, please
>>> help me to figure it out.
>>
>> Have you looked in the apache logs (look in
>> /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>> content of the error log after trying to run the script?
>
> Dear Carn? Draug,
>
> As per your suggestion, I am attaching blast code file currently it is not
> showing any error on error.log.
> Thanks a lot for your valuable reply and will be highly grateful if you can
> get me out of this problem :)


Hi

sorry for the late reply. Please try to always reply to the mailing
list, maybe someone else can help you too. I don't know about the
script as I never used RemoteBlast from bioperl. But given a quick
look at it, you're not loading the CGI module on the script (
http://perldoc.perl.org/CGI.html ). Here's a simple example using the
CGI module ( http://pastebin.com/miMd70wn ) and a HTML page that will
use it ( http://pastebin.com/kWwwMijd ).

If nothing shows up on error.log, take a look in access.log. Try some
simple CGI script first, such as "hello world!" to see if the problem
lies on your bioperl part of the script, or in the web server, or some
other part.

Carn?



From scott at scottcain.net  Wed Sep  7 13:57:31 2011
From: scott at scottcain.net (Scott Cain)
Date: Wed, 7 Sep 2011 13:57:31 -0400
Subject: [Bioperl-l] October GMOD Meeting in Toronto
Message-ID: <CA+JTaoxxMxNQmOu8wbU=vD+-6eRwPVjpXBAszWn=p6_OOkr9ig@mail.gmail.com>

Hello,

The early registration deadline for the October GMOD meeting in
Toronto, Canada is approaching.  Please register by September 13th to
avoid the late registration fee.  You can register here:

  http://gmod.eventbrite.com/

For information about the GMOD meeting please see the page at:

  http://gmod.org/wiki/October_2011_GMOD_Meeting

In addition to the main meeting, there will be a free BioMart workshop
on the following Friday, which you can also register for at the main
meeting registration page.

Thanks,
Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From info at etisalat.com  Wed Sep  7 05:52:00 2011
From: info at etisalat.com (Etisalat Telecommunication Network.)
Date: Wed, 7 Sep 2011 17:52:00 +0800
Subject: [Bioperl-l] Winning No:ETS/G/NG
Message-ID: <20110907092508.M63844@etisalat.com>

Etisalat Telecommunication Network.
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Etisalat Award Promotion
(c)2011 Online Award Promotion Edition  



From longbow0 at gmail.com  Wed Sep  7 16:19:37 2011
From: longbow0 at gmail.com (longbow leo)
Date: Wed, 7 Sep 2011 15:19:37 -0500
Subject: [Bioperl-l] How to determine strains were evolved independently in
	a phylogenetic tree?
Message-ID: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>

Hi,

I have created a phylogenetic for a virus protein which contained about 200
strains. Next I need to do an analysis to check whether several strains in
this tree were evolved independently. Although it is not too difficult to do
manually, I still have litter idea how to do this in a Perl script since
there are some datasets need to do.

At first I tried to use the method "is_monophyletic" in the module
"Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
work as I have thought. According to the description of "is_monophyletic"
method, it "Will do a test of monophyly for the nodes specified in
comparison to a chosen outgroup". Does here test whether the outgroup strain
is monophyletic to the nodes, or test the nodes only? The description sounds
like the latter but the what the script did seemed to be the first.

Are there any suggestions?

Thank you very much!


Haizhou Liu


From greg at ebi.ac.uk  Thu Sep  8 06:40:30 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Thu, 8 Sep 2011 11:40:30 +0100
Subject: [Bioperl-l] How to determine strains were evolved independently
 in a phylogenetic tree?
In-Reply-To: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
References: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
Message-ID: <CA+08rdT4z5W5OzuuBPsC0icz_LWXCTNWO0uv=w=Bg_0EoU44Gw@mail.gmail.com>

Hi Haizhou,

I'm not sure I understand exactly what you're trying to do. But to clarify
the BioPerl code: the is_monophyletic method (for the actual code, see here
https://github.com/bioperl/bioperl-live/blob/master/Bio/Tree/TreeFunctionsI.pm#L832)
tests
whether the single outgroup node falls *within* or *outside* the last common
ancestor of the group of nodes given. If the outgroup node falls *outside*
the subtree defined by this LCA node, then the group of nodes can be called
monophyletic with respect to that outgroup (at least as far as my
understanding of the word 'monophyletic' goes). If the outgroup node falls
*within* the subtree defined by this LCA node, then the group of nodes is
not monophyletic with respect to that outgroup node.

The term "evolved independently" sounds slightly vague to me -- what is it
exactly about the shape of your tree that allows you to call a strain
independent or not? If you gave an example or two of trees where you
consider the evolution to be independent and non-independent, I (or someone
else on the list) may be able to help you find the right method to do this
automatically.

Cheers,
 Greg

On Wed, Sep 7, 2011 at 9:19 PM, longbow leo <longbow0 at gmail.com> wrote:

> Hi,
>
> I have created a phylogenetic for a virus protein which contained about 200
> strains. Next I need to do an analysis to check whether several strains in
> this tree were evolved independently. Although it is not too difficult to
> do
> manually, I still have litter idea how to do this in a Perl script since
> there are some datasets need to do.
>
> At first I tried to use the method "is_monophyletic" in the module
> "Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
> work as I have thought. According to the description of "is_monophyletic"
> method, it "Will do a test of monophyly for the nodes specified in
> comparison to a chosen outgroup". Does here test whether the outgroup
> strain
> is monophyletic to the nodes, or test the nodes only? The description
> sounds
> like the latter but the what the script did seemed to be the first.
>
> Are there any suggestions?
>
> Thank you very much!
>
>
> Haizhou Liu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From manju.rawat2 at gmail.com  Thu Sep  8 02:11:12 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 8 Sep 2011 02:11:12 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
Message-ID: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>

Toady i installed the latest version of bioperl in my system via CPAN..
But this still not sowing the complete result..


I just want to do nucleotide blast using bioperl..but while i am doing blast
with my sequence it shwowing very samll result..
I dnt know whether it is wrong or right...but while i am blasting the same
sequence in NCBI it showing a diffrent result..

and i have also tried to use the orignl module..but it also dnt work..

Pl see reult of the balst in  attached file of this mail..
#!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO;
$blast_report =blast_sequence('acggctgctgtagatctgatgct');
write_blast(">resl.blast",$blast_report);

Thanks.
Manju Rawat
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From cjfields at illinois.edu  Thu Sep  8 09:05:10 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 13:05:10 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <6D4A142B-9455-4CC3-AFDB-F9B3B991B57F@illinois.edu>

Submissions to NCBI BLAST via their web interface have different parameters than those submitted via their QBLAST interface (what is used in BioPerl).  So the fact there are differing results isn't too surprising, particularly if the results fall close to the e-value cutoff for one or the other.  You will need to set the proper parameters, which I don't believe is possible via the (very simple) Bio::Perl interface, but is possible via Bio::Tools::Run::RemoteBlast.

chris

On Sep 8, 2011, at 1:11 AM, Manju Rawat wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
> 
> 
> I just want to do nucleotide blast using bioperl..but while i am doing blast with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same sequence in NCBI it showing a diffrent result..
> 
> and i have also tried to use the orignl module..but it also dnt work..
> 
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
> 
> Thanks.
> Manju Rawat
> 
> 
> <resl.blast>




From David.Messina at sbc.su.se  Thu Sep  8 09:33:19 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 8 Sep 2011 15:33:19 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>

As I think has been said earlier in this thread, it's almost certainly a
discrepancy in the BLAST parameters between what the blast_sequence function
in the Bio::Perl module is sending, and what the BLAST website is doing.


In this case, you have a very short sequence. If you look in the "Algorithm
parameters" section of the BLAST web form, you'll see that there is an
option that is checked by default, "Automatically adjust parameters for
short input sequences".


If I uncheck that option, I get the same results as you did when you
submitted your BLAST through BioPerl (see http://cl.ly/9ynq).


So to get the same results from a BioPerl-submitted BLAST and a BLAST on
NCBI's website, you need to have the same parameters. You can set the
parameters from BioPerl as described in the documentation:

http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Tools/Run/RemoteBlast.pm


As Jason said earlier, the blast_sequence function in Bio::Perl is intended
as a simple demonstration and uses the default BLAST parameters. That
function is a wrapper around the RemoteBlast module. Since you want to do
something a little different, I believe you'll need to use the RemoteBlast
module directly.




Dave




On Thu, Sep 8, 2011 at 08:11, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
>
>
> I just want to do nucleotide blast using bioperl..but while i am doing
> blast
> with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same
> sequence in NCBI it showing a diffrent result..
>
> and i have also tried to use the orignl module..but it also dnt work..
>
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
>
> Thanks.
> Manju Rawat
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From abualiga2 at gmail.com  Thu Sep  8 10:44:39 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 10:44:39 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
	primary tag
Message-ID: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>

Hi,

I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
multiple tags within a primary tag.  E.g., when there are several 'function'
tag-values within a 'CDS' primary tag, I don't know how to link those
'function' tag-values to a particular 'locus_tag'.  As parsed values are
returned as a list, I tried creating an array of hashes, where the hash-key
is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
miserably.  Pasted below is what I managed so far.  At your convenience,
please advise.

thanks!

galeb

#!/usr/local/bin/perl
# parse_gbk.pl
# gsa 09042011
# script to parse out features from gbk
#
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction

use strict; use warnings;
use Bio::SeqIO;

my @loci;
my @seqs;
my @directions;
my @start_coords;
my @end_coords;
my @genes;
my @products;
my @notes;
my @functions;
my %functions;

my $gb_file = shift;
my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
my $seq_obj = $seqio_obj->next_seq;

for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
    if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
                if ($feat_obj->has_tag( 'locus_tag' ) ) {
                push ( @seqs, $feat_obj->seq->seq ); #collect sequences
                    for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
{
                            push ( @loci, $val ); # locus_tags
            }
        }
                if ( $feat_obj->has_tag( 'gene' ) ) {
                           for my $val ( $feat_obj->get_tag_values( 'gene' )
) {
                            push ( @genes, $val ); # gene names
                        }
                }
                else {
                    push ( @genes, "" ); # if gene names are absent, leave
empty
        }
        if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
coordinates
            for my $location ( $feat_obj->location ) {
                push ( @start_coords, $location->start );
                push ( @end_coords, $location->end );
                if ( $location->strand == -1 ) {
                    push ( @directions, "reverse" );
                }
                else {
                    push ( @directions, "forward" );
                }
            }
        }
    }
    # gene products, notes, functions
    if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
$feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
|| $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
        if ( $feat_obj->has_tag( 'product' ) ) {
            for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
                push ( @products, $product );
            }
        }
        else {
            push ( @products, "" );
        }
        if ( $feat_obj->has_tag( 'note' ) ) {
            for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
                push ( @notes, $note );
            }
        }
        else {
            push ( @notes, "" );
        }
        if ( $feat_obj->has_tag( 'function' ) ) {
            for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
                push ( @functions, $function );
            }
        }
        else {
            push ( @functions, "" );
        }

    }
}

print
"locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
# header

for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
    print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
"\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
$directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
$functions[$elem], "\t", $seqs[$elem], "\n";
}


From p.j.a.cock at googlemail.com  Thu Sep  8 11:27:56 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:27:56 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>

On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> Hi,
>
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag. ?E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.

Do you have GenBank features with multiple locus_tag qualifiers?
That would be very unusual...

Peter



From cjfields at illinois.edu  Thu Sep  8 11:32:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 15:32:21 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
Message-ID: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>

On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:

> On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
>> Hi,
>> 
>> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
>> multiple tags within a primary tag.  E.g., when there are several 'function'
>> tag-values within a 'CDS' primary tag, I don't know how to link those
>> 'function' tag-values to a particular 'locus_tag'.
> 
> Do you have GenBank features with multiple locus_tag qualifiers?
> That would be very unusual...
> 
> Peter

Agreed; in order to clarify what you mean, I think we would need to see the record in question to get a better idea of the problem.

chris


From abualiga2 at gmail.com  Thu Sep  8 11:39:20 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:39:20 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
Message-ID: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>

I guess I was not clear. 'locus_tag' qualifiers are single, but there are
mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

# gbk file
LOCUS       NC_011748            5154862 bp    DNA     circular BCT
15-MAY-2010

# example feature
     gene        complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /db_xref="GeneID:7145846"
     CDS             complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /function="7 : Transport and binding proteins"
                     /function="15.10 : Adaptations to atypical conditions"
                     /function="16.1 : Circulate"
                     /inference="ab initio prediction:AMIGene:2.0"
                     /note="the Vibrio parahaemolyticus gene VP2867 was
found
                     to be a potassium/proton antiporter; can rapidly
extrude
                     potassium against a potassium gradient at alkaline pH
when
                     cloned and expressed in Escherichia coli"
                     /codon_start=1
                     /transl_table=11
                     /product="potassium/proton antiporter"
                     /protein_id="YP_002402372.1"
                     /db_xref="GI:218694705"
                     /db_xref="GeneID:7145846"

/translation="MDATTIISLFILGSILVTSSILLSSFSSRLGIPILVIFLAIGML

AGVDGVGGIPFDNYPFAYMVSNLALAIILLDGGMRTQASSFRVALGPALSLATLGVLI

TSGLTGMMAAWLFNLDLIEGLLIGAIVGSTDAAAVFSLLGGKGLNERVGSTLEIESGS

NDPMAVFLTITLIAMIQQHESSVSWMFVVDILQQFGLGIVIGLGGGYLLLQMINRIAL

PAGLYPLLALSGGILIFALTTALEGSGILAVYLCGFLLGNRPIRNRYGILQNFDGLAW

LAQIAMFLVLGLLVNPSDLLPIAIPALILSAWMIFFARPLSVFAGLLPFRGFNLRERV

FISWVGLRGAVPIILAVFPMMAGLENARLFFNVAFFVVLVSLLLQGTSLSWAAKKAKV

VVPPVGRPVSRVGLDIHPENPWEQFVYQLSADKWCVGAALRDLHMPKETRIAALFRDN

QLLHPTGSTRLREGDVLCVIGRERDLPALGKLFSQSPPVALDQRFFGDFILEASAKYA

DVALIYGLEDGREYRDKQQTLGEIVQQLLGAAPVVGDQVEFAGMIWTVAEKEDNEVLK
                     IGVRVAEEEAES"

On Thu, Sep 8, 2011 at 11:32 AM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:
>
> > On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com>
> wrote:
> >> Hi,
> >>
> >> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> >> multiple tags within a primary tag.  E.g., when there are several
> 'function'
> >> tag-values within a 'CDS' primary tag, I don't know how to link those
> >> 'function' tag-values to a particular 'locus_tag'.
> >
> > Do you have GenBank features with multiple locus_tag qualifiers?
> > That would be very unusual...
> >
> > Peter
>
> Agreed; in order to clarify what you mean, I think we would need to see the
> record in question to get a better idea of the problem.
>
> chris


From p.j.a.cock at googlemail.com  Thu Sep  8 11:46:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:46:28 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
Message-ID: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>

On Thu, Sep 8, 2011 at 4:39 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> I guess I was not clear. 'locus_tag' qualifiers are single, but there are
> mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?

Peter


From abualiga2 at gmail.com  Thu Sep  8 11:55:08 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:55:08 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
	<CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
Message-ID: <CANPzzTsCB8DMzQHMYNOh84hBmu2diwrEA6xb8n3i2RFY9_a4kw@mail.gmail.com>

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?


Precisely!
I want to create a tab delim file with 'locus_tag' as the common identifier
to all the features and gene sequences. So far, I parsed out sequences and
single instance qualifiers, but 'function' and 'db_xref' qualifiers give me
grief.

galeb


From abualiga2 at gmail.com  Thu Sep  8 12:14:07 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:14:07 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.



That's right. Products are not the issue in this particular case, as it's
E.coli and there's no alternate splicing as far as I know so there is a
single product per gene. But there are plenty more 'function' qualifiers,
for example, than loci. And I don't know how to create a data structure that
will link a 'gene' (as primary tag) to all other qualifiers, whether they
belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.


From ss2489 at cornell.edu  Thu Sep  8 12:28:40 2011
From: ss2489 at cornell.edu (Surya Saha)
Date: Thu, 8 Sep 2011 12:28:40 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
Message-ID: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

-Surya

On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:

> I only had a quick look at your code, so maybe I'm missing something but
> you are currently pushing all products of all CDSs into the same array,
> i.e. you do not assign them to a datastructure that links a particular
> CDS to a list of products. You then use the same index to print out a
> locus from the @loci array and a product from @products, but the two
> will not match up because you will have more products than loci.
>
>
>
> That's right. Products are not the issue in this particular case, as it's
> E.coli and there's no alternate splicing as far as I know so there is a
> single product per gene. But there are plenty more 'function' qualifiers,
> for example, than loci. And I don't know how to create a data structure
> that
> will link a 'gene' (as primary tag) to all other qualifiers, whether they
> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From fs5 at sanger.ac.uk  Thu Sep  8 12:04:57 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 08 Sep 2011 17:04:57 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags
	within	primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.

Frank



On Thu, 2011-09-08 at 10:44 -0400, galeb abu-ali wrote:
> Hi,
> 
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag.  E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.  As parsed values are
> returned as a list, I tried creating an array of hashes, where the hash-key
> is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
> miserably.  Pasted below is what I managed so far.  At your convenience,
> please advise.
> 
> thanks!
> 
> galeb
> 
> #!/usr/local/bin/perl
> # parse_gbk.pl
> # gsa 09042011
> # script to parse out features from gbk
> #
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction
> 
> use strict; use warnings;
> use Bio::SeqIO;
> 
> my @loci;
> my @seqs;
> my @directions;
> my @start_coords;
> my @end_coords;
> my @genes;
> my @products;
> my @notes;
> my @functions;
> my %functions;
> 
> my $gb_file = shift;
> my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
> my $seq_obj = $seqio_obj->next_seq;
> 
> for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
>     if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
>                 if ($feat_obj->has_tag( 'locus_tag' ) ) {
>                 push ( @seqs, $feat_obj->seq->seq ); #collect sequences
>                     for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
> {
>                             push ( @loci, $val ); # locus_tags
>             }
>         }
>                 if ( $feat_obj->has_tag( 'gene' ) ) {
>                            for my $val ( $feat_obj->get_tag_values( 'gene' )
> ) {
>                             push ( @genes, $val ); # gene names
>                         }
>                 }
>                 else {
>                     push ( @genes, "" ); # if gene names are absent, leave
> empty
>         }
>         if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
> coordinates
>             for my $location ( $feat_obj->location ) {
>                 push ( @start_coords, $location->start );
>                 push ( @end_coords, $location->end );
>                 if ( $location->strand == -1 ) {
>                     push ( @directions, "reverse" );
>                 }
>                 else {
>                     push ( @directions, "forward" );
>                 }
>             }
>         }
>     }
>     # gene products, notes, functions
>     if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
> 'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
> $feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
> || $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
>         if ( $feat_obj->has_tag( 'product' ) ) {
>             for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
>                 push ( @products, $product );
>             }
>         }
>         else {
>             push ( @products, "" );
>         }
>         if ( $feat_obj->has_tag( 'note' ) ) {
>             for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
>                 push ( @notes, $note );
>             }
>         }
>         else {
>             push ( @notes, "" );
>         }
>         if ( $feat_obj->has_tag( 'function' ) ) {
>             for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
>                 push ( @functions, $function );
>             }
>         }
>         else {
>             push ( @functions, "" );
>         }
> 
>     }
> }
> 
> print
> "locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
> # header
> 
> for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
>     print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
> "\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
> $directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
> $functions[$elem], "\t", $seqs[$elem], "\n";
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From cjfields at illinois.edu  Thu Sep  8 12:51:22 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 16:51:22 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>

There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().

chris

-----------------------------
#!/usr/bin/env perl

use Modern::Perl;
use Bio::SeqIO;

my $in = Bio::SeqIO->new(-format => 'genbank',
                         -file => shift);

while (my $seq = $in->next_seq) {
   for my $feat ($seq->get_SeqFeatures) {
       next unless $feat->primary_tag eq 'CDS';
       my ($locus) = $feat->has_tag('locus_tag') ? 
                     $feat->get_tag_values('locus_tag') : '';
       my @funcs = $feat->has_tag('function') ?
           $feat->get_tag_values('function') : ();
       say join("\t", $locus, join(',', at funcs));
   }
}



On Sep 8, 2011, at 11:28 AM, Surya Saha wrote:

> You might want to explore using a hash of complex records that are very
> similar to structures in C/C++. More info at
> http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS
> 
> -Surya
> 
> On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> 
>> I only had a quick look at your code, so maybe I'm missing something but
>> you are currently pushing all products of all CDSs into the same array,
>> i.e. you do not assign them to a datastructure that links a particular
>> CDS to a list of products. You then use the same index to print out a
>> locus from the @loci array and a product from @products, but the two
>> will not match up because you will have more products than loci.
>> 
>> 
>> 
>> That's right. Products are not the issue in this particular case, as it's
>> E.coli and there's no alternate splicing as far as I know so there is a
>> single product per gene. But there are plenty more 'function' qualifiers,
>> for example, than loci. And I don't know how to create a data structure
>> that
>> will link a 'gene' (as primary tag) to all other qualifiers, whether they
>> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From abualiga2 at gmail.com  Thu Sep  8 12:51:42 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:51:42 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <CANPzzTuAkFy-P9WAVe7bzv=mVEXb-MOLFQrZYv8UX7L2rWcZCA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

alright, thanks!


From jskittrell at unmc.edu  Thu Sep  8 12:40:31 2011
From: jskittrell at unmc.edu (Jeff S Kittrell)
Date: Thu, 8 Sep 2011 11:40:31 -0500
Subject: [Bioperl-l] Error when parsing a blast file
Message-ID: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20110908/486df26d/attachment-0003.html>

From cjfields at illinois.edu  Thu Sep  8 13:28:53 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 17:28:53 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
Message-ID: <1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>

What version of bioperl are you using?  I think this issue was addressed a while ago, but it's possible there has been a regression.

chris

On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:

> Hello Gentlemen,
> 
> I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> When the SearchIO parser encounters this record it dies with the error
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no data for midline Query ------------------------------------------------------------
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> -----------------------------------------------------------
> 
> 
> Has anyone encountered this problem before? Am I doing something wrong?
> 
> Thanks
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> Query= 78065535
> 
> Length=523
> Score E
> Sequences producing significant alignments: (Bits) Value
> 
> gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> 
> 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> receptor 123 (GPR123), mRNA
> Length=4298
> 
> Score = 576 bits (638), Expect = 1e-163
> Identities = 466/583 (80%), Gaps = 82/583 (14%)
> Strand=Plus/Minus
> 
> Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> 
> Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> 
> Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> 
> Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> 
> Query ------------------------------------------------------------ 
> 
> Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> 
> Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> 
> Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> 
> Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> 
> Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> 
> Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> ||||||||||||||||||||||||||||||| ||| || ||||
> Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> 
> 
> 
> Lambda K H
> 0.634 0.408 0.912 
> 
> Gapped
> Lambda K H
> 0.625 0.410 0.780 
> 
> Effective search space used: 47712920310
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From abualiga2 at gmail.com  Thu Sep  8 13:51:34 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 13:51:34 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
Message-ID: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>

thanks, Chris! works perfect.
To make sure I understand what's going on, forcing list context on $locus
allows me to get one value at a time, which is then concatenated with \t to
concatenated functions.

thanks again!

galeb

On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> There is no need to do that if one is using the Bio::SeqFeatureI interface.
>  Note that get_tag_values always returns a list, so to snag a single value
> for a tag in a scalar, force list context on the LHS by enclosing the
> variable in ().
>
> chris
>
> -----------------------------
> #!/usr/bin/env perl
>
> use Modern::Perl;
> use Bio::SeqIO;
>
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
>
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>    }
> }
>
>
>
>


From cjfields at illinois.edu  Thu Sep  8 14:27:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:27:06 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
Message-ID: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>

On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:

> thanks, Chris! works perfect. 
> To make sure I understand what's going on, forcing list context on $locus allows me to get one value at a time,...

You have to be careful in this circumstance; doing this:

   my $foo = @bar;

is scalar context on a list, which returns the number of elements in @bar.  The following

   my ($foo) = @bar;

forces list context and assigns the first value in @bar to $foo but tosses the rest.  If you are sure there is only one value in @bar anyway, the above is fine (and is a common perl idiom).  

> which is then concatenated with \t to concatenated functions. 

I'm just using a simple join() to print off the results.  Note the second element in the join list is an embedded join() with comma-sep values for functions.

chris

> thanks again!
> 
> galeb
> 
> On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().
> 
> chris
> 
> -----------------------------
> #!/usr/bin/env perl
> 
> use Modern::Perl;
> use Bio::SeqIO;
> 
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
> 
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>   }
> }
> 
> 
> 




From cjfields at illinois.edu  Thu Sep  8 14:30:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:30:06 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
	<1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>
	<OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
Message-ID: <C7BC7AE9-FF28-460D-83D1-35F0C8A17832@illinois.edu>

Try updating to the latest CPAN release (1.6.901, which is the pre-1.7 release).

chris

On Sep 8, 2011, at 1:19 PM, Jeff S Kittrell wrote:

> chris,
> 
> I am using version 1.6.1
> 
> Thanks,
> 
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> <graycol.gif>"Fields, Christopher J" ---09/08/2011 12:28:56 PM---What version of bioperl are you using? I think this issue was addressed a while ago, but it's possi
> 
> <ecblank.gif>
> From:
> <ecblank.gif>
> "Fields, Christopher J" <cjfields at illinois.edu>
> <ecblank.gif>
> To:
> <ecblank.gif>
> Jeff S Kittrell <jskittrell at unmc.edu>
> <ecblank.gif>
> Cc:
> <ecblank.gif>
> "<bioperl-l at lists.open-bio.org> " <bioperl-l at lists.open-bio.org>
> <ecblank.gif>
> Date:
> <ecblank.gif>
> 09/08/2011 12:28 PM
> <ecblank.gif>
> Subject:
> <ecblank.gif>
> Re: [Bioperl-l] Error when parsing a blast file
> 
> 
> 
> What version of bioperl are you using? I think this issue was addressed a while ago, but it's possible there has been a regression.
> 
> chris
> 
> On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:
> 
> > Hello Gentlemen,
> > 
> > I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> > When the SearchIO parser encounters this record it dies with the error
> > 
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: no data for midline Query ------------------------------------------------------------
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> > STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> > STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> > -----------------------------------------------------------
> > 
> > 
> > Has anyone encountered this problem before? Am I doing something wrong?
> > 
> > Thanks
> > 
> > Jeff Kittrell
> > Department of Genetics, Cell Biology & Anatomy
> > University of Nebraska Medical Center
> > 985805 Nebraska Medical Center
> > Omaha, NE 68198-5805
> > 
> > Query= 78065535
> > 
> > Length=523
> > Score E
> > Sequences producing significant alignments: (Bits) Value
> > 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> > 
> > 
> > > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> > receptor 123 (GPR123), mRNA
> > Length=4298
> > 
> > Score = 576 bits (638), Expect = 1e-163
> > Identities = 466/583 (80%), Gaps = 82/583 (14%)
> > Strand=Plus/Minus
> > 
> > Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> > ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> > Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> > 
> > Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> > |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> > Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> > 
> > Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> > |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> > Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> > 
> > Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> > ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> > Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> > 
> > Query ------------------------------------------------------------ 
> > 
> > Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> > 
> > Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> > |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> > Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> > 
> > Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> > ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> > Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> > 
> > Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> > |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> > Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> > 
> > Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> > ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> > Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> > 
> > Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> > ||||||||||||||||||||||||||||||| ||| || ||||
> > Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> > 
> > 
> > 
> > Lambda K H
> > 0.634 0.408 0.912 
> > 
> > Gapped
> > Lambda K H
> > 0.625 0.410 0.780 
> > 
> > Effective search space used: 47712920310
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 




From abualiga2 at gmail.com  Thu Sep  8 14:34:41 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 14:34:41 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
	<2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
Message-ID: <CANPzzTvxce3b=-bBUh9xNsda=1HrO9X6tRLhZAN5jhxpkKMLAQ@mail.gmail.com>

many thanks again, Chris! I was reading Programming Perl, but this sums it
up better.

On Thu, Sep 8, 2011 at 2:27 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

> On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:
>
> > thanks, Chris! works perfect.
> > To make sure I understand what's going on, forcing list context on $locus
> allows me to get one value at a time,...
>
> You have to be careful in this circumstance; doing this:
>
>   my $foo = @bar;
>
> is scalar context on a list, which returns the number of elements in @bar.
>  The following
>
>   my ($foo) = @bar;
>
> forces list context and assigns the first value in @bar to $foo but tosses
> the rest.  If you are sure there is only one value in @bar anyway, the above
> is fine (and is a common perl idiom).
>
> > which is then concatenated with \t to concatenated functions.
>
> I'm just using a simple join() to print off the results.  Note the second
> element in the join list is an embedded join() with comma-sep values for
> functions.
>
> chris
>
> > thanks again!
> >
> > galeb
> >
> > On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
> > There is no need to do that if one is using the Bio::SeqFeatureI
> interface.  Note that get_tag_values always returns a list, so to snag a
> single value for a tag in a scalar, force list context on the LHS by
> enclosing the variable in ().
> >
> > chris
> >
> > -----------------------------
> > #!/usr/bin/env perl
> >
> > use Modern::Perl;
> > use Bio::SeqIO;
> >
> > my $in = Bio::SeqIO->new(-format => 'genbank',
> >                         -file => shift);
> >
> > while (my $seq = $in->next_seq) {
> >   for my $feat ($seq->get_SeqFeatures) {
> >       next unless $feat->primary_tag eq 'CDS';
> >       my ($locus) = $feat->has_tag('locus_tag') ?
> >                     $feat->get_tag_values('locus_tag') : '';
> >       my @funcs = $feat->has_tag('function') ?
> >           $feat->get_tag_values('function') : ();
> >       say join("\t", $locus, join(',', at funcs));
> >   }
> > }
> >
> >
> >
>
>


From David.Messina at sbc.su.se  Fri Sep  9 05:40:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 11:40:25 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
Message-ID: <CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>

Hi Manju,


But this is not showing all query coverage as it shows in simple balst.(see
> attached file)
>

I'm not sure what you mean by query coverage here, as blast report you
attached doesn't (as far as I can see) include a calculation of the number
or percentage of query bases covered.

But in any case, everything in that blast report is available in the
Bio::SearchIO object that B::T::R::RemoteBlast returns. Have you taken a
look at http://www.bioperl.org/wiki/HOWTO:SearchIO ? That, along with the
module documentation, should help you find the parts of the BLAST report
you're looking for.



> and i also want to write that result in a blast file..Is there any method
> which can write the remoteblast output
> in a file with blast extension?
>

It is possible to write out the results in a format that closely resembles
the native blast report, but it's not recommended. If you want to just run
BLAST and get back a report, there's no need to use BioPerl to parse the
report first and then recreate the report.

This might also be a good time to mention that, if you're doing more than a
few hundred BLAST searches, you'll find it much more efficient to download
the database and the BLAST program from NCBI and run them on your own
computer. NCBI severely limits the speed and frequency of remote BLASTs, and
furthermore it's much more prone to failure.

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
remotely without BioPerl. Check out the --remote command-line option ? it's
my favorite new feature!


Dave



From David.Messina at sbc.su.se  Fri Sep  9 06:53:01 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 12:53:01 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
Message-ID: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>

If you don't want to learn how to do this in BioPerl, then take my previous
suggestion and just use NCBI's tools:

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
> remotely without BioPerl. Check out the --remote command-line option





On Fri, Sep 9, 2011 at 12:07, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I dont no more about Bioperl....
> and i just want to blast my sequences using bioperl...
> ans see the result in a file...
> pls tell me what should i do???
>


From manju.rawat2 at gmail.com  Fri Sep  9 07:05:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 07:05:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
Message-ID: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>

I want to learn...and i am learing it from starting...
My main query is I want to make a program which gives me that
result(sequence) which have no blast result(no matches in any database/or
particular database).
for this i have to do blast may time....but i am not getting desired result
in blast...this is the main problem which i am facing..
now pls tell me whta procedure i should follow...


Manju


From cjfields at illinois.edu  Fri Sep  9 09:03:26 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 9 Sep 2011 13:03:26 +0000
Subject: [Bioperl-l] blast result not matching.
In-Reply-To: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
	<CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
Message-ID: <AB17FEA3-524D-43EC-8C55-FAF7339FAE4A@illinois.edu>

If you are planning on looking against 'everything' (e.g. nt or nr), and you have many sequences to run, I would follow Dave's suggestion and download BLAST locally.  

chris

On Sep 9, 2011, at 6:05 AM, Manju Rawat wrote:

> I want to learn...and i am learing it from starting...
> My main query is I want to make a program which gives me that
> result(sequence) which have no blast result(no matches in any database/or
> particular database).
> for this i have to do blast may time....but i am not getting desired result
> in blast...this is the main problem which i am facing..
> now pls tell me whta procedure i should follow...
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Fri Sep  9 05:01:55 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 05:01:55 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
Message-ID: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>

Thanks to all..Its working..
I tried that module...and got the result follwing result in terminal...


waiting......db is All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
hit name is ref|NM_181451.1|
score is 240
hit name is ref|NM_001008415.1|
score is 234
hit name is ref|XM_002706247.1|
score is 212
hit name is ref|XM_002683856.1|
score is 208
hit name is gb|EF197120.1|
score is 208
hit name is ref|XR_083566.1|
score is 198
hit name is ref|NM_001097567.1|
score is 198
hit name is ref|NM_001098089.1|
score is 198
hit name is ref|XM_002699708.1|
score is 192
hit name is ref|XM_592786.5|
score is 192
hit name is ref|XM_001251693.3|
score is 192
hit name is gb|AF490400.1|
score is 190
hit name is gb|AY075103.1|
score is 190
hit name is ref|XR_083457.1|
score is 178


But this is not showing all query coverage as it shows in simple balst.(see
attached file)
and i also want to write that result in a blast file..Is there any method
which can write the remoteblast output
in a file with blast extension?


Thanks
Manju Rawat.
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From ross at cuhk.edu.hk  Sat Sep 10 02:39:23 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 10 Sep 2011 14:39:23 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick file
Message-ID: <048a01cc6f84$60c41090$224c31b0$@edu.hk>

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"

 

What's the problem? 

 

use Bio::TreeIO;

 

($treefh) = @ARGV;

 

my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;

 

$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);

 

my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);

 

my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";

 

 

#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;



From greg at ebi.ac.uk  Sat Sep 10 11:39:52 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Sat, 10 Sep 2011 16:39:52 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
Message-ID: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>

Hi Ross,

Which version of BioPerl are you using?

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
the following script works for me. Do those values look sensible to you? The
code on the new branch is a bit experimental, so I wouldn't be surprised if
all the edge cases for calculations like this aren't covered.

--greg

use Bio::TreeIO;

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");
my $tree = $treeio->next_tree;
my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");
my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");
my $ma = $tree->find("Mycobacterium_abscessus");
my $distance = $mt->distance($ma);
print "MT - MA: ".$mt->distance($ma)."\n";
print "MT - MS: ".$mt->distance($ms)."\n";
print "MS - MA: ".$ms->distance($ma)."\n";
# MT - MA: 0.24326
# MT - MS: 0.18573
# MS - MA: 0.20729

--greg

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ross at cuhk.edu.hk  Sat Sep 10 19:06:44 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 11 Sep 2011 07:06:44 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
Message-ID: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>

Hi Greg,

 

The values are correct! However, how to install this bioperl-live module? my
bioperl is 1.6.1 but there's an error:

 

Can't locate object method "find" via package "Bio::Tree::Tree" at
TreeCalDist.pl line 32, <GEN0> line 1.

my $mt = $tree->find($keyword);  #line 32

 

 

From: gjuggler at gmail.com [mailto:gjuggler at gmail.com] On Behalf Of Gregory
Jordan
Sent: 2011??9??10?? 23:40
To: bioperl-l List; Ross KK Leung
Subject: Re: [Bioperl-l] fail to obtain node-to-node distance from a newick
file

 

Hi Ross,

 

Which version of BioPerl are you using?

 

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree
/NodeFunctionsI.pm#L406) the following script works for me. Do those values
look sensible to you? The code on the new branch is a bit experimental, so I
wouldn't be surprised if all the edge cases for calculations like this
aren't covered.

 

--greg

 

use Bio::TreeIO;

 

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");

my $tree = $treeio->next_tree;

my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");

my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");

my $ma = $tree->find("Mycobacterium_abscessus");

my $distance = $mt->distance($ma);

print "MT - MA: ".$mt->distance($ma)."\n";

print "MT - MS: ".$mt->distance($ms)."\n";

print "MS - MA: ".$ms->distance($ma)."\n";

# MT - MA: 0.24326

# MT - MS: 0.18573

# MS - MA: 0.20729

 

--greg

 

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"



What's the problem?



use Bio::TreeIO;



($treefh) = @ARGV;



my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;



$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);



my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);



my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";





#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 




From manju.rawat2 at gmail.com  Mon Sep 12 01:37:35 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:37:35 -0400
Subject: [Bioperl-l] no blast result
Message-ID: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>

Hello,
I want to make a program which first generate the random sequence and then
gives me that result(sequence) which have no blast result(no matches in any
database/or particular database).Is there any body who can help me in doing
this.

Pl reply if anybody knows about it..
Thanks
Manju


From zhangchnxp at gmail.com  Mon Sep 12 01:51:59 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 13:51:59 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
Message-ID: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>

Hi,

IMHO, due to the nature of BLAST, it is usually impossible to get no results
from random sequence, but to get a set of matches with lower scores.

What you can do is to focus on the e-value, say, setting a threshold to it.

FYI, http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

On Mon, Sep 12, 2011 at 1:37 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Hello,
> I want to make a program which first generate the random sequence and then
> gives me that result(sequence) which have no blast result(no matches in any
> database/or particular database).Is there any body who can help me in doing
> this.
>
> Pl reply if anybody knows about it..
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From manju.rawat2 at gmail.com  Mon Sep 12 01:58:38 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:58:38 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
Message-ID: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>

Ya i know this....And it is also in my use if i get result with lower
scores.
But how could I do this?


Manju


From zhangchnxp at gmail.com  Mon Sep 12 02:04:17 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 14:04:17 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
Message-ID: <CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>

Please read the documentation for Bio::Tools::Run::StandAloneBlast
and Bio::AlignIO.*
*
On Mon, Sep 12, 2011 at 1:58 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Ya i know this....And it is also in my use if i get result with lower
> scores.
> But how could I do this?
>
>
> Manju
>


From manju.rawat2 at gmail.com  Mon Sep 12 07:12:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 07:12:40 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
Message-ID: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>

I read this..but default program is not runnig fine.it showing many error
that

MSG: cannot find path to blastall..
Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

Am this this is not showing output which i want..

Pl help me..

Manju Rawat


From arguelloj at gmail.com  Sun Sep 11 22:52:42 2011
From: arguelloj at gmail.com (J. Fernando Arguello)
Date: Sun, 11 Sep 2011 19:52:42 -0700
Subject: [Bioperl-l] BioPerl - quick general question
Message-ID: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>

Dear BioPerl,

I'm excited to see a project like this! Basically I have a computer science
background with a few years of development, research and minimal
bioinformatics experience.

Dumb question...where is the best place for a developer to begin on the
BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
BioPerl in the future?

Any input is much appreciated. Thank you all for your time.

Best,
Fernando
jfa


From briano at bioteam.net  Mon Sep 12 09:20:36 2011
From: briano at bioteam.net (Brian Osborne)
Date: Mon, 12 Sep 2011 09:20:36 -0400
Subject: [Bioperl-l] Fwd: cds sequence extract
References: <112c4ef2.641e.1325c4b21cb.Coremail.maliang7121@163.com>
Message-ID: <671CAF11-55A4-462A-BC5B-805C87E1EB0E@bioteam.net>

Liang Ma,

I'm forwarding this to the Bioperl mailing list.

If you're starting out with Bioperl I suggest you read this:

http://www.bioperl.org/wiki/HOWTO:Beginners

Brian O.


Begin forwarded message:

> From: maliang7121 <maliang7121 at 163.com>
> Date: September 12, 2011 2:20:20 AM EDT
> To: briano at bioteam.net
> Subject: cds sequence extract
> 
> Dear Brian:
> 
> I am a student of Chinese Academy of Sience, I begin to love bioperl, but now I have a problem.
> 
> According to the script of the attachment, I could easily dowload sequences from NCBI, now I need extract cds sequence from the genbank format files, and put them all in a single file using fasta format, I can not do it, could you spend a few minite wrinting a script for me?
> 
> Best!
> 
> Liang Ma
> 
> 
> 

Brian O.
--
Brian Osborne, PhD
BioTeam: http://bioteam.net
email: briano at bioteam.net
mobile: 978-317-3101

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From fs5 at sanger.ac.uk  Mon Sep 12 09:54:21 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Mon, 12 Sep 2011 14:54:21 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
Message-ID: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>

looks like BLAST is not install on your system. The BioPerl module only
runs BLAST for you and parses the output but you still need the BLAST
executables installed on your system. Follow the instructions on the
NCBI website to download and install BLAST and try running it on the
commandline with the "blastall" command. If that works then you can run
it also via BioPerl.
Frank


On Mon, 2011-09-12 at 07:12 -0400, Manju Rawat wrote:
> I read this..but default program is not runnig fine.it showing many error
> that
> 
> MSG: cannot find path to blastall..
> Use of uninitialized value $_[0] in join or string at
> /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> Am this this is not showing output which i want..
> 
> Pl help me..
> 
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From p.j.a.cock at googlemail.com  Mon Sep 12 10:00:30 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 12 Sep 2011 15:00:30 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>

On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
> looks like BLAST is not install on your system. The BioPerl module only
> runs BLAST for you and parses the output but you still need the BLAST
> executables installed on your system. Follow the instructions on the
> NCBI website to download and install BLAST and try running it on the
> commandline with the "blastall" command. If that works then you can run
> it also via BioPerl.
> Frank

Hang on - blastall is from the "legacy" BLAST suite, does
BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
blastn and blastp rather then blastall)?

Peter


From cjfields at illinois.edu  Mon Sep 12 13:45:56 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 12 Sep 2011 17:45:56 +0000
Subject: [Bioperl-l] BioPerl - quick general question
In-Reply-To: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
References: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
Message-ID: <62B9B300-96AC-4511-A1B9-CFF36CBE6288@illinois.edu>

On Sep 11, 2011, at 9:52 PM, J. Fernando Arguello wrote:

> Dear BioPerl,
> 
> I'm excited to see a project like this! Basically I have a computer science
> background with a few years of development, research and minimal
> bioinformatics experience.
> 
> Dumb question...where is the best place for a developer to begin on the
> BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
> BioPerl in the future?

The basic starting point: the HOWTOs and the tutorial (not sure how up-to-date some of the latter are, in general they should work):

http://www.bioperl.org/wiki/HOWTOs
http://www.bioperl.org/wiki/Tutorials

> Any input is much appreciated. Thank you all for your time.
> 
> Best,
> Fernando
> jfa

We gladly welcome anyone willing to hack on BioPerl.  The repository is now on github (core is https://github.com/bioperl/bioperl-live), so it's fairly easy to fork the code and make changes.  We are in the middle of splitting up the large codebase into more manageable subdistributions, so it's probably a good idea to ask on list about specific code in case the code is question resides in a separate repository.  

Let us know if you have additional questions!

Cheers!

chris




From shalabh.sharma7 at gmail.com  Mon Sep 12 14:00:16 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Mon, 12 Sep 2011 14:00:16 -0400
Subject: [Bioperl-l] Module for SOCS
Message-ID: <CAA7rn9d37ntxbtMUR3Z41JHTNZypi+2jZQunwGJ5bN8DZ21xtg@mail.gmail.com>

Hi All,
         I am using SOCS for mapping my SOILD data. I was just wondering if
there is any module in bioperl to analyze SOCS output files directly or
mapreads format.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From greg at ebi.ac.uk  Tue Sep 13 04:30:58 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Tue, 13 Sep 2011 09:30:58 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
Message-ID: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>

Hi Ross,

I don't typically 'install' versions of BioPerl from GitHub. Rather, I check
out the code into a directory that's on my Perl search path (and make sure
any other BioPerl code isn't on the path anymore). I think the following
commands should get you the right set of code:

> git clone git://github.com/bioperl/bioperl-live.git
> git checkout topic/tree_api_refresh

After that, I'm afraid I'll have to leave it to you (or someone else on the
list). I'm no Perl guru, so I don't know the "right" way to direct Perl
towards a developmental BioPerl branch.

Cheers,
 Greg

2011/9/11 Ross KK Leung <ross at cuhk.edu.hk>

> Hi Greg,****
>
> ** **
>
> The values are correct! However, how to install this bioperl-live module?
> my bioperl is 1.6.1 but there's an error:****
>
> ** **
>
> Can't locate object method "find" via package "Bio::Tree::Tree" at
> TreeCalDist.pl line 32, <GEN0> line 1.****
>
> my $mt = $tree->find($keyword);  #line 32****
>
> ** **
>
> ** **
>
> *From:* gjuggler at gmail.com [mailto:gjuggler at gmail.com] *On Behalf Of *Gregory
> Jordan
> *Sent:* 2011?9?10? 23:40
> *To:* bioperl-l List; Ross KK Leung
> *Subject:* Re: [Bioperl-l] fail to obtain node-to-node distance from a
> newick file****
>
> ** **
>
> Hi Ross,****
>
> ** **
>
> Which version of BioPerl are you using?****
>
> ** **
>
> With the refactored tree code (available from the tree_api_refresh branch
> on the BioPerl github repo:
> https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
> the following script works for me. Do those values look sensible to you? The
> code on the new branch is a bit experimental, so I wouldn't be surprised if
> all the edge cases for calculations like this aren't covered.****
>
> ** **
>
> --greg****
>
> ** **
>
> use Bio::TreeIO;****
>
> ** **
>
> my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");**
> **
>
> my $tree = $treeio->next_tree;****
>
> my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");****
>
> my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");****
>
> my $ma = $tree->find("Mycobacterium_abscessus");****
>
> my $distance = $mt->distance($ma);****
>
> print "MT - MA: ".$mt->distance($ma)."\n";****
>
> print "MT - MS: ".$mt->distance($ms)."\n";****
>
> print "MS - MA: ".$ms->distance($ma)."\n";****
>
> # MT - MA: 0.24326****
>
> # MT - MS: 0.18573****
>
> # MS - MA: 0.20729****
>
> ** **
>
> --greg****
>
> ** **
>
> On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:**
> **
>
> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l****
>
> ** **
>



From manju.rawat2 at gmail.com  Tue Sep 13 07:20:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 13 Sep 2011 07:20:07 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>

this is the perl code

 #!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO
use Bio::Tools::Run::StandAloneBlast;
 @params = ('database' => 'swissprot',
        'READMETHOD' => 'Blastn');

 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);


 $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
 $blast_report = $factory->blastall($input);


  write_blast(">rs.blast",$blast_report);


It showing error that


Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

MSG: cannot find path to blastall


From fs5 at sanger.ac.uk  Tue Sep 13 11:09:24 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Tue, 13 Sep 2011 16:09:24 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
Message-ID: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>

Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
StandAloneBlast is still set to "blastall" - I'm not sure if it works
with blast+ too.

Manju: as I said previously, you need to check that you can run BLAST on
the command line, i.e. make sure it is actually installed on your
system. Have you done that?
You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
you can manually set the path to your BLAST executable if it is not in
your path. You have to install BLAST fisrt before you can run this
module.
The other error you get from yuor code refers to something that is
outside of the code fragment you show here, so can't comment on that
one.

Frank


On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> this is the perl code
> 
>  #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO
> use Bio::Tools::Run::StandAloneBlast;
>  @params = ('database' => 'swissprot', 
>         'READMETHOD' => 'Blastn');
> 
>  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> 
> 
>  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
>  $blast_report = $factory->blastall($input);
>  
> 
>   write_blast(">rs.blast",$blast_report);
> 
> 
> It showing error that
> 
> 
> Use of uninitialized value $_[0] in join or string
> at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> MSG: cannot find path to blastall
> 
>  



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From David.Messina at sbc.su.se  Tue Sep 13 11:34:20 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 13 Sep 2011 17:34:20 +0200
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAM3TQQWx_QQK96etWHntvmRRnjJ9ZPCJYMcC0rukNoJD5_et1w@mail.gmail.com>

There's a separate Bio::Tools::Run::BlastPlus module for blast+. And a
related HOWTO:
http://www.bioperl.org/wiki/HOWTO:BlastPlus



On Tue, Sep 13, 2011 at 17:09, Frank Schwach <fs5 at sanger.ac.uk> wrote:

> Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
> StandAloneBlast is still set to "blastall" - I'm not sure if it works
> with blast+ too.
>
> Manju: as I said previously, you need to check that you can run BLAST on
> the command line, i.e. make sure it is actually installed on your
> system. Have you done that?
> You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
> you can manually set the path to your BLAST executable if it is not in
> your path. You have to install BLAST fisrt before you can run this
> module.
> The other error you get from yuor code refers to something that is
> outside of the code fragment you show here, so can't comment on that
> one.
>
> Frank
>
>
> On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> > this is the perl code
> >
> >  #!usr/bin/perl -w
> > use Bio::Perl;
> > use Bio::SearchIO
> > use Bio::Tools::Run::StandAloneBlast;
> >  @params = ('database' => 'swissprot',
> >         'READMETHOD' => 'Blastn');
> >
> >  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> >
> >
> >  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
> >  $blast_report = $factory->blastall($input);
> >
> >
> >   write_blast(">rs.blast",$blast_report);
> >
> >
> > It showing error that
> >
> >
> > Use of uninitialized value $_[0] in join or string
> > at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> >
> > MSG: cannot find path to blastall
> >
> >
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Tue Sep 13 15:36:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 13 Sep 2011 19:36:21 +0000
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>

On Sep 12, 2011, at 9:00 AM, Peter Cock wrote:

> On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
>> looks like BLAST is not install on your system. The BioPerl module only
>> runs BLAST for you and parses the output but you still need the BLAST
>> executables installed on your system. Follow the instructions on the
>> NCBI website to download and install BLAST and try running it on the
>> commandline with the "blastall" command. If that works then you can run
>> it also via BioPerl.
>> Frank
> 
> Hang on - blastall is from the "legacy" BLAST suite, does
> BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
> blastn and blastp rather then blastall)?
> 
> Peter

(aside: thought I sent this the other day.  never mix grant writing and open source)

Both BLAST and BLAST+ are supported via different modules.  Some users don't want to use BLAST+ for various reasons, though this may soon be out of their control when NCBI eventually stops supporting legacy BLAST entirely.

chris




From manju.rawat2 at gmail.com  Wed Sep 14 07:32:19 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 14 Sep 2011 07:32:19 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>
	<CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
Message-ID: <CAB2c7yqZ0Eb=7=GTiXidD-6_UzF8qB1JBVv+5h6+8xsR84HXuQ@mail.gmail.com>

On Wed, Sep 14, 2011 at 7:31 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I am trying to install Blast+ in my system.(ubuntu) from this link
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html.
> but i am getting error..
>
> first i downloaded the blast(ncbi-blast-2.2.25+-ia32-linux.tar.gz) from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
> .  and then extract it in the home/abc/ folder.
> after that i set the path for configuration in terminal i.e
>
> *PATH=$PATH:/home/abc/blast-2.2.25+/bin*
>
>
> but when i am  running blast -help in terminal it showing me error that
>
> error while loading shared libraries:
>  libbz2.so.1: cannot open shared object file: No such file or directory.
>
>


-- 
Regards
Manju Rawat
Project Assistant(NAIP)
Genomics Lab
ABTC,NDRI Karnal-132001,Haryana


From kumarsaurabh20 at gmail.com  Thu Sep 15 07:20:47 2011
From: kumarsaurabh20 at gmail.com (kumar Saurabh)
Date: Thu, 15 Sep 2011 13:20:47 +0200
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
Message-ID: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>

Hi,

I need to integrate the primer3 module in one of our pipeline. In a process,
I was testing the initial code given on the CPAN website. But whenever I try
to run this program its giving me error...that "Cannot locate the Object
method add_target via the package Bio::Tools:Run::Primer3Redux...."

The line of codes I am using is as follows:

# design some primers.
  # the output will be put into temp.out
  use Bio::Tools::Primer3Redux;
  use Bio::Tools::Run::Primer3Redux;
  use Bio::SeqIO;

  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
  my $seq = $seqio->next_seq;

  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
                                            -path =>
"/home/singh/Downloads/primer3-2.2.3/src/primer3_core");

  # or after the fact you can change the program_name
  $primer3->program_name('my_superfast_primer3');

  unless ($primer3->executable) {
    print STDERR "primer3 can not be found. Is it installed?\n";
    exit(-1)
  }

  # set the maximum and minimum Tm of the primer
  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);

  # Design the primers. This runs primer3 and returns a
  # Bio::Tools::Primer3::result object with the results
  # Primer3 can run in several modes (see explanation for
  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
  # either call it by its PRIMER_TASK name as in these examples:
  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
  $check_results = $primer3->check_primers();

  # Alternatively, explicitly set the PRIMER_TASK parameter and
  # use the generic 'run' method (this is mainly here for backwards
  # compatibility) :
  $primer3->PRIMER_TASK( 'pick_left_only' );
  $result = $primer3->run( $seq );

  # If no task is set and the 'run' method is called, primer3 will default
to
  # pick pcr primers.

  # see the Bio::Tools::Primer3Redux POD for
  # things that you can get from this. For example:

  print "There were ", $results->num_primer_pairs, " primer pairs\n";


Can anyone help me with this???


Best regards,
Kumar


From fs5 at sanger.ac.uk  Thu Sep 15 09:44:03 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 14:44:03 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
Message-ID: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>

Hi Kumar,

We are currently working on this module and you might want to check out
the latest version on Chris Field's github project:

https://github.com/cjfields/Bio-Tools-Primer3Redux

There will probably be some changes again once I get some time again to
work on a few points we discussed lately. You can also check out my repo
here:
https://github.com/fschwach/Bio-Tools-Primer3Redux

but I will certainly have to make changes to that code because I used
AUTOLAD in the last version, which is probably not a good idea.
My recommendation would be to use Chris' repo and see if that works for
you. If not, feedback would be much appreciated.

Cheers,

Frank




On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> Hi,
> 
> I need to integrate the primer3 module in one of our pipeline. In a process,
> I was testing the initial code given on the CPAN website. But whenever I try
> to run this program its giving me error...that "Cannot locate the Object
> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> 
> The line of codes I am using is as follows:
> 
> # design some primers.
>   # the output will be put into temp.out
>   use Bio::Tools::Primer3Redux;
>   use Bio::Tools::Run::Primer3Redux;
>   use Bio::SeqIO;
> 
>   my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>   my $seq = $seqio->next_seq;
> 
>   my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>                                             -path =>
> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> 
>   # or after the fact you can change the program_name
>   $primer3->program_name('my_superfast_primer3');
> 
>   unless ($primer3->executable) {
>     print STDERR "primer3 can not be found. Is it installed?\n";
>     exit(-1)
>   }
> 
>   # set the maximum and minimum Tm of the primer
>   $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> 
>   # Design the primers. This runs primer3 and returns a
>   # Bio::Tools::Primer3::result object with the results
>   # Primer3 can run in several modes (see explanation for
>   # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>   # either call it by its PRIMER_TASK name as in these examples:
>   $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>   $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>   $check_results = $primer3->check_primers();
> 
>   # Alternatively, explicitly set the PRIMER_TASK parameter and
>   # use the generic 'run' method (this is mainly here for backwards
>   # compatibility) :
>   $primer3->PRIMER_TASK( 'pick_left_only' );
>   $result = $primer3->run( $seq );
> 
>   # If no task is set and the 'run' method is called, primer3 will default
> to
>   # pick pcr primers.
> 
>   # see the Bio::Tools::Primer3Redux POD for
>   # things that you can get from this. For example:
> 
>   print "There were ", $results->num_primer_pairs, " primer pairs\n";
> 
> 
> Can anyone help me with this???
> 
> 
> Best regards,
> Kumar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From cjfields at illinois.edu  Thu Sep 15 10:13:38 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 15 Sep 2011 14:13:38 +0000
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>

I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 

chris

On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:

> Hi Kumar,
> 
> We are currently working on this module and you might want to check out
> the latest version on Chris Field's github project:
> 
> https://github.com/cjfields/Bio-Tools-Primer3Redux
> 
> There will probably be some changes again once I get some time again to
> work on a few points we discussed lately. You can also check out my repo
> here:
> https://github.com/fschwach/Bio-Tools-Primer3Redux
> 
> but I will certainly have to make changes to that code because I used
> AUTOLAD in the last version, which is probably not a good idea.
> My recommendation would be to use Chris' repo and see if that works for
> you. If not, feedback would be much appreciated.
> 
> Cheers,
> 
> Frank
> 
> 
> 
> 
> On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
>> Hi,
>> 
>> I need to integrate the primer3 module in one of our pipeline. In a process,
>> I was testing the initial code given on the CPAN website. But whenever I try
>> to run this program its giving me error...that "Cannot locate the Object
>> method add_target via the package Bio::Tools:Run::Primer3Redux...."
>> 
>> The line of codes I am using is as follows:
>> 
>> # design some primers.
>>  # the output will be put into temp.out
>>  use Bio::Tools::Primer3Redux;
>>  use Bio::Tools::Run::Primer3Redux;
>>  use Bio::SeqIO;
>> 
>>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>>  my $seq = $seqio->next_seq;
>> 
>>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>>                                            -path =>
>> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
>> 
>>  # or after the fact you can change the program_name
>>  $primer3->program_name('my_superfast_primer3');
>> 
>>  unless ($primer3->executable) {
>>    print STDERR "primer3 can not be found. Is it installed?\n";
>>    exit(-1)
>>  }
>> 
>>  # set the maximum and minimum Tm of the primer
>>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
>> 
>>  # Design the primers. This runs primer3 and returns a
>>  # Bio::Tools::Primer3::result object with the results
>>  # Primer3 can run in several modes (see explanation for
>>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>>  # either call it by its PRIMER_TASK name as in these examples:
>>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>>  $check_results = $primer3->check_primers();
>> 
>>  # Alternatively, explicitly set the PRIMER_TASK parameter and
>>  # use the generic 'run' method (this is mainly here for backwards
>>  # compatibility) :
>>  $primer3->PRIMER_TASK( 'pick_left_only' );
>>  $result = $primer3->run( $seq );
>> 
>>  # If no task is set and the 'run' method is called, primer3 will default
>> to
>>  # pick pcr primers.
>> 
>>  # see the Bio::Tools::Primer3Redux POD for
>>  # things that you can get from this. For example:
>> 
>>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
>> 
>> 
>> Can anyone help me with this???
>> 
>> 
>> Best regards,
>> Kumar
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From fs5 at sanger.ac.uk  Thu Sep 15 10:43:48 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 15:43:48 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
	<D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
Message-ID: <1316097828.3797.700.camel@deskpro15336.internal.sanger.ac.uk>

I also haven't had the time yet to work on this again but, yes, we need
to make sure we don't loose track of where we are. 


On Thu, 2011-09-15 at 14:13 +0000, Fields, Christopher J wrote:
> I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 
> 
> chris
> 
> On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:
> 
> > Hi Kumar,
> > 
> > We are currently working on this module and you might want to check out
> > the latest version on Chris Field's github project:
> > 
> > https://github.com/cjfields/Bio-Tools-Primer3Redux
> > 
> > There will probably be some changes again once I get some time again to
> > work on a few points we discussed lately. You can also check out my repo
> > here:
> > https://github.com/fschwach/Bio-Tools-Primer3Redux
> > 
> > but I will certainly have to make changes to that code because I used
> > AUTOLAD in the last version, which is probably not a good idea.
> > My recommendation would be to use Chris' repo and see if that works for
> > you. If not, feedback would be much appreciated.
> > 
> > Cheers,
> > 
> > Frank
> > 
> > 
> > 
> > 
> > On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> >> Hi,
> >> 
> >> I need to integrate the primer3 module in one of our pipeline. In a process,
> >> I was testing the initial code given on the CPAN website. But whenever I try
> >> to run this program its giving me error...that "Cannot locate the Object
> >> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> >> 
> >> The line of codes I am using is as follows:
> >> 
> >> # design some primers.
> >>  # the output will be put into temp.out
> >>  use Bio::Tools::Primer3Redux;
> >>  use Bio::Tools::Run::Primer3Redux;
> >>  use Bio::SeqIO;
> >> 
> >>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
> >>  my $seq = $seqio->next_seq;
> >> 
> >>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
> >>                                            -path =>
> >> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> >> 
> >>  # or after the fact you can change the program_name
> >>  $primer3->program_name('my_superfast_primer3');
> >> 
> >>  unless ($primer3->executable) {
> >>    print STDERR "primer3 can not be found. Is it installed?\n";
> >>    exit(-1)
> >>  }
> >> 
> >>  # set the maximum and minimum Tm of the primer
> >>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> >> 
> >>  # Design the primers. This runs primer3 and returns a
> >>  # Bio::Tools::Primer3::result object with the results
> >>  # Primer3 can run in several modes (see explanation for
> >>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
> >>  # either call it by its PRIMER_TASK name as in these examples:
> >>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
> >>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
> >>  $check_results = $primer3->check_primers();
> >> 
> >>  # Alternatively, explicitly set the PRIMER_TASK parameter and
> >>  # use the generic 'run' method (this is mainly here for backwards
> >>  # compatibility) :
> >>  $primer3->PRIMER_TASK( 'pick_left_only' );
> >>  $result = $primer3->run( $seq );
> >> 
> >>  # If no task is set and the 'run' method is called, primer3 will default
> >> to
> >>  # pick pcr primers.
> >> 
> >>  # see the Bio::Tools::Primer3Redux POD for
> >>  # things that you can get from this. For example:
> >> 
> >>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
> >> 
> >> 
> >> Can anyone help me with this???
> >> 
> >> 
> >> Best regards,
> >> Kumar
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > 
> > 
> > -- 
> > The Wellcome Trust Sanger Institute is operated by Genome Research 
> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose registered 
> > office is 215 Euston Road, London, NW1 2BE. 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From manju.rawat2 at gmail.com  Fri Sep 16 01:09:25 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:09:25 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>

Hello Frank,

Yes,u r rite..I tried to run blast in terminal but its not working..
I have installed the latest version of blast and download the database
correctly..

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.
Manju


From manju.rawat2 at gmail.com  Fri Sep 16 01:12:03 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:12:03 -0400
Subject: [Bioperl-l] Command line error in BLAST+
Message-ID: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>

Hi,


I have installed the latest version of blast and download the database
correctly Using this tutorial
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.

Thanks
Manju


From p.j.a.cock at googlemail.com  Fri Sep 16 04:15:46 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:15:46 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <CAKVJ-_4UF=5oBNc-ZRESAXzO-tC2j+nQGn0Qjh4E51Yrvr2o3A@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:12 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
>
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
>
> Thanks
> Manju

You're using the BioPerl wrapper for legacy blast (blastall),
which is not installed. Instead you have the new blast+
suite which includes a wrapper using the perl script
legacy_blast.pl to imitate the old blastall tool (in this
case it calls the new tool blastn).

Fix 1: Edit legacy_blast.pl to use the path to blastn etc
under your home directory

Fix 2: Install BLAST+ at system level

Fix 3: Use the BioPerl wrapper for BLAST+ instead.

I'd go with option 3.

Peter


From p.j.a.cock at googlemail.com  Fri Sep 16 04:17:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:17:58 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
	<CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
Message-ID: <CAKVJ-_5Omy7h9qx++7S-46YrxFTxbGoQZu61GDgM12C2FmQJsQ@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:09 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello Frank,
>
> Yes,u r rite..I tried to run blast in terminal but its not working..
> I have installed the latest version of blast and download the database
> correctly..
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out
> Can't exec "/usr/bin/blastn": No such file or directory at
> /usr/bin/legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
> Manju

For the benefit of anyone reading the archives later,
I tried to answer this in Manju's new thread:
http://lists.open-bio.org/pipermail/bioperl-l/2011-September/035696.html

Peter


From fs5 at sanger.ac.uk  Fri Sep 16 04:36:37 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 16 Sep 2011 09:36:37 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <1316162197.3797.721.camel@deskpro15336.internal.sanger.ac.uk>

Hi Manju,

Are you on Ubuntu? I think I've seen problems with this bzip library on
Ubuntu before. It's not a problem with BLAST in any case. 
Should be possible to install the missing files through your package
manager. I'm sure Google will know what to do :)
Not sure what went wrong with your blast installation. What happens if
you run blastall directly (without the legacy_blast.pl script)? In any
case, it might be better to ask the NCBI people for help with the BLAST
installation as this is not a BioPerl problem.

cheers,

Frank


On Fri, 2011-09-16 at 01:12 -0400, Manju Rawat wrote:
> Hi,
> 
> 
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
> 
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
> 
> 
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
> 
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
> 
> I have checked everything but not able tp fine the error..
> 
> Pl help me.
> 
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From ross at cuhk.edu.hk  Fri Sep 16 04:51:38 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 16 Sep 2011 16:51:38 +0800
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
Message-ID: <085501cc744d$d90b4500$8b21cf00$@edu.hk>

I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!

 




From cjfields at illinois.edu  Fri Sep 16 09:22:07 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 16 Sep 2011 13:22:07 +0000
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <085501cc744d$d90b4500$8b21cf00$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
Message-ID: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>

That seems like a pretty straightforward thing to do; there isn't an all-in-one way of doing this, but that's a good thing (it's a separation of concerns).

1) Run and parse BLAST results and grab seqID and coordinates for each hit (or each HSP for each hit) (Bio::SearchIO)
2) Pull the right subsequence +/- 20bp using above from the indexed flat file of your reference (Bio::DB::Fasta)

You can get revcomped sequence from Bio::DB::Fasta directly by flipping coordinates:
  
  # raw sequence
  my $seq      = $db->seq('CHROMOSOME_I',4_000_000 => 4_100_000);
  my $revseq   = $db->seq('CHROMOSOME_I',4_100_000 => 4_000_000);

chris


On Sep 16, 2011, at 3:51 AM, Ross KK Leung wrote:

> I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From wsavigne at yahoo.com  Fri Sep 16 16:45:12 2011
From: wsavigne at yahoo.com (Willy Savigne)
Date: Fri, 16 Sep 2011 13:45:12 -0700 (PDT)
Subject: [Bioperl-l] question Bioperl installation
Message-ID: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>

my name is william how do download Bioperl i tried other site but NOTHING? i would like to know info in downloading? bioperl .This is my first? time into knowing? bioinformatic i? just got? a book developing bioinformatic and begginning perl bioinformatic. I do alot Dna and RNA sequencing?? and more.
?
Thank u willy


From ross at cuhk.edu.hk  Sun Sep 18 06:51:05 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 18 Sep 2011 18:51:05 +0800
Subject: [Bioperl-l] snp/frameshift identification
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <08a901cc75f0$dd463b30$97d2b190$@edu.hk>

Dear Bioperl-users,

Following Fields, Christopher J's advice on sequence extraction, I manage to
proceed to the last stage of non-synonymous SNP identification. Now what I
have in hand is thousands of reliable multiple sequence alignment files,
e.g.

>seq1
ATGACAGACACGACGTTGCCGTAG
>seq2
ATGACAGACACGACGTAGCCGTAG
>seq3
ATGACAGACACGACGTTGCCGTAG

Seq2 has a T->A mutation and that leads to a stop codon generation. I wonder
if Bioperl has handled this kind of SNP or frameshift or non-sense mutations
that lead to change of amino acid in the translated protein product.

Thanks again to the community that helps me a great deal so I can catch up
progress during this Sat/Sun!!



From rondonbio at yahoo.com.br  Mon Sep 19 09:46:36 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Mon, 19 Sep 2011 06:46:36 -0700 (PDT)
Subject: [Bioperl-l] help-> SearchIO
Message-ID: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>

Hi guys! I need your help in a loop that I have in SearchIO.
I need to check the nucleotide coverage of querys using BLAST. I'm using the script below. It's open the alignment, create arrays for each query with zeros in each nucleotide position but, when I adds values to the coverage of each nucleotide, the script does it once and passes to another query.
Can you hek me?
Thank you very much,

Rondon
a Brazilian friend.


use Bio::SearchIO;
?
my $alignment = new Bio::SearchIO ( -format => 'blastXML',
? ? ? ? ? ? ? ? ? ? ? ? ?? ? -file ? => $alignment_file );

my %positions;
while (my $result = $alignment->next_result) {
while (my $hit = $result->next_hit) {
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
my @pos = $hsp->seq_inds('query','identical');
for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
foreach my $num (@pos) {
${$positions{$query_name}}[$num -1]++; ? ?#This loop is where I believe that is an error.
}
}
}
}

foreach my $key (keys %positions){
print "$key\t@{$positions{$key}}\n";
}

exit;



From roy.chaudhuri at gmail.com  Mon Sep 19 12:29:41 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:29:41 +0100
Subject: [Bioperl-l] help-> SearchIO
In-Reply-To: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
References: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
Message-ID: <4E776DF5.6040504@gmail.com>

Hi Rondon,

The line where you populate your arrayref with 0 (starting "for 
(0..$tam)") is within the HSP loop, so the data from every successive 
HSP will overwrite the previous one in your hash. You will therefore 
only see the data for the last HSP from each query. If you move that 
line to execute once per result (i.e. just after the line starting 
"while (my result ="), then I think it should work as you intended.

Cheers,
Roy.

On 19/09/2011 14:46, Rondon Neto wrote:
> Hi guys! I need your help in a loop that I have in SearchIO. I need
> to check the nucleotide coverage of querys using BLAST. I'm using the
> script below. It's open the alignment, create arrays for each query
> with zeros in each nucleotide position but, when I adds values to the
> coverage of each nucleotide, the script does it once and passes to
> another query. Can you hek me? Thank you very much,
>
> Rondon a Brazilian friend.
>
> use Bio::SearchIO;
>
> my $alignment = new Bio::SearchIO ( -format =>  'blastXML',
>                               -file   =>  $alignment_file );
>
> my %positions;
> while (my $result = $alignment->next_result) {
> while (my $hit = $result->next_hit) {
> while (my $hsp = $hit->next_hsp) {
> my $query_name = $result->query_name();
> my $tam = $result ->  query_length();
> my @pos = $hsp->seq_inds('query','identical');
> for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
> foreach my $num (@pos) {
> ${$positions{$query_name}}[$num -1]++;    #This loop is where I believe that is an error.
> }
> }
> }
> }
>
> foreach my $key (keys %positions){
> print "$key\t@{$positions{$key}}\n";
> }
>
> exit;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From roy.chaudhuri at gmail.com  Mon Sep 19 12:39:40 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:39:40 +0100
Subject: [Bioperl-l] question Bioperl installation
In-Reply-To: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
References: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
Message-ID: <4E77704C.20604@gmail.com>

Hi Willy,

There are instructions for downloading and installing BioPerl on the wiki:
http://www.bioperl.org/wiki/Getting_BioPerl
http://www.bioperl.org/wiki/Installing_BioPerl

These are the first two results when you Google for "bioperl download".

Note that the wiki is a little out of date, the latest BioPerl version 
is 1.6.901:
http://search.cpan.org/~cjfields/BioPerl-1.6.901/

Cheers,
Roy.

On 16/09/2011 21:45, Willy Savigne wrote:
> my name is william how do download Bioperl i tried other site but
> NOTHING  i would like to know info in downloading  bioperl .This is
> my first  time into knowing  bioinformatic i  just got  a book
> developing bioinformatic and begginning perl bioinformatic. I do alot
> Dna and RNA sequencing   and more.
>
> Thank u willy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From bosborne11 at verizon.net  Tue Sep 20 13:01:21 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 13:01:21 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
Message-ID: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>

All,

I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:

..... get the files etc ....

my %alignparams = (
    -seqtype  => 'nucleo',
    -usetree_nowarn => $guidetreefile,
    -in => $tempfile
);
my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);

# $align is a Bio::SimpleAlign object
my $align = $aligner->align($tempfile);

my %treeparams = (
   -data_type => 'nt',
   -model     => 'K80',  # Kimura
   -tree      => 'BIONJ',
   -bootstrap => 1000
);
my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);

#$tree is a Bio::Tree::Tree object
my $tree = $treemaker->run($align);

My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:

$distance = $tree->subtree_length($internal_node)

Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!

Brian O.


From bosborne11 at verizon.net  Tue Sep 20 15:17:13 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 15:17:13 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
In-Reply-To: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
References: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
Message-ID: <A2EDBACB-963C-4E1C-8E7A-5F769BE89476@verizon.net>

Ah, I see:

my $distances = $tree->distance(-nodes => [$node1,$node2]);

Brian O.


On Sep 20, 2011, at 1:01 PM, Brian Osborne wrote:

> All,
> 
> I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:
> 
> ..... get the files etc ....
> 
> my %alignparams = (
>    -seqtype  => 'nucleo',
>    -usetree_nowarn => $guidetreefile,
>    -in => $tempfile
> );
> my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);
> 
> # $align is a Bio::SimpleAlign object
> my $align = $aligner->align($tempfile);
> 
> my %treeparams = (
>   -data_type => 'nt',
>   -model     => 'K80',  # Kimura
>   -tree      => 'BIONJ',
>   -bootstrap => 1000
> );
> my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);
> 
> #$tree is a Bio::Tree::Tree object
> my $tree = $treemaker->run($align);
> 
> My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:
> 
> $distance = $tree->subtree_length($internal_node)
> 
> Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!
> 
> Brian O.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Thu Sep 22 07:07:39 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 22 Sep 2011 16:37:39 +0530
Subject: [Bioperl-l] database for Bos Touras
Message-ID: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>

Hello To All,

I want to blast my sequence Only in Bos Touras Database Using Local
Blast(Blast+).
But I dnt Know which database I should use for this From this Link.
ftp://ftp.ncbi.nlm.nih.gov/blast/db/

Pl tell me which DB I Should use??

Thanks
Manju


From hrh at fmi.ch  Thu Sep 22 07:44:56 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 13:44:56 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
Message-ID: <4E7B1FB8.8090208@fmi.ch>


assuming you mean 'Bos taurus', it might be easier to get the data from

ucsc:  http://hgdownload.cse.ucsc.edu/downloads.html#cow

or ensembl: ftp://ftp.ensembl.org/pub/release-64/fasta/bos_taurus/dna/



Regards, Hans



On 09/22/2011 01:07 PM, Manju Rawat wrote:
> Hello To All,
>
> I want to blast my sequence Only in Bos Touras Database Using Local
> Blast(Blast+).
> But I dnt Know which database I should use for this From this Link.
> ftp://ftp.ncbi.nlm.nih.gov/blast/db/
>
> Pl tell me which DB I Should use??
>
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From hrh at fmi.ch  Thu Sep 22 08:16:00 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 14:16:00 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
	<4E7B1FB8.8090208@fmi.ch>
	<CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
Message-ID: <4E7B2700.8080904@fmi.ch>


Yes, BLAST uses fasta files. You (may need to concatenate the individual 
chromosomes and the you) need to index them with 'makeblastdb' which is 
also part of the blast+ software package.

see: http://www.ncbi.nlm.nih.gov/books/NBK1762/


Hans

On 09/22/2011 01:49 PM, Manju Rawat wrote:
> It will work on Local Blast or not??????


From bosborne11 at verizon.net  Thu Sep 22 12:16:39 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 22 Sep 2011 12:16:39 -0400
Subject: [Bioperl-l] [bioperl-live] genbank_ref_extractor: new script to
 make search on entrez gene and retrieve related sequences (#23)
In-Reply-To: <bioperl/bioperl-live/pull/23@github.com>
References: <bioperl/bioperl-live/pull/23@github.com>
Message-ID: <245C75D5-61EC-4395-B64F-47D8471568F5@verizon.net>

Carne,

This is impressive looking, it is now in scripts/.

Thanks again,

Brian O.

On Sep 21, 2011, at 11:25 AM, Carn? Draug wrote:

> Hi
> 
> I wrote a script with bioperl that I would like to share back. It takes a list of searches for Entrez Gene and attempts to retrieve the related sequences (genomic, transcripts and proteins). It is also possible to obtain extra upstream and downstream bp for genomic sequences and control the naming of the files. In the end it can save all the results in a CSV file.
> 
> Hope you find it up to your coding standards. Suggestions for improvements are welcome, including for a better name.
> 
> Carn?
> 
> You can merge this Pull Request by running:
> 
>  git pull https://github.com/carandraug/bioperl-live bp_genbank_ref_extractor
> 
> Or you can view, comment on it, or merge it online at:
> 
>  https://github.com/bioperl/bioperl-live/pull/23
> 
> -- Commit Summary --
> 
> * genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences
> 
> -- File Changes --
> 
> A scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl (1064)
> 
> -- Patch Links --
> 
>  https://github.com/bioperl/bioperl-live/pull/23.patch
>  https://github.com/bioperl/bioperl-live/pull/23.diff
> 
> -- 
> Reply to this email directly or view it on GitHub:
> https://github.com/bioperl/bioperl-live/pull/23




From bluecurio at gmail.com  Thu Sep 22 15:32:07 2011
From: bluecurio at gmail.com (Daniel Renfro)
Date: Thu, 22 Sep 2011 14:32:07 -0500
Subject: [Bioperl-l] Download RefSeq revision history programmatically
Message-ID: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>

I am working on a project to find historical differences in GenBank/RefSeq files. I would like to download all the old revisions of a file (for example NC_000913 [http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2?report=girevhist]) using any technology available. I wrote a page-scraper in Perl, but I can't get NCBI to return plaintext, only HTML (which does nobody any good.) 

Does anyone know of a way to get all the "revisions" (not just "versions") of a GenBank/RefSeq file?

-Daniel 
--
http://ecoliwiki.net/User:DanielRenfro
Hu Lab Research Associate
979-862-4055



From ross at cuhk.edu.hk  Tue Sep 27 10:16:14 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 27 Sep 2011 22:16:14 +0800
Subject: [Bioperl-l]  obtain a distance matrix from tree
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>

After using MEGA to generate a newick tree file (phylogram), I wonder if
Bioperl has any convenient functions to derive the (n x n) distance (by NJ,
MP etc) matrix. Thanks for your advice in advance!




From thomas.sharpton at gmail.com  Tue Sep 27 16:02:44 2011
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Tue, 27 Sep 2011 13:02:44 -0700
Subject: [Bioperl-l] obtain a distance matrix from tree
In-Reply-To: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
	<014201cc7d20$03abd4c0$0b037e40$@edu.hk>
Message-ID: <C2ED3ADC-B089-4481-BD63-8D5FDFB51CFA@gmail.com>

Hi Ross,

For very large trees, I found it to be more efficient to do this in R  
using the ape package. I have a script listed in my github repo that  
will convert a tree to a distance matrix via in R at the link below:

https://github.com/sharpton/PhylOTU/blob/master/tree_to_matrix.R

That said, I've also done this in Bioperl using something like the  
following:

use Bio::TreeIO;

my $treein = Bio::TreeIO->new( -fh => "input_tree.nwk", -format =>  
'newick' );
while( my $tree = $treein->next_tree ){
	my %dist_matrix = ();
	my @leaves = $tree->get_leaf_nodes;
	foreach my $leaf1( @leaves ){
		my $id1 = $leaf1->id;	
		foreach my $leaf2( @leaves ){
			my $id2 = $leaf2->id;
			next if $id1 eq $id2;
			next if( defined( $dist_matrix{$id1}->{$id2} ) || defined  
( $dist_matrix{$id2}->{$id1} ) );
			my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] );
			$dist_matrix{$id1}->{$id2} = $distance;
		}
	}
}
#print distance matrix here....

This will put the information you need to create either a full or a  
upper triangle distance matrix into the hash %dist_matrix. I didn't  
test the above, so hopefully there are no bugs....

Someone else may have a more elegant solution.

Best,
Tom

PS: Sorry if you get this twice.

On Sep 27, 2011, at 7:16 AM, Ross KK Leung wrote:

> After using MEGA to generate a newick tree file (phylogram), I  
> wonder if
> Bioperl has any convenient functions to derive the (n x n) distance  
> (by NJ,
> MP etc) matrix. Thanks for your advice in advance!
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From member at linkedin.com  Tue Sep 27 19:45:10 2011
From: member at linkedin.com (Razi Khaja via LinkedIn)
Date: Tue, 27 Sep 2011 23:45:10 +0000 (UTC)
Subject: [Bioperl-l] Invitation to connect on LinkedIn
Message-ID: <1856085440.8574001.1317167110185.JavaMail.app@ela4-bed82.prod>

LinkedIn
------------




    Razi Khaja requested to add you as a connection on LinkedIn:
  
------------------------------------------

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I'd like to add you to my professional network on LinkedIn.

Accept invitation from Razi Khaja
http://www.linkedin.com/e/5drwke-gt3jaequ-6k/uez6TYkHzbaXxXM-lUk23auFwJZodcPlXc2UWC0Ao8h/blk/I3148646357_2/1BpC5vrmRLoRZcjkkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYOnPsRcPoQdzwQcjd9bSsPizpOoltTbP0NdPgMd3kTcPgLrCBxbOYWrSlI/EML_comm_afe/?hs=false&tok=2TjQgihXkh-kU1

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------------------------------------------



From ross at cuhk.edu.hk  Tue Sep 27 23:57:52 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 28 Sep 2011 11:57:52 +0800
Subject: [Bioperl-l]  ancestral state derived from Tree
In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
Message-ID: <017701cc7d92$cba88d20$62f9a760$@edu.hk>


By using Tom's advice, I'm able to obtain the distance matrix for the
following tree by Bioperl TreeIO. 

((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000
00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00
000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(
L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0
.00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,
(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000
):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000
00);

For the last few nodes T, U and V, they should be monophyletic but U and V
should be more closely related. Although I can use TreeIO methods like
is_monophyletic or is_paraphyletic to test in this case, the problem becomes
more tricky for nodes A, B, C, D because D actually makes no difference from
the common ancestor of nodes A, B, C and D. Since is_monophyletic does not
take into account for this case, is there any workaround? I have to pay
attention to such a detail in order to make a better guess for the ancestral
state(s) at various points of this tree.

Thanks again for the TreeIO developers for making tree analysis easier for
us biologists!



From manju.rawat2 at gmail.com  Wed Sep 28 05:54:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 28 Sep 2011 15:24:07 +0530
Subject: [Bioperl-l] how to blast a seq against multiple dbase
Message-ID: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>

Hello,

I have downloaded all the chromosome of Bos Taurus and i'd changed them in
blast format using makeblastdb..and now i want to localy blast my sequence
against these all chromosome..
now i have 29 database.Is there any method by which can i blast my sequence
against all 29 database in my program..


whta should i write in database????

@params = ('database' => '????????', 'outfile' => 'blast2.out',
        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');



Thanks
Manju Rawat


From p.j.a.cock at googlemail.com  Wed Sep 28 06:02:07 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 28 Sep 2011 11:02:07 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <CAKVJ-_7HCbvfm=mgcXEmL_9AH6A3rttnLrW86rs1ecNB0L7=XQ@mail.gmail.com>

On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello,
>
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
>
>
> whta should i write in database????
>
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
> ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn');
>

The simple answer is make a combined database. This
works internally with alias files, have a look at the NR
and NT databases for example - they act like singe
databases but are actually a collection of chunks.

Even simpler would be to combine your Bos taurus
sequence files into a single multi-entry FASTA file,
and make that into a single BLAST database.

Peter



From awitney at sgul.ac.uk  Wed Sep 28 06:42:39 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 28 Sep 2011 11:42:39 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <B2F15B1E-24EB-41B5-8BC4-07A2EF4C8286@sgul.ac.uk>


I think if you want to keep the databases separate you would need to create a factory for each database, something like this

foreach my $db ( @databases ) {
	my $factory = Bio::Tools::Run::StandAloneBlastPlus->new( -db_data => $db ,  < ? any other params ? > );

	? do blast stuff?
}

or as Peter says in another email you could combine your databases and run one query then filter them out in the results.

regards

adam

On 28 Sep 2011, at 10:54, Manju Rawat wrote:

> Hello,
> 
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
> 
> 
> whta should i write in database????
> 
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
>        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');
> 
> 
> 
> Thanks
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Wed Sep 28 07:43:02 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 12:43:02 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
Message-ID: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>

Hi everyone,

is there a recommended way to get the version of a script that is part
of bioperl (the ones in the scripts directory)? Rather than hard
coding the version of the script independent of bioperl, I thought on
using the bioperl version itself. How can this be done?

Thanks in advance,
Carn?



From carandraug+dev at gmail.com  Wed Sep 28 11:00:34 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 16:00:34 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
Message-ID: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>

2011/9/28 longbow leo <longbow0 at gmail.com>:
> Hi, Carn?,
>
> Do you mean this:
>
> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>
> In my machine, the output is

Thank you. Yes this is what I was looking for. I looked down how that
variable comes up and so I think I'll use

use Bio::Root::Version;
say $Bio::Root::Version::VERSION;

Carn?



From pcantalupo at gmail.com  Wed Sep 28 12:54:19 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 28 Sep 2011 12:54:19 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
Message-ID: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>

Hello,

I'm using the most recent copy of bioperl-live (pulled yesterday). I
have a BLASTN (from blast+) output file for 3 query sequences
(https://gist.github.com/1248342). I used this script,
https://gist.github.com/1248338, to print the query id, algorithm and
algorithm_version for each result. When I run the script, I get the
following output:

GFAVMM201BADC0 ?BLASTN ?2.2.25+
GFAVMM201A1JOH ?BLASTN
GFAVMM201D933Z ?BLASTN

Algorithm_version outputs the correct version for the first result but
outputs the empty string for the 2nd and 3rd query. Why? This
functionality worked about a month ago. What has changed to cause this
to happen?

Thank you,

Paul



From rondonbio at yahoo.com.br  Wed Sep 28 15:47:45 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Wed, 28 Sep 2011 12:47:45 -0700 (PDT)
Subject: [Bioperl-l] best Hit
Message-ID: <1317239265.98674.YahooMailNeo@web130214.mail.mud.yahoo.com>

Hi guys.?

I have this subroutine that returns a hash with nucleotide's coverage of each query from a blast alignment.
So, I want to compute uniq hits. If a hit has already been aligned with a query, it must be eliminated from my experiment.
Can anyone check if it's right or can fix it to me? Is there a way to do that directly in blast?

Thank you

Rondon Neto


sub nucleotide_coverage{
#Bio::SearchIO dependent
#This subroutine return a Hash and a file with nucleotide coverage?
#for each query in an blast alignment xlm file. The input is the
#alignment file.

my ($alignment_file) = @_;

my $alignment = new Bio::SearchIO ( -format => 'blastXML',
 ? ?-file ? => $alignment_file );my %positions;my @used_reads;
while (my $result = $alignment->next_result) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
for (0..$tam-1){ ${$positions{$query_name}}[$_] = 0 }?
while (my $hit = $result->next_hit) {
my $hit_name = $hit->name;
# Here is my best hit parser. Is it ok?
foreach my $read (@used_reads) {
if ( $read eq $hit_name ) {
next;
}
}
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my @pos = $hsp->seq_inds('query','identical');
foreach my $num (@pos) {
${$positions{$query_name}}[$num-1]++;
}
}
push (@used_reads, $hit_name);
}
}

my $outfile = "nucleotide_coverage.txt";
open OUT, ">$outfile" or die $!;foreach my $key (keys %positions){print OUT "$key\t@{$positions{$key}}\n";
}

close OUT;

return \%positions;

}


From shalabh.sharma7 at gmail.com  Wed Sep 28 15:53:07 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 28 Sep 2011 15:53:07 -0400
Subject: [Bioperl-l] Getting taxa from gi
Message-ID: <CAA7rn9dYGfeCS-qVccDcdwVenj8KFQs4i89EoT8_63gQk5b42g@mail.gmail.com>

Hi All,
        I know this has been discussed before, but this is kind of a new
problem that i am facing.
I want to get taxonomy (full linage) information from the huge list of GI's.
I am using Bio::DB:Genbak for this with perl-5.12.3.
Here is my small script.

#! /usr/local/perl-5.12.3/bin/perl -w
use strict;
use warnings;
use Bio::DB::GenBank;

my @ids = qw( CP000490 );
my $gbh = Bio::DB::GenBank->new();

foreach my $id( @ids ) {
# say "* ID: $id";
 my $seq = $gbh->get_Seq_by_acc( $id );
 my $org = $seq->species;
 #print "$org\n";
 my $class = join'-', $org->classification;
 print "$class\n";
}

The output is: Paracoccus denitrificans
PD1222-Paracoccus-Rhodobacteraceae-Rhodobacterales-Alphaproteobacteria-Proteobacteria-Bacteria
which is fine but i also want to get the taxa id, and if possible taxa ids
for all the linage classification.

ideally i would like to get something like this: 318586 - - - - - - - 1224 -
2

I would really appreciate your help.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Wed Sep 28 17:36:37 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:36:37 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
Message-ID: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>

On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:

> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>> Hi, Carn?,
>> 
>> Do you mean this:
>> 
>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>> 
>> In my machine, the output is
> 
> Thank you. Yes this is what I was looking for. I looked down how that
> variable comes up and so I think I'll use
> 
> use Bio::Root::Version;
> say $Bio::Root::Version::VERSION;
> 
> Carn?

Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

chris


From cjfields at illinois.edu  Wed Sep 28 17:40:48 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:40:48 +0000
Subject: [Bioperl-l] algorithm_version not working in multi-result
	blast	output
In-Reply-To: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
Message-ID: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>

Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.  

This should be an easy enough fix, but can you submit it as a bug so we can track it?

chris

On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:

> Hello,
> 
> I'm using the most recent copy of bioperl-live (pulled yesterday). I
> have a BLASTN (from blast+) output file for 3 query sequences
> (https://gist.github.com/1248342). I used this script,
> https://gist.github.com/1248338, to print the query id, algorithm and
> algorithm_version for each result. When I run the script, I get the
> following output:
> 
> GFAVMM201BADC0  BLASTN  2.2.25+
> GFAVMM201A1JOH  BLASTN
> GFAVMM201D933Z  BLASTN
> 
> Algorithm_version outputs the correct version for the first result but
> outputs the empty string for the 2nd and 3rd query. Why? This
> functionality worked about a month ago. What has changed to cause this
> to happen?
> 
> Thank you,
> 
> Paul
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Wed Sep 28 18:07:53 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 23:07:53 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
Message-ID: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>

2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>
>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>> Hi, Carn?,
>>>
>>> Do you mean this:
>>>
>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>
>>> In my machine, the output is
>>
>> Thank you. Yes this is what I was looking for. I looked down how that
>> variable comes up and so I think I'll use
>>
>> use Bio::Root::Version;
>> say $Bio::Root::Version::VERSION;
>>
>> Carn?
>
> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

Where will the scripts end up after this restructuration? What I want
is to create a version of the script (not of bioperl). Since the
script is released with bioperl, they are the same. I actually already
made the commit that makes this, just haven't bothered with the pull
request yet.

Also, will there be a release before this change?

Carn?



From shalabh.sharma7 at gmail.com  Thu Sep 29 10:37:53 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 29 Sep 2011 10:37:53 -0400
Subject: [Bioperl-l] GFF to GTF
Message-ID: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>

Hi,
    Is there any module to convert GFF file to GTF?

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Thu Sep 29 11:07:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 29 Sep 2011 15:07:27 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
	<CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
Message-ID: <46733E36-5795-4EB6-9C2B-C978000FFD46@illinois.edu>

On Sep 28, 2011, at 5:07 PM, Carn? Draug wrote:

> 2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
>> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>> 
>>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>>> Hi, Carn?,
>>>> 
>>>> Do you mean this:
>>>> 
>>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>> 
>>>> In my machine, the output is
>>> 
>>> Thank you. Yes this is what I was looking for. I looked down how that
>>> variable comes up and so I think I'll use
>>> 
>>> use Bio::Root::Version;
>>> say $Bio::Root::Version::VERSION;
>>> 
>>> Carn?
>> 
>> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).
> 
> Where will the scripts end up after this restructuration? What I want
> is to create a version of the script (not of bioperl). Since the
> script is released with bioperl, they are the same. I actually already
> made the commit that makes this, just haven't bothered with the pull
> request yet.
> 
> Also, will there be a release before this change?
> 
> Carn?

Scripts will likely go with the distribution that they most closely are tied to, but that's still an area for debate (some may equally fall within one distribution or another, which will be tricky).  

For more on the release aspects see the (currently being revised and thus not complete) wiki page:

http://www.bioperl.org/wiki/BioPerl_Modularization

chris


From pcantalupo at gmail.com  Thu Sep 29 12:13:05 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 29 Sep 2011 12:13:05 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
In-Reply-To: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
	<4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
Message-ID: <CAJqbkv6Cgf8V4x2DDrzJjc7yKyF8j-kMFNz6JGpnhn9QQTZEQg@mail.gmail.com>

Bug submitted: https://redmine.open-bio.org/issues/3298





On Wed, Sep 28, 2011 at 5:40 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.
>
> This should be an easy enough fix, but can you submit it as a bug so we can track it?
>
> chris
>
> On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:
>
>> Hello,
>>
>> I'm using the most recent copy of bioperl-live (pulled yesterday). I
>> have a BLASTN (from blast+) output file for 3 query sequences
>> (https://gist.github.com/1248342). I used this script,
>> https://gist.github.com/1248338, to print the query id, algorithm and
>> algorithm_version for each result. When I run the script, I get the
>> following output:
>>
>> GFAVMM201BADC0 ?BLASTN ?2.2.25+
>> GFAVMM201A1JOH ?BLASTN
>> GFAVMM201D933Z ?BLASTN
>>
>> Algorithm_version outputs the correct version for the first result but
>> outputs the empty string for the 2nd and 3rd query. Why? This
>> functionality worked about a month ago. What has changed to cause this
>> to happen?
>>
>> Thank you,
>>
>> Paul
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



From jluis.lavin at unavarra.es  Fri Sep 30 04:23:19 2011
From: jluis.lavin at unavarra.es (jluis.lavin at unavarra.es)
Date: Fri, 30 Sep 2011 10:23:19 +0200
Subject: [Bioperl-l] Bio-Graphics module
Message-ID: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>


Dear All,

I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
windows machine.

I read about the Bio-Graphics module and it'd be wonderful to install it,
but seems like it is  only available for Perl 5.8...
Is there any other Perl and/or Bioperl module to do the same kind of
genomic and Blast report representation currently available?

Thanks in advance

-- 
Dr. Jos? Luis Lav?n Trueba

Dpto. de Producci?n Agraria
Grupo de Gen?tica y Microbiolog?a
Universidad P?blica de Navarra
31006 Pamplona
Navarra
SPAIN




From cjfields at illinois.edu  Fri Sep 30 08:38:01 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 30 Sep 2011 12:38:01 +0000
Subject: [Bioperl-l] Bio-Graphics module
In-Reply-To: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
Message-ID: <B1F1674B-D8DA-46E2-AAAE-DD9DDBC4C51A@illinois.edu>

It's available for all perl versions from 5.8.8 up.  I have it running with perl 5.14.  Now, I recall there being problems with installation on Mac OS X, though I think that was mainly due to GD.pm and libgd.

chris

On Sep 30, 2011, at 3:23 AM, <jluis.lavin at unavarra.es>
 <jluis.lavin at unavarra.es> wrote:

> 
> Dear All,
> 
> I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
> windows machine.
> 
> I read about the Bio-Graphics module and it'd be wonderful to install it,
> but seems like it is  only available for Perl 5.8...
> Is there any other Perl and/or Bioperl module to do the same kind of
> genomic and Blast report representation currently available?
> 
> Thanks in advance
> 
> -- 
> Dr. Jos? Luis Lav?n Trueba
> 
> Dpto. de Producci?n Agraria
> Grupo de Gen?tica y Microbiolog?a
> Universidad P?blica de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jillianrowe91286 at gmail.com  Wed Sep 28 02:03:32 2011
From: jillianrowe91286 at gmail.com (Jill)
Date: Tue, 27 Sep 2011 23:03:32 -0700 (PDT)
Subject: [Bioperl-l] Gene Type in Entrez gene?
Message-ID: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>

Hi there,

I am using the Bio::DB::Eutilities module to download gene sequences
based on a query.

<code>
while (my $docsum = $summaries->next_DocSum) {
  ## some items in DocSum are also named ChrStart so we pick the
genomic
  ## information item and get the coordinates from it
  my ($genomic_info)  = $docsum->get_Items_by_name('GenomicInfoType');

  ## some entries may have no data on genomic coordinates. This
condition filters then out
  if (!$genomic_info) {
    ## found no genomic coordinates data
    next;
  }

  ## get coordinates of sequence
  ## get_contents_by_name always returns a list
  my ($chr_acc_ver)   = $genomic_info-
>get_contents_by_name("ChrAccVer");
  my ($chr_start)     = $genomic_info-
>get_contents_by_name("ChrStart");
  my ($chr_stop)      = $genomic_info-
>get_contents_by_name("ChrStop");
  my $strand;

  if ($chr_start < $chr_stop) {
    $strand     = 1;
    $chr_start  = $chr_start +1 - $bp5_extra;
    $chr_stop   = $chr_stop  +1 + $bp5_extra;
  } elsif ($chr_start > $chr_stop) {
    $strand     = 2;
    $chr_start  = $chr_start +1 - (-$bp5_extra);
    $chr_stop   = $chr_stop  +1 + (-$bp5_extra);
  } else {
    next;
  }

  while (my $item = $docsum->next_Item('flattened'))  {
	next if ($item->get_name =~ m/NomenclatureName/);
	if($item->get_name =~ m/Description/) {
	  $description = $item->get_content if $item->get_content;
	  $description =~ tr/ /_/;
	  print $description, "\n";}
	if($item->get_name =~ m/Name/) {
	    $name = $item->get_content if $item->get_content;
	    print $name, "\n";
	  }
        printf("%-20s:%s\n",$item->get_name,$item->get_content) if
$item->get_content;
    }
}
</code>

Then I go on to use genbank to download the sequences based on the
chromosome splice. For what I have it works great. But I am trying to
get to the gene type (either protein coding or pseudo) as well. I can
see it in the summary on the Entrez Gene sight, but can't get to it
through bioperl. When I have it print out all the contents of the
summary it doesn't show up there either.

Any help?

Thanks!


From liam.elbourne at mq.edu.au  Thu Sep 29 17:34:04 2011
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Fri, 30 Sep 2011 07:34:04 +1000
Subject: [Bioperl-l] GFF to GTF
In-Reply-To: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
References: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
Message-ID: <8D027281-44E6-467C-8D22-D2D2F87D04B6@mq.edu.au>

Hi Shalabh,

Not sure about bioperl (I looked a while back and either missed it or it's not there) but there is a program associated with the cufflinks suite called gffread that should convert. 

Regards,
Liam Elbourne. 



On 30/09/2011, at 12:37 AM, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:

> Hi,
>    Is there any module to convert GFF file to GTF?
> 
> Thanks
> Shalabh
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Fri Sep 30 09:18:04 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 30 Sep 2011 14:18:04 +0100
Subject: [Bioperl-l] Gene Type in Entrez gene?
In-Reply-To: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
References: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
Message-ID: <CAPOrs_2QOMOyPsZ90iYc3fMd8YE9HGnPcVqELGo+rYRRxJu9NQ@mail.gmail.com>

On 28 September 2011 07:03, Jill <jillianrowe91286 at gmail.com> wrote:
> Hi there,
>
> I am using the Bio::DB::Eutilities module to download gene sequences
> based on a query.
>
> <code>
> [...]
> }
> </code>
>
> Then I go on to use genbank to download the sequences based on the
> chromosome splice. For what I have it works great. But I am trying to
> get to the gene type (either protein coding or pseudo) as well. I can
> see it in the summary on the Entrez Gene sight, but can't get to it
> through bioperl. When I have it print out all the contents of the
> summary it doesn't show up there either.
>
> Any help?

Hi Jill,

there's already a script in bioperl that does what you want, it's just
not part of the current stable release. You can get it here

https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl

You can download the script alone, it will work fine in previous
releases of bioperl, no need to write another one.

Carn? Draug



From manju.rawat2 at gmail.com  Thu Sep  1 06:53:53 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 1 Sep 2011 02:53:53 -0400
Subject: [Bioperl-l] Bioperl query....
In-Reply-To: <CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
References: <CAB2c7yp6p2e_8p7M9wVL2xzU7g+mZ-NVXwLs4PUassRs4PgrTQ@mail.gmail.com>
	<4E5CC8AC.8050800@gmail.com>
	<CAA7rn9fsSsduEYUBo271zuXX++2eqC-Yhzuyaf7gvQ4E6QQ4YQ@mail.gmail.com>
Message-ID: <CAB2c7yobL=KRW_XWOCfgEwJS17A8Mne4FJhVp88xjJfBqZMHGw@mail.gmail.com>

Thanks For The Reply..
I have already seen this link..But I am confused.

I used to following code and run it...

my $in = Bio::SearchIO->new(-format => 'blast',
                -file => 'seqs.blast');
while( my $result = $in->next_result ) {
  ## $result is a Bio::Search::Result::ResultI compliant object
  while( my $hit = $result->next_hit ) {
    ## $hit is a Bio::Search::Hit::HitI compliant object
    while( my $hsp = $hit->next_hsp ) {
      ## $hsp is a Bio::Search::HSP::HSPI compliant object
      if( $hsp->length('total') > 50 ) {
        if ( $hsp->percent_identity >= 75 ) {
          print "Query=",   $result->query_name,
            " Hit=",        $hit->name,
            " Length=",     $hsp->length('total'),
    " gaps=",            $hsp->gaps,
            " Percent_id=", $hsp->percent_identity, "\n";
        }     } }    }}



and it showing me following output with an error that..


*Erro--*rArgument "" isn't numeric in numeric lt (<) at
/usr/local/share/perl/5.10.1/Bio/SearchIO/SearchResultEventBuilder.pm line
279, <GEN1> line 4113.

Query=NM_181451 Hit=ref|NM_181451.1| Length=1349 gaps=1 Percent_id=100
Query=NM_181451 Hit=ref|XM_002706247.1| Length=1345 gaps=13
Percent_id=93.8289962825279
Query=NM_181451 Hit=ref|NM_001098089.1| Length=1323 gaps=7
Percent_id=91.9123204837491
Query=NM_181451 Hit=ref|NM_001008415.1| Length=1211 gaps=5
Percent_id=94.9628406275805
Query=NM_181451 Hit=ref|XM_001251693.3| Length=1320 gaps=5
Percent_id=91.969696969697
Query=NM_181451 Hit=ref|NM_001097567.1| Length=1338 gaps=4
Percent_id=91.5545590433483
Query=NM_181451 Hit=gb|AY075103.1| Length=1334 gaps=1
Percent_id=91.304347826087
................
..........

Pl Find.whats the error i this code...

Thanks
Manju Rawat.


From locarpau at upvnet.upv.es  Thu Sep  1 14:49:06 2011
From: locarpau at upvnet.upv.es (Lorenzo Carretero Paulet)
Date: Thu,  1 Sep 2011 16:49:06 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
Message-ID: <1314888546.4e5f9b628ecea@webmail.upv.es>

Hi all,
I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:

my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
if ( my $paml_result = $parserF->next_result )
{
say Dumper $paml_result; #Prints Ok
	for ( my $model_result= $paml_result->get_NSSite_results )
	{
        #say Dumper $model_result; #Prints nothing
        $ns_string = "model ".$model_result->model_num."\n
".$model_result->model_description()."\n ".$model_result->time_used."\n";
	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
	#say Dumper $dnds_site_classes;
	for my $sites ( $model_result->get_BEB_pos_selected_sites )
        ...
         ...
          ...

The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
object is not being properly instantiated, as I get the error message:

"Can't call method "model_num" without a package or object reference at ..."

What am I missing?
Best,
Lorenzo




From jason.stajich at gmail.com  Thu Sep  1 20:23:47 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Thu, 1 Sep 2011 13:23:47 -0700
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <1314888546.4e5f9b628ecea@webmail.upv.es>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com><9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu><4DF56976.8080704@upvnet.upv.es><AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com><9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
Message-ID: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>

Lorenzo -

I am sure this is a problem with changes in the output from PAML - this is classic problem with this suite.  This requires some debugging of the parser, not sure if there is anyone out there with time to do the debugging.
I can say all this worked before on an earlier version of PAML but I don't know specifically what is going on with the latest paml4.4 version.

Jason


On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:

> Hi all,
> I'm trying to parse mlc output files from PAML using Bio::Tools::Phylo::PAML as:
> 
> my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> if ( my $paml_result = $parserF->next_result )
> {
> say Dumper $paml_result; #Prints Ok
> 	for ( my $model_result= $paml_result->get_NSSite_results )
> 	{
>        #say Dumper $model_result; #Prints nothing
>        $ns_string = "model ".$model_result->model_num."\n
> ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> 	$dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> 	#say Dumper $dnds_site_classes;
> 	for my $sites ( $model_result->get_BEB_pos_selected_sites )
>        ...
>         ...
>          ...
> 
> The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> DUmper. In contrast, it seems that the Bio::Tools::Phylo::PAML::ModelResult
> object is not being properly instantiated, as I get the error message:
> 
> "Can't call method "model_num" without a package or object reference at ..."
> 
> What am I missing?
> Best,
> Lorenzo
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Scott.Markel at accelrys.com  Thu Sep  1 21:22:21 2011
From: Scott.Markel at accelrys.com (Scott Markel)
Date: Thu, 1 Sep 2011 14:22:21 -0700
Subject: [Bioperl-l] file format for alignment plus features for aligned
	sequences
Message-ID: <5ACBA19439E77B43A06F4CAB897EC97702F8302A05@EXCH1-COLO.accelrys.net>

A question on behalf of the Discovery Studio group at Accelrys -

They have alignment data with annotations, e.g., visualization settings or alignment properties.  The aligned sequences also have features, e.g., domain boundaries or secondary structure motifs.  They currently use BSML to save sequences and features.

Is there an extension of BSML that can also save the alignment information?

Are there any good file formats that can be used to store an alignment plus features associated with the aligned sequences?

Are there other mailing lists that might be more appropriate for these questions?

Scott

Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (Pipeline Pilot R&D)       mobile: +1 858 205 3653
10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
San Diego, CA 92121                 fax:    +1 858 799 5222
USA                                 web:    http://www.accelrys.com

http://www.linkedin.com/in/smarkel
Secretary, Board of Directors:
    International Society for Computational Biology
Chair: ISCB Publications Committee
Associate Editor: PLoS Computational Biology
Editorial Board: Briefings in Bioinformatics






From ihok at hotmail.com  Fri Sep  2 03:49:50 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Thu, 1 Sep 2011 23:49:50 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
Message-ID: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>

I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty 
quiet codebase these days... Is it dead?

Does anyone have a spec file for building an SRPM for it for RHEL 6?


From cjfields at illinois.edu  Fri Sep  2 04:31:17 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 04:31:17 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
Message-ID: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>

Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.

chris

On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:

> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> 
> Does anyone have a spec file for building an SRPM for it for RHEL 6?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Fri Sep  2 08:44:07 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 10:44:07 +0200
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
Message-ID: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>

As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
http://toolkit.tuebingen.mpg.de/hhpred


He got it working thus:

> Hi Dave,
> thanks a lot. i made it work. The error i got later on was:

 relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making
> a shared object;
> recompile with -fPIC
>


> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared
> --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/<http://forums.fedoraforum.org/showthread.php?t=232607>
> showthread.php?t=232607<http://forums.fedoraforum.org/showthread.php?t=232607>




Dave





On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J
<cjfields at illinois.edu>wrote:

> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone
> who has packaged that up in a while, if ever.
>
> chris
>
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty
> quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From David.Messina at sbc.su.se  Fri Sep  2 09:30:33 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 2 Sep 2011 11:30:33 +0200
Subject: [Bioperl-l] Parsing PAML mlc files
In-Reply-To: <E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
References: <BANLkTikyVRMaVJ_1FPSfbqv-MSTDY3mKSA@mail.gmail.com>
	<9645AF32-5EC3-41FA-9A32-45B6B92E31FD@illinois.edu>
	<4DF56976.8080704@upvnet.upv.es>
	<AA153EEB-8DDE-41C4-966A-7554D2D1D2EC@gmail.com>
	<9866C4A4-AC36-4A25-B38F-3006A7BB0F11@illinois.edu>
	<1314636433.4e5bc291a40c6@webmail.upv.es>
	<1A4207F8295607498283FE9E93B775B407CCB2D3@EX02.asurite.ad.asu.edu>
	<1314659986.4e5c1e9268078@webmail.upv.es>
	<A6E9DEB7-8192-47BE-A538-7897BB7EF7C4@gmail.com>
	<1314888546.4e5f9b628ecea@webmail.upv.es>
	<E5506749-2532-49A9-8CC8-2187E4D2329F@gmail.com>
Message-ID: <CAM3TQQU6YV0+5HEf6_PhNDuh3SK0eYZgHE5kT+F3MbTH8ktsNw@mail.gmail.com>

Looking back at the commit history, back in April and May 2010, I made some
updates for the January 2010 edition of PAML 4.4. All tests passed at that
time, but:

- the tests may be incomplete
- PAML has undoubtedly changed since then, even if it's still called version
4.4


I can't look at this right now myself, but please file a bug report on this,
and hopefully someone else can.


Dave




On Thu, Sep 1, 2011 at 22:23, Jason Stajich <jason.stajich at gmail.com> wrote:

> Lorenzo -
>
> I am sure this is a problem with changes in the output from PAML - this is
> classic problem with this suite.  This requires some debugging of the
> parser, not sure if there is anyone out there with time to do the debugging.
> I can say all this worked before on an earlier version of PAML but I don't
> know specifically what is going on with the latest paml4.4 version.
>
> Jason
>
>
> On Sep 1, 2011, at 7:49 AM, Lorenzo Carretero Paulet wrote:
>
> > Hi all,
> > I'm trying to parse mlc output files from PAML using
> Bio::Tools::Phylo::PAML as:
> >
> > my $mlcfile = "/Applications/Bioinformatics/paml44/bin/mlc";
> > my $parserF = Bio::Tools::Phylo::PAML->new (-file =>$mclfile);
> > if ( my $paml_result = $parserF->next_result )
> > {
> > say Dumper $paml_result; #Prints Ok
> >       for ( my $model_result= $paml_result->get_NSSite_results )
> >       {
> >        #say Dumper $model_result; #Prints nothing
> >        $ns_string = "model ".$model_result->model_num."\n
> > ".$model_result->model_description()."\n ".$model_result->time_used."\n";
> >       $dnds_site_classes = $model_result->dnds_site_classes; #a hashref
> >       #say Dumper $dnds_site_classes;
> >       for my $sites ( $model_result->get_BEB_pos_selected_sites )
> >        ...
> >         ...
> >          ...
> >
> > The Bio::Tools::Phylo::PAML::Result object is ok, as I can print it using
> > DUmper. In contrast, it seems that the
> Bio::Tools::Phylo::PAML::ModelResult
> > object is not being properly instantiated, as I get the error message:
> >
> > "Can't call method "model_num" without a package or object reference at
> ..."
> >
> > What am I missing?
> > Best,
> > Lorenzo
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Fri Sep  2 13:00:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 2 Sep 2011 13:00:27 +0000
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
Message-ID: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>

I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/

chris

On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:

> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
> http://toolkit.tuebingen.mpg.de/hhpred
> 
> 
> He got it working thus:
> Hi Dave,
> thanks a lot. i made it work. The error i got later on was: 
> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
> recompile with -fPIC 
>  
> the solution is:
> perl Makefile.PL PREFIX=<path to installation> /fftwsingle --enable-shared --with-pic --enable-single
> <edit Makefile to add -fPIC to CFLAGS>
> make
> make install
> http://forums.fedoraforum.org/showthread.php?t=232607
> 
> 
> 
> Dave
> 
> 
> 
> 
> 
> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J <cjfields at illinois.edu> wrote:
> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
> 
> chris
> 
> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
> 
> > I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
> >
> > Does anyone have a spec file for building an SRPM for it for RHEL 6?
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From ihok at hotmail.com  Fri Sep  2 15:20:44 2011
From: ihok at hotmail.com (Jack Tanner)
Date: Fri, 2 Sep 2011 11:20:44 -0400
Subject: [Bioperl-l] Bio::Ext::Align?
In-Reply-To: <81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
References: <BLU0-SMTP37BA9C57D1D35A6B66432FCA180@phx.gbl>
	<82213CB3-C02A-415D-A4F3-66471D44C31C@illinois.edu>
	<CAM3TQQX=grNeEPvFjjVO5XcpuJLwpabxp8Ddo32yBByq3mSzmQ@mail.gmail.com>
	<81EEC2D4-D039-41D5-A10F-91DD26B4D21E@illinois.edu>
Message-ID: <BLU0-SMTP2075F7F67ABC5C1860ED380CA180@phx.gbl>

I also see that someone's forked it on Github and made some packaging fixes.

It'd be nice to see it revived.

On 9/2/2011 9:00 AM, Fields, Christopher J wrote:
> I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/
>
> chris
>
> On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:
>
>> As it happens, a colleague of mine needed Bio::Ext::Align for hhrpred:
>> http://toolkit.tuebingen.mpg.de/hhpred
>>
>>
>> He got it working thus:
>> Hi Dave,
>> thanks a lot. i made it work. The error i got later on was:
>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
>> recompile with -fPIC
>>
>> the solution is:
>> perl Makefile.PL PREFIX=<path to installation>  /fftwsingle --enable-shared --with-pic --enable-single
>> <edit Makefile to add -fPIC to CFLAGS>
>> make
>> make install
>> http://forums.fedoraforum.org/showthread.php?t=232607
>>
>>
>>
>> Dave
>>
>>
>>
>>
>>
>> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J<cjfields at illinois.edu>  wrote:
>> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
>>
>> chris
>>
>> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>>
>>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
>>>
>>> Does anyone have a spec file for building an SRPM for it for RHEL 6?
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>



From manju.rawat2 at gmail.com  Sat Sep  3 05:29:56 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 01:29:56 -0400
Subject: [Bioperl-l] hsps_successfully_gapped: 47
Message-ID: <CAB2c7yr8qHCPO2L6nczPUTWi-L94Bz9kQtyLP-U03=nhWS+66Q@mail.gmail.com>

Hello,


Is There any method in BioPerl through which we can extract
number_of_hsps_successfully_gapped:
from a blast file..
If any one know about the it Pl help me...


Thanks
Manju Rawat


From manju.rawat2 at gmail.com  Sat Sep  3 10:00:22 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Sat, 3 Sep 2011 06:00:22 -0400
Subject: [Bioperl-l] blast result not matching.
Message-ID: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


and Output..

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat


From florent.angly at gmail.com  Mon Sep  5 02:14:37 2011
From: florent.angly at gmail.com (Florent Angly)
Date: Mon, 05 Sep 2011 12:14:37 +1000
Subject: [Bioperl-l] Bio::SeqIO can't guess the format of data from a
 pipe
In-Reply-To: <F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
References: <CAFAnT677UmaEsudqoj9UsefdeK9Wx0E_W8iM3zmMAJx8PHzBjA@mail.gmail.com>
	<2E070303-ADDF-472B-835B-6D3959B83E9A@illinois.edu>
	<CAFAnT64JhkP-xzi8TpqHiTJTm3UMgT7SPMWVm+-UhSFwk0G3gQ@mail.gmail.com>
	<E89E20DA-9B27-4D42-ACF8-96A176C85259@illinois.edu>
	<4E58D105.7050805@gmail.com>
	<A249C76A-A0BC-414E-AE78-A2B6CA7B4A9A@drycafe.net>
	<4E5A0590.2010805@gmail.com>
	<8D639B95-0666-4F09-8E9E-88C8CDF76ABC@illinois.edu>
	<4E5AC2B8.9060808@gmail.com>
	<F7E233D7-D1B5-4126-AE89-85098BC19A59@illinois.edu>
Message-ID: <4E64308D.5060304@gmail.com>


Thanks for your advice Chris. I put a format() and variant() method in 
Bio::Root::IO. All the Bio::*IO methods inherit these methods.

Regarding the module naming, 8 follow the convention Bio::*IO and 8 
follow the Bio::*::IO convention. If we decide to rename some IO modules 
for consistency, I would prefer the Bio::*::IO convention.

Regards,

Florent


On 29/08/11 11:10, Chris Fields wrote:
> On Aug 28, 2011, at 5:35 PM, Florent Angly wrote:
>
>> Hi,
>>
>> I implemented the format() getter method in Bio::SeqIO as discussed, essentially following the way proposed by Hilmar. The variant() method is not needed since Bio::SeqIO::fastq already has a get/set method for that.
> Right, but the method could be used by other modules if it were moved to Bio::SeqIO. for instance.
>
>> I noticed that there are plenty more Bio*IO modules that could benefit from having a format() method, e.g.:
>>     Bio::AlignIO
>>     Bio::ClusterIO
>>     Bio::FeatureIO
>>     Bio::MapIO
>>     Bio::OntologyIO
>>     Bio::SearchIO
>>     Bio::TreeIO
>>     Bio::Assembly::IO *
>> The code could be copy-pasted for each of them but it is not very graceful. Is there a way we could have all these IO modules share the same format() method?
> Move the method to Bio::Root::IO, the common base class for all of the above.
>
>> * Note how the IO class for Bio::Assembly is called Bio::Assembly::IO, and not Bio::AssemblyIO like for other classes. This may be something to change in the future for consistency.
>>
>> Florent
> That's possible; one could take advantage of that for redesign/API issues if it were needed.
>
> chris



From manju.rawat2 at gmail.com  Mon Sep  5 07:53:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 03:53:40 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
Message-ID: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>

Hi,
I doing blast using bioperl...but it not showing me complete result..


my program is following...

#!usr/bin/perl -w
use Bio::Perl;
# this script will only work with an internet connection
# on the computer it is run on
$seq = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


*and Output..*

BLASTN 2.2.25+


Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.

Query= blast-sequence-temp-id
       (30 letters)

Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
           14,527,398 sequences; 37,346,598,701 total letters

                                                                 Score
E
Sequences producing significant alignments:                      (bits)
value


  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Sep 2, 2011  4:14 PM
    Number of letters in database: 37,346,598,701
    Number of sequences in database: 14,527,398

  Matrix: blastn matrix:2 -3
  Gap Penalties Existence: 5, Extension: 2
expect: 1e-10
allowgaps: yes
Search Statistics
A: 0
Hits_to_DB: 737,387
S1: 23
S1_bits: 22.0
S2: 77
S2_bits: 70.7
X1: 22
X1_bits: 20.1
X2: 33
X2_bits: 29.8
X3: 110
X3_bits: 99.2
dbentries: 14,527,398
dbletters: -1308106959
effectivedblength: 36,954,358,955
effectivespace: 110,863,076,865
effectivespaceused: 110,863,076,865
entropy: 0.912
entropy_gapped: 0.780
kappa: 0.408
kappa_gapped: 0.410
lambda: 0.634
lambda_gapped: 0.625
length_adjustment: 27
num_extensions: 8,057
num_successful_extensions: 8,057
number_of_hsps_better_than_expect_value_cutoff_without_gapping: 0
number_of_hsps_gapped: 8,057
number_of_hsps_successfully_gapped: 0
querylength: 3
seqs_better_than_1e-10: 0


this result is not matching with with NCBI result...
Is there anything wrong..


Thanks
Manju Rawat


From p.j.a.cock at googlemail.com  Mon Sep  5 09:44:06 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 10:44:06 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
Message-ID: <CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>

On Mon, Sep 5, 2011 at 8:53 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
> I doing blast using bioperl...but it not showing me complete result..
>
>
> my program is following...
> ...
>
> this result is not matching with with NCBI result...
> Is there anything wrong..

The NCBI website for BLAST uses different default values
to the BLAST command line tools. Check things like the
gap parameters if you want to use the same settings.

Peter


From p.j.a.cock at googlemail.com  Mon Sep  5 10:25:15 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 5 Sep 2011 11:25:15 +0100
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
Message-ID: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>

Please CC the mailing list.

On Mon, Sep 5, 2011 at 11:19 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
> Thanks for the reply...
> but when i am blasting after getting sequence of any gene (from NCBI using
> bioperl see below)..it showing me same result as shown in NCBI..
>
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq_object = get_sequence('NCBI',"NM_181451");
> $blast_result = blast_sequence($seq);
> write_blast(">roa1.blast",$blast_report);
>
>
> I dnt know why its not working when i am blasting my own sequence..
>

Maybe you need give the sequence as a FASTA entry
rather than a plain string?

Peter


From manju.rawat2 at gmail.com  Mon Sep  5 10:40:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 5 Sep 2011 06:40:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
Message-ID: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>

No..i also tried this..this also dont work..
pls help me..


From cjfields at illinois.edu  Mon Sep  5 19:42:49 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 5 Sep 2011 19:42:49 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
Message-ID: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>

Are you using the latest BioPerl?  I believe there had been some fixes addressing remote blast.

chris

On Sep 5, 2011, at 5:40 AM, Manju Rawat wrote:

> No..i also tried this..this also dont work..
> pls help me..
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Tue Sep  6 10:59:50 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 6 Sep 2011 06:59:50 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
Message-ID: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>

bioperl 1.6.9 version is installed in my system..
its not the reason bcs blast is working fine when i am blasting with
follwing code..

#!usr/bin/perl -w
use Bio::Perl;
$seq = get_sequence('NCBI',"NM_181451");
$blast_result=blast_sequence($seq);
write_blast(">xyz.blast",$blast_result);


Manju


From sidd.basu at gmail.com  Tue Sep  6 15:51:09 2011
From: sidd.basu at gmail.com (Siddhartha Basu)
Date: Tue, 6 Sep 2011 10:51:09 -0500
Subject: [Bioperl-l] Bioinformatics Job Opening at dictyBase in Chicago
Message-ID: <20110906155106.GB1841@Macintosh-388.local>

Hi All, 
We have an open position for a Bioinformatics Software Engineer at dictyBase(Northwestern
University in Chicago). The job involves developing web application and middleware for
a genome database using modern perl(DBIx-Class/Moose/MVC web frameworks etc)
as well as integration of various genomic tools(gbrowse, intermine, apollo,
biomart, pathway tools etc..). 
For full details please see:
 http://www.dictybase.org/dictybase_jobs.html.


thanks, 
-siddhartha

Siddhartha Basu
Software developer,  dictybase
http://www.dictybase.org



From slucky at ibab.ac.in  Wed Sep  7 13:39:03 2011
From: slucky at ibab.ac.in (Lucky Singh)
Date: Wed, 07 Sep 2011 19:09:03 +0530
Subject: [Bioperl-l] Fwd: Re:  Problem using Bio::Tools::Run::RemoteBlast
Message-ID: <4E6773F7.7000703@ibab.ac.in>



-------- Original Message --------
Subject: 	Re: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
Date: 	Sat, 27 Aug 2011 20:36:58 +0530
From: 	Lucky Singh <slucky at ibab.ac.in>
To: 	Carn? Draug <carandraug+dev at gmail.com>



On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>  On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in>   wrote:
>>  Now I
>>  wanted to host it from web server, but This program is not working from it
>>  may be it is not able to create or write on file from web server but in
>>  command line it is working fine. I don't know the possible reason, please
>>  help me to figure it out.
>  Have you looked in the apache logs (look in
>  /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>  content of the error log after trying to run the script?
Dear Carn? Draug,

As per your suggestion, I am attaching blast code file currently it is
not showing any error on error.log.
Thanks a lot for your valuable reply and will be highly grateful if you
can get me out of this problem :)


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From jason.stajich at gmail.com  Wed Sep  7 16:13:46 2011
From: jason.stajich at gmail.com (Jason Stajich)
Date: Wed, 7 Sep 2011 09:13:46 -0700
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
Message-ID: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>

I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.


On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:

> bioperl 1.6.9 version is installed in my system..
> its not the reason bcs blast is working fine when i am blasting with
> follwing code..
> 
> #!usr/bin/perl -w
> use Bio::Perl;
> $seq = get_sequence('NCBI',"NM_181451");
> $blast_result=blast_sequence($seq);
> write_blast(">xyz.blast",$blast_result);
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Wed Sep  7 16:33:52 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 7 Sep 2011 16:33:52 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
Message-ID: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>

I think there was an issue with Bio::Perl BLAST submissions fixed in the 1.6.901 release (1.6.9 != 1.6.901, the latter is newer).  From CPAN:

1.6.901 May 18, 2011

...

    [Bug fixes]

    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
      docs [genehack, cjfields]

chris

On Sep 7, 2011, at 11:13 AM, Jason Stajich wrote:

> I don't think it works. I am not sure why - probably a bug - but can you go back to what it is you are trying to do? The Bio::Perl functions in that modules are intended to be shortcuts but the original modules should work.
> Can you recap what it is you want to accomplish, it may be better to do this with the Bio::Perl module but instead use a more direct use of the underlying modules.
> 
> 
> On Sep 6, 2011, at 3:59 AM, Manju Rawat wrote:
> 
>> bioperl 1.6.9 version is installed in my system..
>> its not the reason bcs blast is working fine when i am blasting with
>> follwing code..
>> 
>> #!usr/bin/perl -w
>> use Bio::Perl;
>> $seq = get_sequence('NCBI',"NM_181451");
>> $blast_result=blast_sequence($seq);
>> write_blast(">xyz.blast",$blast_result);
>> 
>> 
>> Manju
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From carandraug+dev at gmail.com  Wed Sep  7 16:47:16 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 7 Sep 2011 17:47:16 +0100
Subject: [Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast
In-Reply-To: <4E590812.9030006@ibab.ac.in>
References: <37711.192.168.1.254.1313992876.squirrel@webmail.ibab.ac.in>
	<CAPOrs_1TX=+A=hA0bCP56bsW5XdPy5N5mpcnAL=NPugP-4j03Q@mail.gmail.com>
	<4E590812.9030006@ibab.ac.in>
Message-ID: <CAPOrs_2MbWXbtrhj+eOphpDfyaUhdpWvUE8kaMXxKrQe_3m_kw@mail.gmail.com>

2011/8/27 Lucky Singh <slucky at ibab.ac.in>:
> On Friday 26 August 2011 07:50 PM, Carn? Draug wrote:
>>
>> On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in> ?wrote:
>>>
>>> Now I
>>> wanted to host it from web server, but This program is not working from
>>> it
>>> may be it is not able to create or write on file from web server but in
>>> command line it is working fine. I don't know the possible reason, please
>>> help me to figure it out.
>>
>> Have you looked in the apache logs (look in
>> /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>> content of the error log after trying to run the script?
>
> Dear Carn? Draug,
>
> As per your suggestion, I am attaching blast code file currently it is not
> showing any error on error.log.
> Thanks a lot for your valuable reply and will be highly grateful if you can
> get me out of this problem :)


Hi

sorry for the late reply. Please try to always reply to the mailing
list, maybe someone else can help you too. I don't know about the
script as I never used RemoteBlast from bioperl. But given a quick
look at it, you're not loading the CGI module on the script (
http://perldoc.perl.org/CGI.html ). Here's a simple example using the
CGI module ( http://pastebin.com/miMd70wn ) and a HTML page that will
use it ( http://pastebin.com/kWwwMijd ).

If nothing shows up on error.log, take a look in access.log. Try some
simple CGI script first, such as "hello world!" to see if the problem
lies on your bioperl part of the script, or in the web server, or some
other part.

Carn?



From scott at scottcain.net  Wed Sep  7 17:57:31 2011
From: scott at scottcain.net (Scott Cain)
Date: Wed, 7 Sep 2011 13:57:31 -0400
Subject: [Bioperl-l] October GMOD Meeting in Toronto
Message-ID: <CA+JTaoxxMxNQmOu8wbU=vD+-6eRwPVjpXBAszWn=p6_OOkr9ig@mail.gmail.com>

Hello,

The early registration deadline for the October GMOD meeting in
Toronto, Canada is approaching.  Please register by September 13th to
avoid the late registration fee.  You can register here:

  http://gmod.eventbrite.com/

For information about the GMOD meeting please see the page at:

  http://gmod.org/wiki/October_2011_GMOD_Meeting

In addition to the main meeting, there will be a free BioMart workshop
on the following Friday, which you can also register for at the main
meeting registration page.

Thanks,
Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?? scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)? ? ? ? ? ? ? ? ? ?? 216-392-3087
Ontario Institute for Cancer Research



From info at etisalat.com  Wed Sep  7 09:52:00 2011
From: info at etisalat.com (Etisalat Telecommunication Network.)
Date: Wed, 7 Sep 2011 17:52:00 +0800
Subject: [Bioperl-l] Winning No:ETS/G/NG
Message-ID: <20110907092508.M63844@etisalat.com>

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From longbow0 at gmail.com  Wed Sep  7 20:19:37 2011
From: longbow0 at gmail.com (longbow leo)
Date: Wed, 7 Sep 2011 15:19:37 -0500
Subject: [Bioperl-l] How to determine strains were evolved independently in
	a phylogenetic tree?
Message-ID: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>

Hi,

I have created a phylogenetic for a virus protein which contained about 200
strains. Next I need to do an analysis to check whether several strains in
this tree were evolved independently. Although it is not too difficult to do
manually, I still have litter idea how to do this in a Perl script since
there are some datasets need to do.

At first I tried to use the method "is_monophyletic" in the module
"Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
work as I have thought. According to the description of "is_monophyletic"
method, it "Will do a test of monophyly for the nodes specified in
comparison to a chosen outgroup". Does here test whether the outgroup strain
is monophyletic to the nodes, or test the nodes only? The description sounds
like the latter but the what the script did seemed to be the first.

Are there any suggestions?

Thank you very much!


Haizhou Liu


From greg at ebi.ac.uk  Thu Sep  8 10:40:30 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Thu, 8 Sep 2011 11:40:30 +0100
Subject: [Bioperl-l] How to determine strains were evolved independently
 in a phylogenetic tree?
In-Reply-To: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
References: <CAKPXXkeVVidy8jtTjo0KpZAjNvdyT8LLcNfJtv8s2J9dt-7N8w@mail.gmail.com>
Message-ID: <CA+08rdT4z5W5OzuuBPsC0icz_LWXCTNWO0uv=w=Bg_0EoU44Gw@mail.gmail.com>

Hi Haizhou,

I'm not sure I understand exactly what you're trying to do. But to clarify
the BioPerl code: the is_monophyletic method (for the actual code, see here
https://github.com/bioperl/bioperl-live/blob/master/Bio/Tree/TreeFunctionsI.pm#L832)
tests
whether the single outgroup node falls *within* or *outside* the last common
ancestor of the group of nodes given. If the outgroup node falls *outside*
the subtree defined by this LCA node, then the group of nodes can be called
monophyletic with respect to that outgroup (at least as far as my
understanding of the word 'monophyletic' goes). If the outgroup node falls
*within* the subtree defined by this LCA node, then the group of nodes is
not monophyletic with respect to that outgroup node.

The term "evolved independently" sounds slightly vague to me -- what is it
exactly about the shape of your tree that allows you to call a strain
independent or not? If you gave an example or two of trees where you
consider the evolution to be independent and non-independent, I (or someone
else on the list) may be able to help you find the right method to do this
automatically.

Cheers,
 Greg

On Wed, Sep 7, 2011 at 9:19 PM, longbow leo <longbow0 at gmail.com> wrote:

> Hi,
>
> I have created a phylogenetic for a virus protein which contained about 200
> strains. Next I need to do an analysis to check whether several strains in
> this tree were evolved independently. Although it is not too difficult to
> do
> manually, I still have litter idea how to do this in a Perl script since
> there are some datasets need to do.
>
> At first I tried to use the method "is_monophyletic" in the module
> "Bio::Tree::TreeFunctionsI" to do this analysis, but it seems it doesn't
> work as I have thought. According to the description of "is_monophyletic"
> method, it "Will do a test of monophyly for the nodes specified in
> comparison to a chosen outgroup". Does here test whether the outgroup
> strain
> is monophyletic to the nodes, or test the nodes only? The description
> sounds
> like the latter but the what the script did seemed to be the first.
>
> Are there any suggestions?
>
> Thank you very much!
>
>
> Haizhou Liu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From manju.rawat2 at gmail.com  Thu Sep  8 06:11:12 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 8 Sep 2011 02:11:12 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
Message-ID: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>

Toady i installed the latest version of bioperl in my system via CPAN..
But this still not sowing the complete result..


I just want to do nucleotide blast using bioperl..but while i am doing blast
with my sequence it shwowing very samll result..
I dnt know whether it is wrong or right...but while i am blasting the same
sequence in NCBI it showing a diffrent result..

and i have also tried to use the orignl module..but it also dnt work..

Pl see reult of the balst in  attached file of this mail..
#!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO;
$blast_report =blast_sequence('acggctgctgtagatctgatgct');
write_blast(">resl.blast",$blast_report);

Thanks.
Manju Rawat
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From cjfields at illinois.edu  Thu Sep  8 13:05:10 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 13:05:10 +0000
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <6D4A142B-9455-4CC3-AFDB-F9B3B991B57F@illinois.edu>

Submissions to NCBI BLAST via their web interface have different parameters than those submitted via their QBLAST interface (what is used in BioPerl).  So the fact there are differing results isn't too surprising, particularly if the results fall close to the e-value cutoff for one or the other.  You will need to set the proper parameters, which I don't believe is possible via the (very simple) Bio::Perl interface, but is possible via Bio::Tools::Run::RemoteBlast.

chris

On Sep 8, 2011, at 1:11 AM, Manju Rawat wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
> 
> 
> I just want to do nucleotide blast using bioperl..but while i am doing blast with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same sequence in NCBI it showing a diffrent result..
> 
> and i have also tried to use the orignl module..but it also dnt work..
> 
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
> 
> Thanks.
> Manju Rawat
> 
> 
> <resl.blast>




From David.Messina at sbc.su.se  Thu Sep  8 13:33:19 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 8 Sep 2011 15:33:19 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
Message-ID: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>

As I think has been said earlier in this thread, it's almost certainly a
discrepancy in the BLAST parameters between what the blast_sequence function
in the Bio::Perl module is sending, and what the BLAST website is doing.


In this case, you have a very short sequence. If you look in the "Algorithm
parameters" section of the BLAST web form, you'll see that there is an
option that is checked by default, "Automatically adjust parameters for
short input sequences".


If I uncheck that option, I get the same results as you did when you
submitted your BLAST through BioPerl (see http://cl.ly/9ynq).


So to get the same results from a BioPerl-submitted BLAST and a BLAST on
NCBI's website, you need to have the same parameters. You can set the
parameters from BioPerl as described in the documentation:

http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Tools/Run/RemoteBlast.pm


As Jason said earlier, the blast_sequence function in Bio::Perl is intended
as a simple demonstration and uses the default BLAST parameters. That
function is a wrapper around the RemoteBlast module. Since you want to do
something a little different, I believe you'll need to use the RemoteBlast
module directly.




Dave




On Thu, Sep 8, 2011 at 08:11, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Toady i installed the latest version of bioperl in my system via CPAN..
> But this still not sowing the complete result..
>
>
> I just want to do nucleotide blast using bioperl..but while i am doing
> blast
> with my sequence it shwowing very samll result..
> I dnt know whether it is wrong or right...but while i am blasting the same
> sequence in NCBI it showing a diffrent result..
>
> and i have also tried to use the orignl module..but it also dnt work..
>
> Pl see reult of the balst in  attached file of this mail..
> #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO;
> $blast_report =blast_sequence('acggctgctgtagatctgatgct');
> write_blast(">resl.blast",$blast_report);
>
> Thanks.
> Manju Rawat
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From abualiga2 at gmail.com  Thu Sep  8 14:44:39 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 10:44:39 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
	primary tag
Message-ID: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>

Hi,

I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
multiple tags within a primary tag.  E.g., when there are several 'function'
tag-values within a 'CDS' primary tag, I don't know how to link those
'function' tag-values to a particular 'locus_tag'.  As parsed values are
returned as a list, I tried creating an array of hashes, where the hash-key
is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
miserably.  Pasted below is what I managed so far.  At your convenience,
please advise.

thanks!

galeb

#!/usr/local/bin/perl
# parse_gbk.pl
# gsa 09042011
# script to parse out features from gbk
#
http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction

use strict; use warnings;
use Bio::SeqIO;

my @loci;
my @seqs;
my @directions;
my @start_coords;
my @end_coords;
my @genes;
my @products;
my @notes;
my @functions;
my %functions;

my $gb_file = shift;
my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
my $seq_obj = $seqio_obj->next_seq;

for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
    if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
                if ($feat_obj->has_tag( 'locus_tag' ) ) {
                push ( @seqs, $feat_obj->seq->seq ); #collect sequences
                    for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
{
                            push ( @loci, $val ); # locus_tags
            }
        }
                if ( $feat_obj->has_tag( 'gene' ) ) {
                           for my $val ( $feat_obj->get_tag_values( 'gene' )
) {
                            push ( @genes, $val ); # gene names
                        }
                }
                else {
                    push ( @genes, "" ); # if gene names are absent, leave
empty
        }
        if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
coordinates
            for my $location ( $feat_obj->location ) {
                push ( @start_coords, $location->start );
                push ( @end_coords, $location->end );
                if ( $location->strand == -1 ) {
                    push ( @directions, "reverse" );
                }
                else {
                    push ( @directions, "forward" );
                }
            }
        }
    }
    # gene products, notes, functions
    if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
$feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
|| $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
        if ( $feat_obj->has_tag( 'product' ) ) {
            for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
                push ( @products, $product );
            }
        }
        else {
            push ( @products, "" );
        }
        if ( $feat_obj->has_tag( 'note' ) ) {
            for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
                push ( @notes, $note );
            }
        }
        else {
            push ( @notes, "" );
        }
        if ( $feat_obj->has_tag( 'function' ) ) {
            for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
                push ( @functions, $function );
            }
        }
        else {
            push ( @functions, "" );
        }

    }
}

print
"locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
# header

for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
    print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
"\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
$directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
$functions[$elem], "\t", $seqs[$elem], "\n";
}


From p.j.a.cock at googlemail.com  Thu Sep  8 15:27:56 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:27:56 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>

On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> Hi,
>
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag. ?E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.

Do you have GenBank features with multiple locus_tag qualifiers?
That would be very unusual...

Peter



From cjfields at illinois.edu  Thu Sep  8 15:32:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 15:32:21 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
Message-ID: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>

On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:

> On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
>> Hi,
>> 
>> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
>> multiple tags within a primary tag.  E.g., when there are several 'function'
>> tag-values within a 'CDS' primary tag, I don't know how to link those
>> 'function' tag-values to a particular 'locus_tag'.
> 
> Do you have GenBank features with multiple locus_tag qualifiers?
> That would be very unusual...
> 
> Peter

Agreed; in order to clarify what you mean, I think we would need to see the record in question to get a better idea of the problem.

chris


From abualiga2 at gmail.com  Thu Sep  8 15:39:20 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:39:20 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
Message-ID: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>

I guess I was not clear. 'locus_tag' qualifiers are single, but there are
mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

# gbk file
LOCUS       NC_011748            5154862 bp    DNA     circular BCT
15-MAY-2010

# example feature
     gene        complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /db_xref="GeneID:7145846"
     CDS             complement(1336169..1337905)
                     /gene="cvrA"
                     /locus_tag="EC55989_1287"
                     /function="7 : Transport and binding proteins"
                     /function="15.10 : Adaptations to atypical conditions"
                     /function="16.1 : Circulate"
                     /inference="ab initio prediction:AMIGene:2.0"
                     /note="the Vibrio parahaemolyticus gene VP2867 was
found
                     to be a potassium/proton antiporter; can rapidly
extrude
                     potassium against a potassium gradient at alkaline pH
when
                     cloned and expressed in Escherichia coli"
                     /codon_start=1
                     /transl_table=11
                     /product="potassium/proton antiporter"
                     /protein_id="YP_002402372.1"
                     /db_xref="GI:218694705"
                     /db_xref="GeneID:7145846"

/translation="MDATTIISLFILGSILVTSSILLSSFSSRLGIPILVIFLAIGML

AGVDGVGGIPFDNYPFAYMVSNLALAIILLDGGMRTQASSFRVALGPALSLATLGVLI

TSGLTGMMAAWLFNLDLIEGLLIGAIVGSTDAAAVFSLLGGKGLNERVGSTLEIESGS

NDPMAVFLTITLIAMIQQHESSVSWMFVVDILQQFGLGIVIGLGGGYLLLQMINRIAL

PAGLYPLLALSGGILIFALTTALEGSGILAVYLCGFLLGNRPIRNRYGILQNFDGLAW

LAQIAMFLVLGLLVNPSDLLPIAIPALILSAWMIFFARPLSVFAGLLPFRGFNLRERV

FISWVGLRGAVPIILAVFPMMAGLENARLFFNVAFFVVLVSLLLQGTSLSWAAKKAKV

VVPPVGRPVSRVGLDIHPENPWEQFVYQLSADKWCVGAALRDLHMPKETRIAALFRDN

QLLHPTGSTRLREGDVLCVIGRERDLPALGKLFSQSPPVALDQRFFGDFILEASAKYA

DVALIYGLEDGREYRDKQQTLGEIVQQLLGAAPVVGDQVEFAGMIWTVAEKEDNEVLK
                     IGVRVAEEEAES"

On Thu, Sep 8, 2011 at 11:32 AM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> On Sep 8, 2011, at 10:27 AM, Peter Cock wrote:
>
> > On Thu, Sep 8, 2011 at 3:44 PM, galeb abu-ali <abualiga2 at gmail.com>
> wrote:
> >> Hi,
> >>
> >> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> >> multiple tags within a primary tag.  E.g., when there are several
> 'function'
> >> tag-values within a 'CDS' primary tag, I don't know how to link those
> >> 'function' tag-values to a particular 'locus_tag'.
> >
> > Do you have GenBank features with multiple locus_tag qualifiers?
> > That would be very unusual...
> >
> > Peter
>
> Agreed; in order to clarify what you mean, I think we would need to see the
> record in question to get a better idea of the problem.
>
> chris


From p.j.a.cock at googlemail.com  Thu Sep  8 15:46:28 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Thu, 8 Sep 2011 16:46:28 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
Message-ID: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>

On Thu, Sep 8, 2011 at 4:39 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> I guess I was not clear. 'locus_tag' qualifiers are single, but there are
> mutliple 'function' qualifiers within a primary feature (e.g. 'CDS').

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?

Peter


From abualiga2 at gmail.com  Thu Sep  8 15:55:08 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 11:55:08 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<CAKVJ-_7Dtdnu9w2hDJ8XcL4ZZSomCTsXF6ZRUHP7aytguSYgYA@mail.gmail.com>
	<ABC483B3-971C-4B4C-93D6-AA36FB3E7521@illinois.edu>
	<CANPzzTsY83tHci58mtdJq-ytHtqcK02QWN+XJWjUt9WiH+6NqQ@mail.gmail.com>
	<CAKVJ-_7X2YBgps3wYnLxygZmKVC7+w6pwGthwUXE4PvLeWz=ig@mail.gmail.com>
Message-ID: <CANPzzTsCB8DMzQHMYNOh84hBmu2diwrEA6xb8n3i2RFY9_a4kw@mail.gmail.com>

So are your intending to look at all the CDS features only, and
build a hash using the locus_tag as the key, and a list of the
'function' qualifiers as values?


Precisely!
I want to create a tab delim file with 'locus_tag' as the common identifier
to all the features and gene sequences. So far, I parsed out sequences and
single instance qualifiers, but 'function' and 'db_xref' qualifiers give me
grief.

galeb


From abualiga2 at gmail.com  Thu Sep  8 16:14:07 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:14:07 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.



That's right. Products are not the issue in this particular case, as it's
E.coli and there's no alternate splicing as far as I know so there is a
single product per gene. But there are plenty more 'function' qualifiers,
for example, than loci. And I don't know how to create a data structure that
will link a 'gene' (as primary tag) to all other qualifiers, whether they
belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.


From ss2489 at cornell.edu  Thu Sep  8 16:28:40 2011
From: ss2489 at cornell.edu (Surya Saha)
Date: Thu, 8 Sep 2011 12:28:40 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
Message-ID: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

-Surya

On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:

> I only had a quick look at your code, so maybe I'm missing something but
> you are currently pushing all products of all CDSs into the same array,
> i.e. you do not assign them to a datastructure that links a particular
> CDS to a list of products. You then use the same index to print out a
> locus from the @loci array and a product from @products, but the two
> will not match up because you will have more products than loci.
>
>
>
> That's right. Products are not the issue in this particular case, as it's
> E.coli and there's no alternate splicing as far as I know so there is a
> single product per gene. But there are plenty more 'function' qualifiers,
> for example, than loci. And I don't know how to create a data structure
> that
> will link a 'gene' (as primary tag) to all other qualifiers, whether they
> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From fs5 at sanger.ac.uk  Thu Sep  8 16:04:57 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 08 Sep 2011 17:04:57 +0100
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags
	within	primary tag
In-Reply-To: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
Message-ID: <1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>

I only had a quick look at your code, so maybe I'm missing something but
you are currently pushing all products of all CDSs into the same array,
i.e. you do not assign them to a datastructure that links a particular
CDS to a list of products. You then use the same index to print out a
locus from the @loci array and a product from @products, but the two
will not match up because you will have more products than loci.

Frank



On Thu, 2011-09-08 at 10:44 -0400, galeb abu-ali wrote:
> Hi,
> 
> I'm parsing a genbank file with Bio::SeqIO and am stuck on instances of
> multiple tags within a primary tag.  E.g., when there are several 'function'
> tag-values within a 'CDS' primary tag, I don't know how to link those
> 'function' tag-values to a particular 'locus_tag'.  As parsed values are
> returned as a list, I tried creating an array of hashes, where the hash-key
> is 'locus_tag' and hash-values are multiple 'function' tags, but am failing
> miserably.  Pasted below is what I managed so far.  At your convenience,
> please advise.
> 
> thanks!
> 
> galeb
> 
> #!/usr/local/bin/perl
> # parse_gbk.pl
> # gsa 09042011
> # script to parse out features from gbk
> #
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Customizing_Sequence_Object_Construction
> 
> use strict; use warnings;
> use Bio::SeqIO;
> 
> my @loci;
> my @seqs;
> my @directions;
> my @start_coords;
> my @end_coords;
> my @genes;
> my @products;
> my @notes;
> my @functions;
> my %functions;
> 
> my $gb_file = shift;
> my $seqio_obj = Bio::SeqIO->new(-file => $gb_file );
> my $seq_obj = $seqio_obj->next_seq;
> 
> for my $feat_obj ( $seq_obj->get_SeqFeatures ) {
>     if ( $feat_obj->primary_tag eq ( 'gene' ) ) {
>                 if ($feat_obj->has_tag( 'locus_tag' ) ) {
>                 push ( @seqs, $feat_obj->seq->seq ); #collect sequences
>                     for my $val ( $feat_obj->get_tag_values( 'locus_tag' ) )
> {
>                             push ( @loci, $val ); # locus_tags
>             }
>         }
>                 if ( $feat_obj->has_tag( 'gene' ) ) {
>                            for my $val ( $feat_obj->get_tag_values( 'gene' )
> ) {
>                             push ( @genes, $val ); # gene names
>                         }
>                 }
>                 else {
>                     push ( @genes, "" ); # if gene names are absent, leave
> empty
>         }
>         if ( $feat_obj->location->isa( 'Bio::Location::Simple' ) ) { # gene
> coordinates
>             for my $location ( $feat_obj->location ) {
>                 push ( @start_coords, $location->start );
>                 push ( @end_coords, $location->end );
>                 if ( $location->strand == -1 ) {
>                     push ( @directions, "reverse" );
>                 }
>                 else {
>                     push ( @directions, "forward" );
>                 }
>             }
>         }
>     }
>     # gene products, notes, functions
>     if ( $feat_obj->primary_tag eq ( 'CDS' ) || $feat_obj->primary_tag eq (
> 'misc_feature' ) || $feat_obj->primary_tag eq ( 'ncRNA' ) ||
> $feat_obj->primary_tag eq ( 'rRNA' ) || $feat_obj->primary_tag eq ( 'tRNA' )
> || $feat_obj->primary_tag eq ( 'misc_RNA' ) ) {
>         if ( $feat_obj->has_tag( 'product' ) ) {
>             for my $product ( $feat_obj->get_tag_values( 'product' ) ) {
>                 push ( @products, $product );
>             }
>         }
>         else {
>             push ( @products, "" );
>         }
>         if ( $feat_obj->has_tag( 'note' ) ) {
>             for my $note ( $feat_obj->get_tag_values( 'note' ) ) {
>                 push ( @notes, $note );
>             }
>         }
>         else {
>             push ( @notes, "" );
>         }
>         if ( $feat_obj->has_tag( 'function' ) ) {
>             for my $function ( $feat_obj->get_tag_values( 'function' ) ) {
>                 push ( @functions, $function );
>             }
>         }
>         else {
>             push ( @functions, "" );
>         }
> 
>     }
> }
> 
> print
> "locus\tgene_name\tstart_nt\tend_nt\tlength_nt\tdirection\tproduct\tnote\tfunction\tsequence_nt\n";
> # header
> 
> for ( my $elem = 0; $elem < scalar @loci; ++$elem ) {
>     print $loci[$elem], "\t",$genes[$elem], "\t", $start_coords[$elem],
> "\t", $end_coords[$elem], "\t", length( $seqs[$elem] ), "\t",
> $directions[$elem], "\t", $products[$elem], "\t", $notes[$elem], "\t",
> $functions[$elem], "\t", $seqs[$elem], "\n";
> }
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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From cjfields at illinois.edu  Thu Sep  8 16:51:22 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 16:51:22 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>

There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().

chris

-----------------------------
#!/usr/bin/env perl

use Modern::Perl;
use Bio::SeqIO;

my $in = Bio::SeqIO->new(-format => 'genbank',
                         -file => shift);

while (my $seq = $in->next_seq) {
   for my $feat ($seq->get_SeqFeatures) {
       next unless $feat->primary_tag eq 'CDS';
       my ($locus) = $feat->has_tag('locus_tag') ? 
                     $feat->get_tag_values('locus_tag') : '';
       my @funcs = $feat->has_tag('function') ?
           $feat->get_tag_values('function') : ();
       say join("\t", $locus, join(',', at funcs));
   }
}



On Sep 8, 2011, at 11:28 AM, Surya Saha wrote:

> You might want to explore using a hash of complex records that are very
> similar to structures in C/C++. More info at
> http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS
> 
> -Surya
> 
> On Thu, Sep 8, 2011 at 12:14 PM, galeb abu-ali <abualiga2 at gmail.com> wrote:
> 
>> I only had a quick look at your code, so maybe I'm missing something but
>> you are currently pushing all products of all CDSs into the same array,
>> i.e. you do not assign them to a datastructure that links a particular
>> CDS to a list of products. You then use the same index to print out a
>> locus from the @loci array and a product from @products, but the two
>> will not match up because you will have more products than loci.
>> 
>> 
>> 
>> That's right. Products are not the issue in this particular case, as it's
>> E.coli and there's no alternate splicing as far as I know so there is a
>> single product per gene. But there are plenty more 'function' qualifiers,
>> for example, than loci. And I don't know how to create a data structure
>> that
>> will link a 'gene' (as primary tag) to all other qualifiers, whether they
>> belong to 'CDS', 'Misc_RNA', 'Misc_feature', or other primary tags.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From abualiga2 at gmail.com  Thu Sep  8 16:51:42 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 12:51:42 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
Message-ID: <CANPzzTuAkFy-P9WAVe7bzv=mVEXb-MOLFQrZYv8UX7L2rWcZCA@mail.gmail.com>

You might want to explore using a hash of complex records that are very
similar to structures in C/C++. More info at
http://perldoc.perl.org/perldsc.html#Declaration-of-a-HASH-OF-COMPLEX-RECORDS

alright, thanks!


From jskittrell at unmc.edu  Thu Sep  8 16:40:31 2011
From: jskittrell at unmc.edu (Jeff S Kittrell)
Date: Thu, 8 Sep 2011 11:40:31 -0500
Subject: [Bioperl-l] Error when parsing a blast file
Message-ID: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>

An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20110908/486df26d/attachment-0004.html>

From cjfields at illinois.edu  Thu Sep  8 17:28:53 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 17:28:53 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
Message-ID: <1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>

What version of bioperl are you using?  I think this issue was addressed a while ago, but it's possible there has been a regression.

chris

On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:

> Hello Gentlemen,
> 
> I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> When the SearchIO parser encounters this record it dies with the error
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no data for midline Query ------------------------------------------------------------
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> -----------------------------------------------------------
> 
> 
> Has anyone encountered this problem before? Am I doing something wrong?
> 
> Thanks
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> Query= 78065535
> 
> Length=523
> Score E
> Sequences producing significant alignments: (Bits) Value
> 
> gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> 
> 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> receptor 123 (GPR123), mRNA
> Length=4298
> 
> Score = 576 bits (638), Expect = 1e-163
> Identities = 466/583 (80%), Gaps = 82/583 (14%)
> Strand=Plus/Minus
> 
> Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> 
> Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> 
> Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> 
> Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> 
> Query ------------------------------------------------------------ 
> 
> Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> 
> Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> 
> Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> 
> Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> 
> Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> 
> Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> ||||||||||||||||||||||||||||||| ||| || ||||
> Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> 
> 
> 
> Lambda K H
> 0.634 0.408 0.912 
> 
> Gapped
> Lambda K H
> 0.625 0.410 0.780 
> 
> Effective search space used: 47712920310
> 
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From abualiga2 at gmail.com  Thu Sep  8 17:51:34 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 13:51:34 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
Message-ID: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>

thanks, Chris! works perfect.
To make sure I understand what's going on, forcing list context on $locus
allows me to get one value at a time, which is then concatenated with \t to
concatenated functions.

thanks again!

galeb

On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> There is no need to do that if one is using the Bio::SeqFeatureI interface.
>  Note that get_tag_values always returns a list, so to snag a single value
> for a tag in a scalar, force list context on the LHS by enclosing the
> variable in ().
>
> chris
>
> -----------------------------
> #!/usr/bin/env perl
>
> use Modern::Perl;
> use Bio::SeqIO;
>
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
>
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>    }
> }
>
>
>
>


From cjfields at illinois.edu  Thu Sep  8 18:27:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:27:06 +0000
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
Message-ID: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>

On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:

> thanks, Chris! works perfect. 
> To make sure I understand what's going on, forcing list context on $locus allows me to get one value at a time,...

You have to be careful in this circumstance; doing this:

   my $foo = @bar;

is scalar context on a list, which returns the number of elements in @bar.  The following

   my ($foo) = @bar;

forces list context and assigns the first value in @bar to $foo but tosses the rest.  If you are sure there is only one value in @bar anyway, the above is fine (and is a common perl idiom).  

> which is then concatenated with \t to concatenated functions. 

I'm just using a simple join() to print off the results.  Note the second element in the join list is an embedded join() with comma-sep values for functions.

chris

> thanks again!
> 
> galeb
> 
> On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:
> There is no need to do that if one is using the Bio::SeqFeatureI interface.  Note that get_tag_values always returns a list, so to snag a single value for a tag in a scalar, force list context on the LHS by enclosing the variable in ().
> 
> chris
> 
> -----------------------------
> #!/usr/bin/env perl
> 
> use Modern::Perl;
> use Bio::SeqIO;
> 
> my $in = Bio::SeqIO->new(-format => 'genbank',
>                         -file => shift);
> 
> while (my $seq = $in->next_seq) {
>   for my $feat ($seq->get_SeqFeatures) {
>       next unless $feat->primary_tag eq 'CDS';
>       my ($locus) = $feat->has_tag('locus_tag') ?
>                     $feat->get_tag_values('locus_tag') : '';
>       my @funcs = $feat->has_tag('function') ?
>           $feat->get_tag_values('function') : ();
>       say join("\t", $locus, join(',', at funcs));
>   }
> }
> 
> 
> 




From cjfields at illinois.edu  Thu Sep  8 18:30:06 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 8 Sep 2011 18:30:06 +0000
Subject: [Bioperl-l] Error when parsing a blast file
In-Reply-To: <OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
References: <OF709E7248.539E61A7-ON86257905.005AAEFC-86257905.005B99A8@unmc.edu>
	<1F3664C5-6D6B-409C-BE5A-C5EB08975231@illinois.edu>
	<OF55CFA678.2145D3DF-ON86257905.0064A4FA-86257905.0064B220@unmc.edu>
Message-ID: <C7BC7AE9-FF28-460D-83D1-35F0C8A17832@illinois.edu>

Try updating to the latest CPAN release (1.6.901, which is the pre-1.7 release).

chris

On Sep 8, 2011, at 1:19 PM, Jeff S Kittrell wrote:

> chris,
> 
> I am using version 1.6.1
> 
> Thanks,
> 
> 
> Jeff Kittrell
> Department of Genetics, Cell Biology & Anatomy
> University of Nebraska Medical Center
> 985805 Nebraska Medical Center
> Omaha, NE 68198-5805
> 
> <graycol.gif>"Fields, Christopher J" ---09/08/2011 12:28:56 PM---What version of bioperl are you using? I think this issue was addressed a while ago, but it's possi
> 
> <ecblank.gif>
> From:
> <ecblank.gif>
> "Fields, Christopher J" <cjfields at illinois.edu>
> <ecblank.gif>
> To:
> <ecblank.gif>
> Jeff S Kittrell <jskittrell at unmc.edu>
> <ecblank.gif>
> Cc:
> <ecblank.gif>
> "<bioperl-l at lists.open-bio.org> " <bioperl-l at lists.open-bio.org>
> <ecblank.gif>
> Date:
> <ecblank.gif>
> 09/08/2011 12:28 PM
> <ecblank.gif>
> Subject:
> <ecblank.gif>
> Re: [Bioperl-l] Error when parsing a blast file
> 
> 
> 
> What version of bioperl are you using? I think this issue was addressed a while ago, but it's possible there has been a regression.
> 
> chris
> 
> On Sep 8, 2011, at 11:40 AM, Jeff S Kittrell wrote:
> 
> > Hello Gentlemen,
> > 
> > I am using BioPerl to a parse a blast output file but have run into some difficulties. I've pin pointed the problem and have pasted an example below. If you look at query position 223-224 you will see a large insertion 65ish nucleotides. Since the insertion spans the entire line there are no nucleotide position numbers at the end or beginning of the line nor any nucleotides within the line (dashes only). 
> > When the SearchIO parser encounters this record it dies with the error
> > 
> > ------------- EXCEPTION: Bio::Root::Exception -------------
> > MSG: no data for midline Query ------------------------------------------------------------
> > STACK: Error::throw
> > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368
> > STACK: Bio::SearchIO::blast::next_result /usr/local/share/perl5/Bio/SearchIO/blast.pm:1805
> > STACK: BlastParseNucleotideForDBTopHitCONTIGSQUERY.pl:24
> > -----------------------------------------------------------
> > 
> > 
> > Has anyone encountered this problem before? Am I doing something wrong?
> > 
> > Thanks
> > 
> > Jeff Kittrell
> > Department of Genetics, Cell Biology & Anatomy
> > University of Nebraska Medical Center
> > 985805 Nebraska Medical Center
> > Omaha, NE 68198-5805
> > 
> > Query= 78065535
> > 
> > Length=523
> > Score E
> > Sequences producing significant alignments: (Bits) Value
> > 
> > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled... 576 1e-163
> > 
> > 
> > > gi|144922664|ref|NM_001083909.1| Homo sapiens G protein-coupled 
> > receptor 123 (GPR123), mRNA
> > Length=4298
> > 
> > Score = 576 bits (638), Expect = 1e-163
> > Identities = 466/583 (80%), Gaps = 82/583 (14%)
> > Strand=Plus/Minus
> > 
> > Query 1 CAGGACTCCGTGG-----ATGGCATCTCGGGCAGGGCCACGCTGGGGTCTGGGTGGGTCC 55
> > ||||||||||||| | ||||||||||||||||||| |||||||||| ||||||||
> > Sbjct 2537 CAGGACTCCGTGGGCAGCAGGGCATCTCGGGCAGGGCCATGCTGGGGTCTCAGTGGGTCC 2478
> > 
> > Query 56 TTTGATGGAAGCCCCTGCTCTGCCTCTGGGGCGCCCCAGGACTGGAGGCCACAGGACAGA 115
> > |||||||||| |||||||||||||||| ||| ||||||||||||||| ||||||||||||
> > Sbjct 2477 TTTGATGGAATCCCCTGCTCTGCCTCTAGGGTGCCCCAGGACTGGAGACCACAGGACAGA 2418
> > 
> > Query 116 AACCAGATGACCTTGTGCAGGGACGAGCACGTGGAACTGGGATAAAAGGAGTGGGCGTGG 175
> > |||| ||||||| ||||| ||||| |||||| |||| |||||||| |||||||||||||
> > Sbjct 2417 AACCGGATGACCGTGTGC-GGGACCAGCACGCGGAATTGGGATAAGGGGAGTGGGCGTGG 2359
> > 
> > Query 176 CCCAGAGCTTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGT------------ 223
> > ||| |||| ||||||||||||||||||||||||||||||||||||||| 
> > Sbjct 2358 CCCGGAGCGTTTCCCCGCTGAGGTCTTTCACAAGGAAGGGGCAGGGGTGTGATCACAAGG 2299
> > 
> > Query ------------------------------------------------------------ 
> > 
> > Sbjct 2298 AAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGGGGTGTGATCACAAGGAAGGGGCAGG 2239
> > 
> > Query 224 ---GTGAACTGCTTCCGAAAGGTGGGGTCACTTTGGTGCCCCCAGTGACCTCATGTGGCA 280
> > |||||| ||||| |||||| |||||||||| ||| ||||||||||||||||||||||
> > Sbjct 2238 GGTGTGAACGGCTTCTGAAAGGCGGGGTCACTTCGGTACCCCCAGTGACCTCATGTGGCA 2179
> > 
> > Query 281 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACTGTGTCCCCTG-CTCCGCC 339
> > ||||||||||||||||||||||||||||||||||||||||| |||||| ||| | || |
> > Sbjct 2178 GATGGGCCCCCCACTCTGCTCTGAAGCTCCTCCAGGAACACCGTGTCCTCTGCCCCCATC 2119
> > 
> > Query 340 TACACAGTAGTTTCATTTTTCCAGGGTCCTGTTCGGATGTTGCCGGTCCCATCGGTGCCA 399
> > |||||||||||||| |||||||||||||| |||||||||||||||||||| |||||||||
> > Sbjct 2118 TACACAGTAGTTTCGTTTTTCCAGGGTCCCGTTCGGATGTTGCCGGTCCCGTCGGTGCCA 2059
> > 
> > Query 400 AACGGCAGGTCTTCTAGCAAGTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 459
> > ||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||||
> > Sbjct 2058 AACGGCAGGCCTTCTAGCAATTTACCCTTGGGCAGCCCGTTCTGGCTGGGGCCACCAAAG 1999
> > 
> > Query 460 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAGGTGACCAGGCC 502
> > ||||||||||||||||||||||||||||||| ||| || ||||
> > Sbjct 1998 GGCAGGGACTGTGTCCTCCGCAGCATCTCCAAGTGGCCGGGCC 1956
> > 
> > 
> > 
> > Lambda K H
> > 0.634 0.408 0.912 
> > 
> > Gapped
> > Lambda K H
> > 0.625 0.410 0.780 
> > 
> > Effective search space used: 47712920310
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 




From abualiga2 at gmail.com  Thu Sep  8 18:34:41 2011
From: abualiga2 at gmail.com (galeb abu-ali)
Date: Thu, 8 Sep 2011 14:34:41 -0400
Subject: [Bioperl-l] genbank parsing of multiple 'function' tags within
 primary tag
In-Reply-To: <2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
References: <CANPzzTsFkUWQuVgiM6wiOiia+eP1ucWENOmEo9syhqY+sGWh1Q@mail.gmail.com>
	<1315497897.3797.443.camel@deskpro15336.internal.sanger.ac.uk>
	<CANPzzTuT-nAGxTSdrS2CdwFVSzs+RHwzMy9=TDA4u2y2=P3U1Q@mail.gmail.com>
	<CAEiaqD=-eQ=uq+8OM83nyW7_2OoXWy3N0c0459vgxVPJ3K_OUA@mail.gmail.com>
	<D6E019DF-6A7C-4C41-B0FE-1ABFC61C3E9F@illinois.edu>
	<CANPzzTt_P6tXP55VVOSBbA8B2-nXb3JF4hhqCD2E9x5FD6MKzw@mail.gmail.com>
	<2CDD8237-140E-410B-A18C-68FAF54719D5@illinois.edu>
Message-ID: <CANPzzTvxce3b=-bBUh9xNsda=1HrO9X6tRLhZAN5jhxpkKMLAQ@mail.gmail.com>

many thanks again, Chris! I was reading Programming Perl, but this sums it
up better.

On Thu, Sep 8, 2011 at 2:27 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

> On Sep 8, 2011, at 12:51 PM, galeb abu-ali wrote:
>
> > thanks, Chris! works perfect.
> > To make sure I understand what's going on, forcing list context on $locus
> allows me to get one value at a time,...
>
> You have to be careful in this circumstance; doing this:
>
>   my $foo = @bar;
>
> is scalar context on a list, which returns the number of elements in @bar.
>  The following
>
>   my ($foo) = @bar;
>
> forces list context and assigns the first value in @bar to $foo but tosses
> the rest.  If you are sure there is only one value in @bar anyway, the above
> is fine (and is a common perl idiom).
>
> > which is then concatenated with \t to concatenated functions.
>
> I'm just using a simple join() to print off the results.  Note the second
> element in the join list is an embedded join() with comma-sep values for
> functions.
>
> chris
>
> > thanks again!
> >
> > galeb
> >
> > On Thu, Sep 8, 2011 at 12:51 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
> > There is no need to do that if one is using the Bio::SeqFeatureI
> interface.  Note that get_tag_values always returns a list, so to snag a
> single value for a tag in a scalar, force list context on the LHS by
> enclosing the variable in ().
> >
> > chris
> >
> > -----------------------------
> > #!/usr/bin/env perl
> >
> > use Modern::Perl;
> > use Bio::SeqIO;
> >
> > my $in = Bio::SeqIO->new(-format => 'genbank',
> >                         -file => shift);
> >
> > while (my $seq = $in->next_seq) {
> >   for my $feat ($seq->get_SeqFeatures) {
> >       next unless $feat->primary_tag eq 'CDS';
> >       my ($locus) = $feat->has_tag('locus_tag') ?
> >                     $feat->get_tag_values('locus_tag') : '';
> >       my @funcs = $feat->has_tag('function') ?
> >           $feat->get_tag_values('function') : ();
> >       say join("\t", $locus, join(',', at funcs));
> >   }
> > }
> >
> >
> >
>
>


From David.Messina at sbc.su.se  Fri Sep  9 09:40:25 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 11:40:25 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
Message-ID: <CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>

Hi Manju,


But this is not showing all query coverage as it shows in simple balst.(see
> attached file)
>

I'm not sure what you mean by query coverage here, as blast report you
attached doesn't (as far as I can see) include a calculation of the number
or percentage of query bases covered.

But in any case, everything in that blast report is available in the
Bio::SearchIO object that B::T::R::RemoteBlast returns. Have you taken a
look at http://www.bioperl.org/wiki/HOWTO:SearchIO ? That, along with the
module documentation, should help you find the parts of the BLAST report
you're looking for.



> and i also want to write that result in a blast file..Is there any method
> which can write the remoteblast output
> in a file with blast extension?
>

It is possible to write out the results in a format that closely resembles
the native blast report, but it's not recommended. If you want to just run
BLAST and get back a report, there's no need to use BioPerl to parse the
report first and then recreate the report.

This might also be a good time to mention that, if you're doing more than a
few hundred BLAST searches, you'll find it much more efficient to download
the database and the BLAST program from NCBI and run them on your own
computer. NCBI severely limits the speed and frequency of remote BLASTs, and
furthermore it's much more prone to failure.

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
remotely without BioPerl. Check out the --remote command-line option ? it's
my favorite new feature!


Dave



From David.Messina at sbc.su.se  Fri Sep  9 10:53:01 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 9 Sep 2011 12:53:01 +0200
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
Message-ID: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>

If you don't want to learn how to do this in BioPerl, then take my previous
suggestion and just use NCBI's tools:

Also, if you're using BLAST+, you can run your BLASTs on NCBI's computers
> remotely without BioPerl. Check out the --remote command-line option





On Fri, Sep 9, 2011 at 12:07, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I dont no more about Bioperl....
> and i just want to blast my sequences using bioperl...
> ans see the result in a file...
> pls tell me what should i do???
>


From manju.rawat2 at gmail.com  Fri Sep  9 11:05:57 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 07:05:57 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
Message-ID: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>

I want to learn...and i am learing it from starting...
My main query is I want to make a program which gives me that
result(sequence) which have no blast result(no matches in any database/or
particular database).
for this i have to do blast may time....but i am not getting desired result
in blast...this is the main problem which i am facing..
now pls tell me whta procedure i should follow...


Manju


From cjfields at illinois.edu  Fri Sep  9 13:03:26 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 9 Sep 2011 13:03:26 +0000
Subject: [Bioperl-l] blast result not matching.
In-Reply-To: <CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
	<CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>
	<CAM3TQQWERXRyXGh=-1Dn5cWYSeqwsO_o=zHYa-Dm_SSQaYtiMg@mail.gmail.com>
	<CAB2c7ypVvgHmcaToT7GwpP-e0S9OsCjSfebmiAQwqTpHaSVqxg@mail.gmail.com>
	<CAM3TQQWyC2XBYTrXmZiC_Tbu2c8vP3CxPT73q2E_UDQjUJ2gYw@mail.gmail.com>
	<CAB2c7yotbDt=XeOSjSj+YZ3Y4EDOC-WEHTeKNAAO_5dzw80JPw@mail.gmail.com>
Message-ID: <AB17FEA3-524D-43EC-8C55-FAF7339FAE4A@illinois.edu>

If you are planning on looking against 'everything' (e.g. nt or nr), and you have many sequences to run, I would follow Dave's suggestion and download BLAST locally.  

chris

On Sep 9, 2011, at 6:05 AM, Manju Rawat wrote:

> I want to learn...and i am learing it from starting...
> My main query is I want to make a program which gives me that
> result(sequence) which have no blast result(no matches in any database/or
> particular database).
> for this i have to do blast may time....but i am not getting desired result
> in blast...this is the main problem which i am facing..
> now pls tell me whta procedure i should follow...
> 
> 
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Fri Sep  9 09:01:55 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 9 Sep 2011 05:01:55 -0400
Subject: [Bioperl-l] Fwd: blast result not matching.
In-Reply-To: <CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
References: <CAB2c7yp-Ea=3W4cPx2svYH-pdkqxFFK6QWDdWt9_VodTcY6RyA@mail.gmail.com>
	<CAB2c7ypqdEKVXxrG_ELN06hq2J6gHZpFU4vxFnxG0eZgiPoOdw@mail.gmail.com>
	<CAKVJ-_6rgdFeUiLdGB1bCB3YaTzNA+fB6_dvcfLr3cMjCJpGzg@mail.gmail.com>
	<CAB2c7yrNB-=nbuAkAJEhQG=cuPPACP6j9u=up5v-92Y1F=+_NQ@mail.gmail.com>
	<CAKVJ-_6wh0H1F73thgsuP4EU6BAOGTjNsD50PD1QerMLT+tuyg@mail.gmail.com>
	<CAB2c7yrJmW4S9-5-Vryg9KSYAUi3MG4NKDp4CSF2LJZxSQCJOg@mail.gmail.com>
	<4AF09F30-CB69-4285-90A2-40AFEEEBD222@illinois.edu>
	<CAB2c7yqUiMJ6mkrP-W+LXVnV6=hW0cB_ApVvVxEqtk7rSD71Tg@mail.gmail.com>
	<8FB3525D-3B2B-4D17-80D4-AA85B3D2AE8B@gmail.com>
	<C4272278-EC8F-4263-8706-8BA287631CAC@illinois.edu>
	<CAB2c7ypVgh3r4e297RjGSzadpObTfCY86g_XxMvxmzpA+Yq3fQ@mail.gmail.com>
	<CAM3TQQVpHmQarfU8Hxwp8XD=zzyHpwRw-byEYDzaDGgwvkBSOA@mail.gmail.com>
Message-ID: <CAB2c7ypR05bGYsCxXMzxivwcCayOdXOF_8q9vgAo3j5y27e6VA@mail.gmail.com>

Thanks to all..Its working..
I tried that module...and got the result follwing result in terminal...


waiting......db is All GenBank+EMBL+DDBJ+PDB sequences (but no EST,
STS,GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
hit name is ref|NM_181451.1|
score is 240
hit name is ref|NM_001008415.1|
score is 234
hit name is ref|XM_002706247.1|
score is 212
hit name is ref|XM_002683856.1|
score is 208
hit name is gb|EF197120.1|
score is 208
hit name is ref|XR_083566.1|
score is 198
hit name is ref|NM_001097567.1|
score is 198
hit name is ref|NM_001098089.1|
score is 198
hit name is ref|XM_002699708.1|
score is 192
hit name is ref|XM_592786.5|
score is 192
hit name is ref|XM_001251693.3|
score is 192
hit name is gb|AF490400.1|
score is 190
hit name is gb|AY075103.1|
score is 190
hit name is ref|XR_083457.1|
score is 178


But this is not showing all query coverage as it shows in simple balst.(see
attached file)
and i also want to write that result in a blast file..Is there any method
which can write the remoteblast output
in a file with blast extension?


Thanks
Manju Rawat.
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From ross at cuhk.edu.hk  Sat Sep 10 06:39:23 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sat, 10 Sep 2011 14:39:23 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick file
Message-ID: <048a01cc6f84$60c41090$224c31b0$@edu.hk>

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"

 

What's the problem? 

 

use Bio::TreeIO;

 

($treefh) = @ARGV;

 

my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;

 

$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);

 

my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);

 

my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";

 

 

#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;



From greg at ebi.ac.uk  Sat Sep 10 15:39:52 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Sat, 10 Sep 2011 16:39:52 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
Message-ID: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>

Hi Ross,

Which version of BioPerl are you using?

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
the following script works for me. Do those values look sensible to you? The
code on the new branch is a bit experimental, so I wouldn't be surprised if
all the edge cases for calculations like this aren't covered.

--greg

use Bio::TreeIO;

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");
my $tree = $treeio->next_tree;
my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");
my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");
my $ma = $tree->find("Mycobacterium_abscessus");
my $distance = $mt->distance($ma);
print "MT - MA: ".$mt->distance($ma)."\n";
print "MT - MS: ".$mt->distance($ms)."\n";
print "MS - MA: ".$ms->distance($ma)."\n";
# MT - MA: 0.24326
# MT - MS: 0.18573
# MS - MA: 0.20729

--greg

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From ross at cuhk.edu.hk  Sat Sep 10 23:06:44 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 11 Sep 2011 07:06:44 +0800
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
Message-ID: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>

Hi Greg,

 

The values are correct! However, how to install this bioperl-live module? my
bioperl is 1.6.1 but there's an error:

 

Can't locate object method "find" via package "Bio::Tree::Tree" at
TreeCalDist.pl line 32, <GEN0> line 1.

my $mt = $tree->find($keyword);  #line 32

 

 

From: gjuggler at gmail.com [mailto:gjuggler at gmail.com] On Behalf Of Gregory
Jordan
Sent: 2011?9?10? 23:40
To: bioperl-l List; Ross KK Leung
Subject: Re: [Bioperl-l] fail to obtain node-to-node distance from a newick
file

 

Hi Ross,

 

Which version of BioPerl are you using?

 

With the refactored tree code (available from the tree_api_refresh branch on
the BioPerl github repo:
https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree
/NodeFunctionsI.pm#L406) the following script works for me. Do those values
look sensible to you? The code on the new branch is a bit experimental, so I
wouldn't be surprised if all the edge cases for calculations like this
aren't covered.

 

--greg

 

use Bio::TreeIO;

 

my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");

my $tree = $treeio->next_tree;

my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");

my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");

my $ma = $tree->find("Mycobacterium_abscessus");

my $distance = $mt->distance($ma);

print "MT - MA: ".$mt->distance($ma)."\n";

print "MT - MS: ".$mt->distance($ms)."\n";

print "MS - MA: ".$ms->distance($ma)."\n";

# MT - MA: 0.24326

# MT - MS: 0.18573

# MS - MA: 0.20729

 

--greg

 

On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:

I use the following code to derive the distance between two nodes but an
error "MSG: could not find the lca of supplied nodes; can't find distance
either"



What's the problem?



use Bio::TreeIO;



($treefh) = @ARGV;



my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");

my $tree = $treeio->next_tree;



$keyword="Mycobacterium_tuberculosis_H37Rv";

my $Tnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_smegmatis_str._MC2_155";

my $Mnodes = $tree->find_node(-id => $keyword);

$keyword="Mycobacterium_abscessus";

my $Anodes = $tree->find_node(-id => $keyword);



my @root = $tree->get_root_node;

#my $distances = $tree->distance(-nodes => [$node[0],$root]);



my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);

print "Dist:$distances\n";





#### the following is the infile

(((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
-R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
_tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
_T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
.4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
_ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
:0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
)100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
.9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
)100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
_35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
.11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
_hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
.00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
:0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
:0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
_ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
)100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
)100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
_tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
:0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
_H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
_tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
-4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

 




From manju.rawat2 at gmail.com  Mon Sep 12 05:37:35 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:37:35 -0400
Subject: [Bioperl-l] no blast result
Message-ID: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>

Hello,
I want to make a program which first generate the random sequence and then
gives me that result(sequence) which have no blast result(no matches in any
database/or particular database).Is there any body who can help me in doing
this.

Pl reply if anybody knows about it..
Thanks
Manju


From zhangchnxp at gmail.com  Mon Sep 12 05:51:59 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 13:51:59 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
Message-ID: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>

Hi,

IMHO, due to the nature of BLAST, it is usually impossible to get no results
from random sequence, but to get a set of matches with lower scores.

What you can do is to focus on the e-value, say, setting a threshold to it.

FYI, http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

On Mon, Sep 12, 2011 at 1:37 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Hello,
> I want to make a program which first generate the random sequence and then
> gives me that result(sequence) which have no blast result(no matches in any
> database/or particular database).Is there any body who can help me in doing
> this.
>
> Pl reply if anybody knows about it..
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From manju.rawat2 at gmail.com  Mon Sep 12 05:58:38 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 01:58:38 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
Message-ID: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>

Ya i know this....And it is also in my use if i get result with lower
scores.
But how could I do this?


Manju


From zhangchnxp at gmail.com  Mon Sep 12 06:04:17 2011
From: zhangchnxp at gmail.com (Zhang chn)
Date: Mon, 12 Sep 2011 14:04:17 +0800
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
Message-ID: <CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>

Please read the documentation for Bio::Tools::Run::StandAloneBlast
and Bio::AlignIO.*
*
On Mon, Sep 12, 2011 at 1:58 PM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> Ya i know this....And it is also in my use if i get result with lower
> scores.
> But how could I do this?
>
>
> Manju
>


From manju.rawat2 at gmail.com  Mon Sep 12 11:12:40 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Mon, 12 Sep 2011 07:12:40 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
Message-ID: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>

I read this..but default program is not runnig fine.it showing many error
that

MSG: cannot find path to blastall..
Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

Am this this is not showing output which i want..

Pl help me..

Manju Rawat


From arguelloj at gmail.com  Mon Sep 12 02:52:42 2011
From: arguelloj at gmail.com (J. Fernando Arguello)
Date: Sun, 11 Sep 2011 19:52:42 -0700
Subject: [Bioperl-l] BioPerl - quick general question
Message-ID: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>

Dear BioPerl,

I'm excited to see a project like this! Basically I have a computer science
background with a few years of development, research and minimal
bioinformatics experience.

Dumb question...where is the best place for a developer to begin on the
BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
BioPerl in the future?

Any input is much appreciated. Thank you all for your time.

Best,
Fernando
jfa


From briano at bioteam.net  Mon Sep 12 13:20:36 2011
From: briano at bioteam.net (Brian Osborne)
Date: Mon, 12 Sep 2011 09:20:36 -0400
Subject: [Bioperl-l] Fwd: cds sequence extract
References: <112c4ef2.641e.1325c4b21cb.Coremail.maliang7121@163.com>
Message-ID: <671CAF11-55A4-462A-BC5B-805C87E1EB0E@bioteam.net>

Liang Ma,

I'm forwarding this to the Bioperl mailing list.

If you're starting out with Bioperl I suggest you read this:

http://www.bioperl.org/wiki/HOWTO:Beginners

Brian O.


Begin forwarded message:

> From: maliang7121 <maliang7121 at 163.com>
> Date: September 12, 2011 2:20:20 AM EDT
> To: briano at bioteam.net
> Subject: cds sequence extract
> 
> Dear Brian:
> 
> I am a student of Chinese Academy of Sience, I begin to love bioperl, but now I have a problem.
> 
> According to the script of the attachment, I could easily dowload sequences from NCBI, now I need extract cds sequence from the genbank format files, and put them all in a single file using fasta format, I can not do it, could you spend a few minite wrinting a script for me?
> 
> Best!
> 
> Liang Ma
> 
> 
> 

Brian O.
--
Brian Osborne, PhD
BioTeam: http://bioteam.net
email: briano at bioteam.net
mobile: 978-317-3101

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From fs5 at sanger.ac.uk  Mon Sep 12 13:54:21 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Mon, 12 Sep 2011 14:54:21 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
Message-ID: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>

looks like BLAST is not install on your system. The BioPerl module only
runs BLAST for you and parses the output but you still need the BLAST
executables installed on your system. Follow the instructions on the
NCBI website to download and install BLAST and try running it on the
commandline with the "blastall" command. If that works then you can run
it also via BioPerl.
Frank


On Mon, 2011-09-12 at 07:12 -0400, Manju Rawat wrote:
> I read this..but default program is not runnig fine.it showing many error
> that
> 
> MSG: cannot find path to blastall..
> Use of uninitialized value $_[0] in join or string at
> /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> Am this this is not showing output which i want..
> 
> Pl help me..
> 
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From p.j.a.cock at googlemail.com  Mon Sep 12 14:00:30 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Mon, 12 Sep 2011 15:00:30 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>

On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
> looks like BLAST is not install on your system. The BioPerl module only
> runs BLAST for you and parses the output but you still need the BLAST
> executables installed on your system. Follow the instructions on the
> NCBI website to download and install BLAST and try running it on the
> commandline with the "blastall" command. If that works then you can run
> it also via BioPerl.
> Frank

Hang on - blastall is from the "legacy" BLAST suite, does
BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
blastn and blastp rather then blastall)?

Peter


From cjfields at illinois.edu  Mon Sep 12 17:45:56 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Mon, 12 Sep 2011 17:45:56 +0000
Subject: [Bioperl-l] BioPerl - quick general question
In-Reply-To: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
References: <CABGEYBOHXr_9V-zRvMcNfVEXy9e-fx3YWshqa_h2+3CwkeWZEw@mail.gmail.com>
Message-ID: <62B9B300-96AC-4511-A1B9-CFF36CBE6288@illinois.edu>

On Sep 11, 2011, at 9:52 PM, J. Fernando Arguello wrote:

> Dear BioPerl,
> 
> I'm excited to see a project like this! Basically I have a computer science
> background with a few years of development, research and minimal
> bioinformatics experience.
> 
> Dumb question...where is the best place for a developer to begin on the
> BioPerl wiki(s), who is wanting to contribute new code or bug fixes to
> BioPerl in the future?

The basic starting point: the HOWTOs and the tutorial (not sure how up-to-date some of the latter are, in general they should work):

http://www.bioperl.org/wiki/HOWTOs
http://www.bioperl.org/wiki/Tutorials

> Any input is much appreciated. Thank you all for your time.
> 
> Best,
> Fernando
> jfa

We gladly welcome anyone willing to hack on BioPerl.  The repository is now on github (core is https://github.com/bioperl/bioperl-live), so it's fairly easy to fork the code and make changes.  We are in the middle of splitting up the large codebase into more manageable subdistributions, so it's probably a good idea to ask on list about specific code in case the code is question resides in a separate repository.  

Let us know if you have additional questions!

Cheers!

chris




From shalabh.sharma7 at gmail.com  Mon Sep 12 18:00:16 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Mon, 12 Sep 2011 14:00:16 -0400
Subject: [Bioperl-l] Module for SOCS
Message-ID: <CAA7rn9d37ntxbtMUR3Z41JHTNZypi+2jZQunwGJ5bN8DZ21xtg@mail.gmail.com>

Hi All,
         I am using SOCS for mapping my SOILD data. I was just wondering if
there is any module in bioperl to analyze SOCS output files directly or
mapreads format.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From greg at ebi.ac.uk  Tue Sep 13 08:30:58 2011
From: greg at ebi.ac.uk (Gregory Jordan)
Date: Tue, 13 Sep 2011 09:30:58 +0100
Subject: [Bioperl-l] fail to obtain node-to-node distance from a newick
	file
In-Reply-To: <04a601cc700e$4f051d10$ed0f5730$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
Message-ID: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>

Hi Ross,

I don't typically 'install' versions of BioPerl from GitHub. Rather, I check
out the code into a directory that's on my Perl search path (and make sure
any other BioPerl code isn't on the path anymore). I think the following
commands should get you the right set of code:

> git clone git://github.com/bioperl/bioperl-live.git
> git checkout topic/tree_api_refresh

After that, I'm afraid I'll have to leave it to you (or someone else on the
list). I'm no Perl guru, so I don't know the "right" way to direct Perl
towards a developmental BioPerl branch.

Cheers,
 Greg

2011/9/11 Ross KK Leung <ross at cuhk.edu.hk>

> Hi Greg,****
>
> ** **
>
> The values are correct! However, how to install this bioperl-live module?
> my bioperl is 1.6.1 but there's an error:****
>
> ** **
>
> Can't locate object method "find" via package "Bio::Tree::Tree" at
> TreeCalDist.pl line 32, <GEN0> line 1.****
>
> my $mt = $tree->find($keyword);  #line 32****
>
> ** **
>
> ** **
>
> *From:* gjuggler at gmail.com [mailto:gjuggler at gmail.com] *On Behalf Of *Gregory
> Jordan
> *Sent:* 2011?9?10? 23:40
> *To:* bioperl-l List; Ross KK Leung
> *Subject:* Re: [Bioperl-l] fail to obtain node-to-node distance from a
> newick file****
>
> ** **
>
> Hi Ross,****
>
> ** **
>
> Which version of BioPerl are you using?****
>
> ** **
>
> With the refactored tree code (available from the tree_api_refresh branch
> on the BioPerl github repo:
> https://github.com/bioperl/bioperl-live/blob/topic/tree_api_refresh/Bio/Tree/NodeFunctionsI.pm#L406)
> the following script works for me. Do those values look sensible to you? The
> code on the new branch is a bit experimental, so I wouldn't be surprised if
> all the edge cases for calculations like this aren't covered.****
>
> ** **
>
> --greg****
>
> ** **
>
> use Bio::TreeIO;****
>
> ** **
>
> my $treeio = new Bio::TreeIO(-file   => 'temp.nh', -format => "newick");**
> **
>
> my $tree = $treeio->next_tree;****
>
> my $mt = $tree->find("Mycobacterium_tuberculosis_H37Rv");****
>
> my $ms = $tree->find("Mycobacterium_smegmatis_str._MC2_155");****
>
> my $ma = $tree->find("Mycobacterium_abscessus");****
>
> my $distance = $mt->distance($ma);****
>
> print "MT - MA: ".$mt->distance($ma)."\n";****
>
> print "MT - MS: ".$mt->distance($ms)."\n";****
>
> print "MS - MA: ".$ms->distance($ma)."\n";****
>
> # MT - MA: 0.24326****
>
> # MT - MS: 0.18573****
>
> # MS - MA: 0.20729****
>
> ** **
>
> --greg****
>
> ** **
>
> On Sat, Sep 10, 2011 at 7:39 AM, Ross KK Leung <ross at cuhk.edu.hk> wrote:**
> **
>
> I use the following code to derive the distance between two nodes but an
> error "MSG: could not find the lca of supplied nodes; can't find distance
> either"
>
>
>
> What's the problem?
>
>
>
> use Bio::TreeIO;
>
>
>
> ($treefh) = @ARGV;
>
>
>
> my $treeio = new Bio::TreeIO(-file   => $treefh, -format => "newick");
>
> my $tree = $treeio->next_tree;
>
>
>
> $keyword="Mycobacterium_tuberculosis_H37Rv";
>
> my $Tnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_smegmatis_str._MC2_155";
>
> my $Mnodes = $tree->find_node(-id => $keyword);
>
> $keyword="Mycobacterium_abscessus";
>
> my $Anodes = $tree->find_node(-id => $keyword);
>
>
>
> my @root = $tree->get_root_node;
>
> #my $distances = $tree->distance(-nodes => [$node[0],$root]);
>
>
>
> my $distances = $tree->distance(-nodes => [$Tnode,$Mnodes]);
>
> print "Dist:$distances\n";
>
>
>
>
>
> #### the following is the infile
>
>
> (((Mycobacterium_tuberculosis_SUMu006:4.1E-4,(Mycobacterium_tuberculosis_SUM
>
> u002:8.9E-4,Mycobacterium_tuberculosis_SUMu005:1.7E-4)31:1.4E-4)30:1.4E-4,(M
>
> ycobacterium_tuberculosis_SUMu007:4.3E-4,Mycobacterium_tuberculosis_SUMu009:
>
> 1.2E-4)22:1.4E-4)8:1.4E-4,(Mycobacterium_tuberculosis_SUMu004:3.7E-4,Mycobac
>
> terium_tuberculosis_SUMu008:2.0E-4)19:1.0E-4,(Mycobacterium_tuberculosis_SUM
>
> u003:1.4E-4,(((((Mycobacterium_tuberculosis_EAS054:0.00165,(Mycobacterium_tu
>
> berculosis_94_M4241A:0.0011,((Mycobacterium_tuberculosis_T17:0.00257,Mycobac
>
> terium_tuberculosis_KZN_605:0.00259)8:1.9E-4,(Mycobacterium_tuberculosis_'98
>
> -R604_INH-RIF-EM':9.9E-4,(Mycobacterium_tuberculosis_C:0.00293,Mycobacterium
>
> _tuberculosis_str._Haarlem:0.00271)28:1.4E-4)1:1.3E-4)0:1.6E-4)0:1.7E-4)0:1.
>
> 6E-4,(Mycobacterium_tuberculosis_02_1987:0.00186,(Mycobacterium_tuberculosis
>
> _T85:0.00229,Mycobacterium_tuberculosis_210:0.00175)41:1.4E-4)22:1.1E-4)0:1.
>
> 4E-4,(((Mycobacterium_kansasii_ATCC_12478:0.03353,(Mycobacterium_marinum_M:8
>
> .4E-4,Mycobacterium_ulcerans_Agy99:0.00621)100:0.03843)100:0.01058,((Mycobac
>
> terium_leprae_Br4923:1.7E-4,Mycobacterium_leprae_TN:1.6E-4)100:0.07379,(((My
>
> cobacterium_abscessus:0.09172,((Nocardia_farcinica_IFM_10152:0.09312,(Rhodoc
>
> occus_equi_103S:0.04972,((Rhodococcus_erythropolis_PR4:0.00223,Rhodococcus_e
>
> rythropolis_SK121:0.00169)100:0.05311,(Rhodococcus_jostii_RHA1:0.00657,Rhodo
>
> coccus_opacus_B4:0.00665)100:0.03198)100:0.02608)100:0.03679)100:0.0322,(((D
>
> ietzia_cinnamea_P4:0.17703,(Corynebacterium_amycolatum_SK46:0.16548,((Coryne
>
> bacterium_kroppenstedtii_DSM_44385:0.19137,(Corynebacterium_variabile_DSM_44
>
> 702:0.14307,(Corynebacterium_urealyticum_DSM_7109:0.11864,(Corynebacterium_r
>
> esistens_DSM_45100:0.08617,(Corynebacterium_jeikeium_ATCC_43734:0.00292,Cory
>
> nebacterium_jeikeium_K411:0.00277)100:0.08012)100:0.02749)100:0.03867)100:0.
>
> 05776)100:0.02728,((Corynebacterium_glucuronolyticum_ATCC_51866:0.00103,Cory
>
> nebacterium_glucuronolyticum_ATCC_51867:0.00137)100:0.2108,(((Corynebacteriu
>
> m_efficiens_YS-314:0.04795,Corynebacterium_glutamicum_R:0.05369)100:0.07449,
>
> ((Corynebacterium_matruchotii_ATCC_14266:0.00162,Corynebacterium_matruchotii
>
> _ATCC_33806:0.00183)100:0.13467,(Corynebacterium_diphtheriae_NCTC_13129:0.07
>
> 465,((Corynebacterium_pseudotuberculosis_C231:1.6E-4,Corynebacterium_pseudot
>
> uberculosis_I19:1.1E-4)55:1.8E-4,(Corynebacterium_pseudotuberculosis_1002:4.
>
> 2E-4,Corynebacterium_pseudotuberculosis_FRC41:1.2E-4)100:1.3E-4)100:0.0698)1
>
> 00:0.03816)100:0.03537)100:0.01906,((Corynebacterium_ammoniagenes_DSM_20306:
>
> 0.10393,(((Corynebacterium_accolens_ATCC_49725:0.00229,Corynebacterium_accol
>
> ens_ATCC_49726:0.00293)100:0.03941,(Corynebacterium_pseudogenitalium_ATCC_33
>
> 035:0.00268,Corynebacterium_tuberculostearicum_SK141:0.00306)100:0.02483)100
>
> :0.04295,(Corynebacterium_aurimucosum_ATCC_700975:0.05398,Corynebacterium_st
>
> riatum_ATCC_6940:0.05404)100:0.02088)100:0.03132)100:0.05481,(Corynebacteriu
>
> m_genitalium_ATCC_33030:0.09551,Corynebacterium_lipophiloflavum_DSM_44291:0.
>
> 09316)100:0.0783)100:0.03398)100:0.02921)100:0.04667)100:0.02447)100:0.11754
>
> )100:0.06305,(((Pseudonocardia_sp._P1:0.18877,(Saccharopolyspora_erythraea_N
>
> RRL_2338:0.1213,(Actinosynnema_mirum_DSM_43827:0.11851,(Saccharomonospora_vi
>
> ridis_DSM_43017:0.0927,(Amycolatopsis_mediterranei_U32:0.04231,Streptomyces_
>
> sp._AA4:0.04144)100:0.05565)100:0.05467)55:0.01703)100:0.03241)100:0.02581,(
>
> Nakamurella_multipartita_DSM_44233:0.23119,(Geodermatophilus_obscurus_DSM_43
>
> 160:0.21546,((Stackebrandtia_nassauensis_DSM_44728:0.21272,((Salinispora_are
>
> nicola_CNS-205:0.01818,Salinispora_tropica_CNB-440:0.02452)100:0.03265,(Micr
>
> omonospora_sp._ATCC_39149:0.0329,(Micromonospora_aurantiaca_ATCC_27029:0.001
>
> 16,Micromonospora_sp._L5:7.7E-4)100:0.03199)100:0.01352)100:0.11098)100:0.09
>
> 308,((((((Propionibacterium_freudenreichii_subsp._shermanii_CIRM-BIA1:0.2696
>
> 8,(Propionibacterium_acnes_J139:0.00475,(Propionibacterium_acnes_KPA171202:6
>
> .9E-4,(Propionibacterium_acnes_SK187:9.6E-4,(Propionibacterium_acnes_J165:6.
>
> 2E-4,Propionibacterium_acnes_SK137:8.8E-4)100:6.3E-4)100:0.00181)100:0.00315
>
> )100:0.24712)45:0.13659,(Kribbella_flavida_DSM_17836:0.17436,(Nocardioidacea
>
> e_bacterium_Broad-1:0.13638,Nocardioides_sp._JS614:0.08869)100:0.11094)73:0.
>
> 02696)43:0.0456,((Kytococcus_sedentarius_DSM_20547:0.25655,(Dermacoccus_sp._
>
> Ellin185:0.19062,(Intrasporangium_calvum_DSM_43043:0.13866,Janibacter_sp._HT
>
> CC2649:0.1412)100:0.04228)58:0.02864)100:0.06896,(Kineococcus_radiotolerans_
>
> SRS30216:0.21207,((((Propionibacterium_acidifaciens_F0233:1.06116,Rubrobacte
>
> r_xylanophilus_DSM_9941:0.5414)87:0.41816,(((Tropheryma_whipplei_TW08/27:0.0
>
> 0122,Tropheryma_whipplei_str._Twist:9.8E-4)100:0.6263,(Microbacterium_testac
>
> eum_StLB037:0.17489,(Leifsonia_xyli_subsp._xyli_str._CTCB07:0.12936,(marine_
>
> actinobacterium_PHSC20C1:0.15679,(Clavibacter_michiganensis_subsp._michigane
>
> nsis_NCPPB_382:0.00662,Clavibacter_michiganensis_subsp._sepedonicus:0.00756)
>
> 100:0.1194)100:0.03032)100:0.03729)100:0.05755)100:0.10753,((Kocuria_rhizoph
>
> ila_DC2201:0.15484,(Rothia_dentocariosa_M567:0.0599,(Rothia_mucilaginosa_ATC
>
> C_25296:0.00472,Rothia_mucilaginosa_DY-18:0.00351)100:0.05376)100:0.16477)10
>
> 0:0.06018,((Micrococcus_luteus_NCTC_2665:0.0060,Micrococcus_luteus_SK58:0.00
>
> 536)100:0.2105,(Arthrobacter_arilaitensis_Re117:0.19987,(Renibacterium_salmo
>
> ninarum_ATCC_33209:0.11862,(Arthrobacter_aurescens_TC1:0.0397,(Arthrobacter_
>
> sp._FB24:0.03191,(Arthrobacter_chlorophenolicus_A6:0.02327,Arthrobacter_phen
>
> anthrenivorans_Sphe3:0.0208)100:0.01937)100:0.01749)100:0.05605)100:0.05138)
>
> 54:0.02994)100:0.02418)100:0.06667)66:0.02055)2:0.00737,(Brevibacterium_line
>
> ns_BL2:0.16126,Brevibacterium_mcbrellneri_ATCC_49030:0.16657)100:0.16995)18:
>
> 0.03558,(Brachybacterium_faecium_DSM_4810:0.31488,(((Actinomyces_sp._oral_ta
>
> xon_848_str._F0332:0.18095,Arcanobacterium_haemolyticum_DSM_20595:0.23121)10
>
> 0:0.1195,((Actinomyces_urogenitalis_DSM_15434:0.07685,(Actinomyces_sp._oral_
>
> taxon_171_str._F0337:0.01337,(Actinomyces_oris_K20:0.00655,Actinomyces_visco
>
> sus_C505:0.00531)100:0.00537)100:0.07249)100:0.1364,(((Mobiluncus_mulieris_2
>
> 8-1:0.00136,(Mobiluncus_mulieris_ATCC_35243:8.3E-4,(Mobiluncus_mulieris_ATCC
>
> _35239:8.2E-4,Mobiluncus_mulieris_FB024-16:0.00149)77:5.2E-4)68:4.7E-4)100:0
>
> .11036,(Mobiluncus_curtisii_ATCC_51333:0.00379,(Mobiluncus_curtisii_ATCC_430
>
> 63:0.00217,Mobiluncus_curtisii_subsp._holmesii_ATCC_35242:0.00188)100:0.0018
>
> 7)100:0.10314)100:0.23714,(Actinomyces_coleocanis_DSM_15436:0.23053,(Actinom
>
> yces_sp._oral_taxon_178_str._F0338:0.07648,(Actinomyces_sp._oral_taxon_180_s
>
> tr._F0310:0.034,(Actinomyces_odontolyticus_ATCC_17982:0.00322,Actinomyces_od
>
> ontolyticus_F0309:0.00348)100:0.02875)100:0.05144)100:0.13371)100:0.05044)10
>
> 0:0.03821)98:0.03296)99:0.07932,(Beutenbergia_cavernae_DSM_12333:0.17071,(Ce
>
> llulomonas_flavigena_DSM_20109:0.11998,(Xylanimonas_cellulosilytica_DSM_1589
>
> 4:0.13952,(Sanguibacter_keddieii_DSM_10542:0.0926,Jonesia_denitrificans_DSM_
>
> 20603:0.19099)100:0.037)100:0.02528)100:0.03933)100:0.03437)90:0.02763)87:0.
>
> 02582)25:0.02892)16:0.01907)26:0.05274)57:0.03588,(Catenulispora_acidiphila_
>
> DSM_44928:0.19325,((Streptomyces_bingchenggensis_BCW-1:0.02661,(Streptomyces
>
> _hygroscopicus_ATCC_53653:0.02627,Streptomyces_violaceusniger_Tu_4113:0.0226
>
> 6)100:0.0122)100:0.02739,(((Streptomyces_avermitilis_MA-4680:0.02562,((Strep
>
> tomyces_viridochromogenes_DSM_40736:0.02687,((Streptomyces_ghanaensis_ATCC_1
>
> 4672:0.0209,Streptomyces_griseoflavus_Tu4000:0.02075)100:0.01066,(Streptomyc
>
> es_sp._e14:0.03193,(Streptomyces_coelicolor_A3_2_:5.2E-4,Streptomyces_livida
>
> ns_TK24:6.7E-4)100:0.02763)21:0.00492)22:0.00461)100:0.00897,(Streptomyces_s
>
> viceus_ATCC_29083:0.02794,Streptomyces_scabiei_87.22:0.03155)79:0.00685)98:0
>
> .00896)100:0.02063,(Streptomyces_albus_J1074:0.04846,(Streptomyces_sp._SPB74
>
> :0.01027,(Streptomyces_sp._SPB78:0.0027,(Streptomyces_sp._SA3_actF:0.00376,S
>
> treptomyces_sp._SA3_actG:2.4E-4)100:6.7E-4)100:0.00617)100:0.05981)100:0.015
>
> 63)100:0.00959,((Streptomyces_sp._C:0.01998,Streptomyces_sp._Mg1:0.02056)100
>
> :0.0383,(Streptomyces_pristinaespiralis_ATCC_25486:0.03823,(Streptomyces_sp.
>
> _ACTE:0.02415,((Streptomyces_griseus_subsp._griseus_NBRC_13350:4.1E-4,Strept
>
> omyces_sp._ACT-1:5.2E-4)100:0.00769,(Streptomyces_roseosporus_NRRL_11379:2.2
>
> E-4,Streptomyces_roseosporus_NRRL_15998:0.00209)100:0.00782)100:0.017)100:0.
>
> 02297)60:0.00742)100:0.00985)100:0.0215)100:0.11349)100:0.05)46:0.02214,(Aci
>
> dothermus_cellulolyticus_11B:0.25166,((Nocardiopsis_dassonvillei_subsp._dass
>
> onvillei_DSM_43111:0.11961,Thermobifida_fusca_YX:0.09198)100:0.09418,(Thermo
>
> monospora_curvata_DSM_43183:0.12535,(Streptosporangium_roseum_DSM_43021:0.09
>
> 754,Thermobispora_bispora_DSM_43833:0.08434)100:0.06253)100:0.0273)100:0.045
>
> 43)74:0.02856)40:0.02885,(Frankia_symbiont_of_Datisca_glomerata:0.09569,(Fra
>
> nkia_sp._EuI1c:0.10847,((Frankia_alni_ACN14a:0.0351,Frankia_sp._CcI3:0.03651
>
> )100:0.04249,(Frankia_sp._EAN1pec:0.03101,Frankia_sp._EUN1f:0.0394)100:0.046
>
> 88)100:0.02188)100:0.03014)100:0.16741)88:0.0315)65:0.02571)88:0.05354)88:0.
>
> 03348)88:0.06784,(Segniliparus_rotundus_DSM_44985:0.04795,Segniliparus_rugos
>
> us_ATCC_BAA-974:0.03891)100:0.23144)81:0.0205)88:0.02214,(Tsukamurella_pauro
>
> metabola_DSM_20162:0.13958,(Gordonia_bronchialis_DSM_43247:0.08238,Gordonia_
>
> neofelifaecis_NRRL_B-59395:0.10412)100:0.06124)100:0.03199)84:0.01596)88:0.0
>
> 6919)88:0.04069,(Mycobacterium_smegmatis_str._MC2_155:0.05174,((Mycobacteriu
>
> m_sp._JLS:0.00135,(Mycobacterium_sp._KMS:1.4E-4,Mycobacterium_sp._MCS:2.3E-4
>
> )100:0.00177)100:0.04943,(Mycobacterium_vanbaalenii_PYR-1:0.02631,(Mycobacte
>
> rium_gilvum_PYR-GCK:0.0011,Mycobacterium_sp._Spyr1:9.2E-4)100:0.03388)100:0.
>
> 03536)100:0.01213)100:0.02314)88:0.04937,(Mycobacterium_parascrofulaceum_ATC
>
> C_BAA-614:0.02796,(Mycobacterium_intracellulare_ATCC_13950:0.02159,(Mycobact
>
> erium_avium_subsp._paratuberculosis_K-10:0.0020,(Mycobacterium_avium_104:0.0
>
> 032,Mycobacterium_avium_subsp._avium_ATCC_25291:0.00216)91:6.3E-4)100:0.0194
>
> 3)100:0.01235)100:0.0158)88:0.01054)62:0.0066)88:0.04218,(Mycobacterium_tube
>
> rculosis_T46:7.6E-4,(Mycobacterium_tuberculosis_CPHL_A:5.8E-4,(Mycobacterium
>
> _tuberculosis_K85:8.0E-4,(Mycobacterium_bovis_AF2122/97:1.4E-4,(Mycobacteriu
>
> m_bovis_BCG_str._Pasteur_1173P2:1.4E-4,Mycobacterium_bovis_BCG_str._Tokyo_17
>
> 2:1.4E-4)100:1.3E-4)100:1.8E-4)38:1.1E-4)33:1.4E-4)0:1.4E-4)1:1.5E-4)0:1.5E-
>
> 4,(Mycobacterium_tuberculosis_CDC1551:2.2E-4,(Mycobacterium_tuberculosis_T92
>
> :0.00262,Mycobacterium_tuberculosis_GM_1503:0.00427)3:1.3E-4)0:1.4E-4)13:1.4
>
> E-4,(((Mycobacterium_tuberculosis_SUMu012:8.5E-4,(Mycobacterium_tuberculosis
>
> _H37Ra_WGS_:0.00109,(Mycobacterium_tuberculosis_H37Ra:1.4E-4,Mycobacterium_t
>
> uberculosis_H37Rv:1.4E-4)58:1.4E-4)41:1.4E-4)72:1.4E-4,(Mycobacterium_tuberc
>
> ulosis_SUMu001:2.9E-4,(Mycobacterium_tuberculosis_SUMu010:1.1E-4,Mycobacteri
>
> um_tuberculosis_SUMu011:8.7E-4)58:1.4E-4)65:1.6E-4)61:0.00102,(Mycobacterium
>
> _tuberculosis_F11:1.1E-4,((Mycobacterium_tuberculosis_KZN_4207:1.4E-4,Mycoba
>
> cterium_tuberculosis_KZN_R506:1.4E-4)58:1.4E-4,(Mycobacterium_tuberculosis_K
>
> ZN_1435:1.4E-4,Mycobacterium_tuberculosis_KZN_V2475:1.4E-4)74:1.4E-4)78:1.1E
> -4)36:1.4E-4)3:1.4E-4)46:1.4E-4)4:1.4E-4)88;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l****
>
> ** **
>



From manju.rawat2 at gmail.com  Tue Sep 13 11:20:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Tue, 13 Sep 2011 07:20:07 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>

this is the perl code

 #!usr/bin/perl -w
use Bio::Perl;
use Bio::SearchIO
use Bio::Tools::Run::StandAloneBlast;
 @params = ('database' => 'swissprot',
        'READMETHOD' => 'Blastn');

 $factory = Bio::Tools::Run::StandAloneBlast->new(@params);


 $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
 $blast_report = $factory->blastall($input);


  write_blast(">rs.blast",$blast_report);


It showing error that


Use of uninitialized value $_[0] in join or string at
/usr/share/perl/5.10/File/Spec/Unix.pm line 41.

MSG: cannot find path to blastall


From fs5 at sanger.ac.uk  Tue Sep 13 15:09:24 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Tue, 13 Sep 2011 16:09:24 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
Message-ID: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>

Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
StandAloneBlast is still set to "blastall" - I'm not sure if it works
with blast+ too.

Manju: as I said previously, you need to check that you can run BLAST on
the command line, i.e. make sure it is actually installed on your
system. Have you done that?
You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
you can manually set the path to your BLAST executable if it is not in
your path. You have to install BLAST fisrt before you can run this
module.
The other error you get from yuor code refers to something that is
outside of the code fragment you show here, so can't comment on that
one.

Frank


On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> this is the perl code
> 
>  #!usr/bin/perl -w
> use Bio::Perl;
> use Bio::SearchIO
> use Bio::Tools::Run::StandAloneBlast;
>  @params = ('database' => 'swissprot', 
>         'READMETHOD' => 'Blastn');
> 
>  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> 
> 
>  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
>  $blast_report = $factory->blastall($input);
>  
> 
>   write_blast(">rs.blast",$blast_report);
> 
> 
> It showing error that
> 
> 
> Use of uninitialized value $_[0] in join or string
> at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> 
> MSG: cannot find path to blastall
> 
>  



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From David.Messina at sbc.su.se  Tue Sep 13 15:34:20 2011
From: David.Messina at sbc.su.se (Dave Messina)
Date: Tue, 13 Sep 2011 17:34:20 +0200
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAM3TQQWx_QQK96etWHntvmRRnjJ9ZPCJYMcC0rukNoJD5_et1w@mail.gmail.com>

There's a separate Bio::Tools::Run::BlastPlus module for blast+. And a
related HOWTO:
http://www.bioperl.org/wiki/HOWTO:BlastPlus



On Tue, Sep 13, 2011 at 17:09, Frank Schwach <fs5 at sanger.ac.uk> wrote:

> Peter: in BioPerl 1.6 the default executable name in Bio::Tools::Run
> StandAloneBlast is still set to "blastall" - I'm not sure if it works
> with blast+ too.
>
> Manju: as I said previously, you need to check that you can run BLAST on
> the command line, i.e. make sure it is actually installed on your
> system. Have you done that?
> You can also check the Bio::Tools::Run::StandAloneBlast docs to see how
> you can manually set the path to your BLAST executable if it is not in
> your path. You have to install BLAST fisrt before you can run this
> module.
> The other error you get from yuor code refers to something that is
> outside of the code fragment you show here, so can't comment on that
> one.
>
> Frank
>
>
> On Tue, 2011-09-13 at 07:20 -0400, Manju Rawat wrote:
> > this is the perl code
> >
> >  #!usr/bin/perl -w
> > use Bio::Perl;
> > use Bio::SearchIO
> > use Bio::Tools::Run::StandAloneBlast;
> >  @params = ('database' => 'swissprot',
> >         'READMETHOD' => 'Blastn');
> >
> >  $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> >
> >
> >  $input = Bio::Seq->new(-id=>"testquery",-seq=>"gatcgtataccgtacagct");
> >  $blast_report = $factory->blastall($input);
> >
> >
> >   write_blast(">rs.blast",$blast_report);
> >
> >
> > It showing error that
> >
> >
> > Use of uninitialized value $_[0] in join or string
> > at /usr/share/perl/5.10/File/Spec/Unix.pm line 41.
> >
> > MSG: cannot find path to blastall
> >
> >
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From cjfields at illinois.edu  Tue Sep 13 19:36:21 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 13 Sep 2011 19:36:21 +0000
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
Message-ID: <6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>

On Sep 12, 2011, at 9:00 AM, Peter Cock wrote:

> On Mon, Sep 12, 2011 at 2:54 PM, Frank Schwach <fs5 at sanger.ac.uk> wrote:
>> looks like BLAST is not install on your system. The BioPerl module only
>> runs BLAST for you and parses the output but you still need the BLAST
>> executables installed on your system. Follow the instructions on the
>> NCBI website to download and install BLAST and try running it on the
>> commandline with the "blastall" command. If that works then you can run
>> it also via BioPerl.
>> Frank
> 
> Hang on - blastall is from the "legacy" BLAST suite, does
> BioPerl still talk to that or the new BLAST+ suite (e.g. binaries
> blastn and blastp rather then blastall)?
> 
> Peter

(aside: thought I sent this the other day.  never mix grant writing and open source)

Both BLAST and BLAST+ are supported via different modules.  Some users don't want to use BLAST+ for various reasons, though this may soon be out of their control when NCBI eventually stops supporting legacy BLAST entirely.

chris




From manju.rawat2 at gmail.com  Wed Sep 14 11:32:19 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 14 Sep 2011 07:32:19 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<6570DEC6-B485-44B0-868A-AAC6329B3224@illinois.edu>
	<CAB2c7ypU_0oY_VG-9EQgNyWU3aVwh=+Jh2E7RTpDvVfDb52nig@mail.gmail.com>
Message-ID: <CAB2c7yqZ0Eb=7=GTiXidD-6_UzF8qB1JBVv+5h6+8xsR84HXuQ@mail.gmail.com>

On Wed, Sep 14, 2011 at 7:31 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:

> I am trying to install Blast+ in my system.(ubuntu) from this link
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html.
> but i am getting error..
>
> first i downloaded the blast(ncbi-blast-2.2.25+-ia32-linux.tar.gz) from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
> .  and then extract it in the home/abc/ folder.
> after that i set the path for configuration in terminal i.e
>
> *PATH=$PATH:/home/abc/blast-2.2.25+/bin*
>
>
> but when i am  running blast -help in terminal it showing me error that
>
> error while loading shared libraries:
>  libbz2.so.1: cannot open shared object file: No such file or directory.
>
>


-- 
Regards
Manju Rawat
Project Assistant(NAIP)
Genomics Lab
ABTC,NDRI Karnal-132001,Haryana


From kumarsaurabh20 at gmail.com  Thu Sep 15 11:20:47 2011
From: kumarsaurabh20 at gmail.com (kumar Saurabh)
Date: Thu, 15 Sep 2011 13:20:47 +0200
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
Message-ID: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>

Hi,

I need to integrate the primer3 module in one of our pipeline. In a process,
I was testing the initial code given on the CPAN website. But whenever I try
to run this program its giving me error...that "Cannot locate the Object
method add_target via the package Bio::Tools:Run::Primer3Redux...."

The line of codes I am using is as follows:

# design some primers.
  # the output will be put into temp.out
  use Bio::Tools::Primer3Redux;
  use Bio::Tools::Run::Primer3Redux;
  use Bio::SeqIO;

  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
  my $seq = $seqio->next_seq;

  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
                                            -path =>
"/home/singh/Downloads/primer3-2.2.3/src/primer3_core");

  # or after the fact you can change the program_name
  $primer3->program_name('my_superfast_primer3');

  unless ($primer3->executable) {
    print STDERR "primer3 can not be found. Is it installed?\n";
    exit(-1)
  }

  # set the maximum and minimum Tm of the primer
  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);

  # Design the primers. This runs primer3 and returns a
  # Bio::Tools::Primer3::result object with the results
  # Primer3 can run in several modes (see explanation for
  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
  # either call it by its PRIMER_TASK name as in these examples:
  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
  $check_results = $primer3->check_primers();

  # Alternatively, explicitly set the PRIMER_TASK parameter and
  # use the generic 'run' method (this is mainly here for backwards
  # compatibility) :
  $primer3->PRIMER_TASK( 'pick_left_only' );
  $result = $primer3->run( $seq );

  # If no task is set and the 'run' method is called, primer3 will default
to
  # pick pcr primers.

  # see the Bio::Tools::Primer3Redux POD for
  # things that you can get from this. For example:

  print "There were ", $results->num_primer_pairs, " primer pairs\n";


Can anyone help me with this???


Best regards,
Kumar


From fs5 at sanger.ac.uk  Thu Sep 15 13:44:03 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 14:44:03 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
Message-ID: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>

Hi Kumar,

We are currently working on this module and you might want to check out
the latest version on Chris Field's github project:

https://github.com/cjfields/Bio-Tools-Primer3Redux

There will probably be some changes again once I get some time again to
work on a few points we discussed lately. You can also check out my repo
here:
https://github.com/fschwach/Bio-Tools-Primer3Redux

but I will certainly have to make changes to that code because I used
AUTOLAD in the last version, which is probably not a good idea.
My recommendation would be to use Chris' repo and see if that works for
you. If not, feedback would be much appreciated.

Cheers,

Frank




On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> Hi,
> 
> I need to integrate the primer3 module in one of our pipeline. In a process,
> I was testing the initial code given on the CPAN website. But whenever I try
> to run this program its giving me error...that "Cannot locate the Object
> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> 
> The line of codes I am using is as follows:
> 
> # design some primers.
>   # the output will be put into temp.out
>   use Bio::Tools::Primer3Redux;
>   use Bio::Tools::Run::Primer3Redux;
>   use Bio::SeqIO;
> 
>   my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>   my $seq = $seqio->next_seq;
> 
>   my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>                                             -path =>
> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> 
>   # or after the fact you can change the program_name
>   $primer3->program_name('my_superfast_primer3');
> 
>   unless ($primer3->executable) {
>     print STDERR "primer3 can not be found. Is it installed?\n";
>     exit(-1)
>   }
> 
>   # set the maximum and minimum Tm of the primer
>   $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> 
>   # Design the primers. This runs primer3 and returns a
>   # Bio::Tools::Primer3::result object with the results
>   # Primer3 can run in several modes (see explanation for
>   # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>   # either call it by its PRIMER_TASK name as in these examples:
>   $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>   $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>   $check_results = $primer3->check_primers();
> 
>   # Alternatively, explicitly set the PRIMER_TASK parameter and
>   # use the generic 'run' method (this is mainly here for backwards
>   # compatibility) :
>   $primer3->PRIMER_TASK( 'pick_left_only' );
>   $result = $primer3->run( $seq );
> 
>   # If no task is set and the 'run' method is called, primer3 will default
> to
>   # pick pcr primers.
> 
>   # see the Bio::Tools::Primer3Redux POD for
>   # things that you can get from this. For example:
> 
>   print "There were ", $results->num_primer_pairs, " primer pairs\n";
> 
> 
> Can anyone help me with this???
> 
> 
> Best regards,
> Kumar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From cjfields at illinois.edu  Thu Sep 15 14:13:38 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 15 Sep 2011 14:13:38 +0000
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>

I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 

chris

On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:

> Hi Kumar,
> 
> We are currently working on this module and you might want to check out
> the latest version on Chris Field's github project:
> 
> https://github.com/cjfields/Bio-Tools-Primer3Redux
> 
> There will probably be some changes again once I get some time again to
> work on a few points we discussed lately. You can also check out my repo
> here:
> https://github.com/fschwach/Bio-Tools-Primer3Redux
> 
> but I will certainly have to make changes to that code because I used
> AUTOLAD in the last version, which is probably not a good idea.
> My recommendation would be to use Chris' repo and see if that works for
> you. If not, feedback would be much appreciated.
> 
> Cheers,
> 
> Frank
> 
> 
> 
> 
> On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
>> Hi,
>> 
>> I need to integrate the primer3 module in one of our pipeline. In a process,
>> I was testing the initial code given on the CPAN website. But whenever I try
>> to run this program its giving me error...that "Cannot locate the Object
>> method add_target via the package Bio::Tools:Run::Primer3Redux...."
>> 
>> The line of codes I am using is as follows:
>> 
>> # design some primers.
>>  # the output will be put into temp.out
>>  use Bio::Tools::Primer3Redux;
>>  use Bio::Tools::Run::Primer3Redux;
>>  use Bio::SeqIO;
>> 
>>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>>  my $seq = $seqio->next_seq;
>> 
>>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>>                                            -path =>
>> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
>> 
>>  # or after the fact you can change the program_name
>>  $primer3->program_name('my_superfast_primer3');
>> 
>>  unless ($primer3->executable) {
>>    print STDERR "primer3 can not be found. Is it installed?\n";
>>    exit(-1)
>>  }
>> 
>>  # set the maximum and minimum Tm of the primer
>>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
>> 
>>  # Design the primers. This runs primer3 and returns a
>>  # Bio::Tools::Primer3::result object with the results
>>  # Primer3 can run in several modes (see explanation for
>>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>>  # either call it by its PRIMER_TASK name as in these examples:
>>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>>  $check_results = $primer3->check_primers();
>> 
>>  # Alternatively, explicitly set the PRIMER_TASK parameter and
>>  # use the generic 'run' method (this is mainly here for backwards
>>  # compatibility) :
>>  $primer3->PRIMER_TASK( 'pick_left_only' );
>>  $result = $primer3->run( $seq );
>> 
>>  # If no task is set and the 'run' method is called, primer3 will default
>> to
>>  # pick pcr primers.
>> 
>>  # see the Bio::Tools::Primer3Redux POD for
>>  # things that you can get from this. For example:
>> 
>>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
>> 
>> 
>> Can anyone help me with this???
>> 
>> 
>> Best regards,
>> Kumar
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> -- 
> The Wellcome Trust Sanger Institute is operated by Genome Research 
> Limited, a charity registered in England with number 1021457 and a 
> company registered in England with number 2742969, whose registered 
> office is 215 Euston Road, London, NW1 2BE. 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From fs5 at sanger.ac.uk  Thu Sep 15 14:43:48 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Thu, 15 Sep 2011 15:43:48 +0100
Subject: [Bioperl-l] issue with Bio::Tools::Run::Primer3Redux
In-Reply-To: <D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
References: <CAJxEoEADJADMiL0NaKPejaZgyxzn-6700z+ROv9zhbCa7EJJJg@mail.gmail.com>
	<1316094243.3797.669.camel@deskpro15336.internal.sanger.ac.uk>
	<D31419E8-2CC3-4A78-9D76-7D5D91655D59@illinois.edu>
Message-ID: <1316097828.3797.700.camel@deskpro15336.internal.sanger.ac.uk>

I also haven't had the time yet to work on this again but, yes, we need
to make sure we don't loose track of where we are. 


On Thu, 2011-09-15 at 14:13 +0000, Fields, Christopher J wrote:
> I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 
> 
> chris
> 
> On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:
> 
> > Hi Kumar,
> > 
> > We are currently working on this module and you might want to check out
> > the latest version on Chris Field's github project:
> > 
> > https://github.com/cjfields/Bio-Tools-Primer3Redux
> > 
> > There will probably be some changes again once I get some time again to
> > work on a few points we discussed lately. You can also check out my repo
> > here:
> > https://github.com/fschwach/Bio-Tools-Primer3Redux
> > 
> > but I will certainly have to make changes to that code because I used
> > AUTOLAD in the last version, which is probably not a good idea.
> > My recommendation would be to use Chris' repo and see if that works for
> > you. If not, feedback would be much appreciated.
> > 
> > Cheers,
> > 
> > Frank
> > 
> > 
> > 
> > 
> > On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> >> Hi,
> >> 
> >> I need to integrate the primer3 module in one of our pipeline. In a process,
> >> I was testing the initial code given on the CPAN website. But whenever I try
> >> to run this program its giving me error...that "Cannot locate the Object
> >> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> >> 
> >> The line of codes I am using is as follows:
> >> 
> >> # design some primers.
> >>  # the output will be put into temp.out
> >>  use Bio::Tools::Primer3Redux;
> >>  use Bio::Tools::Run::Primer3Redux;
> >>  use Bio::SeqIO;
> >> 
> >>  my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
> >>  my $seq = $seqio->next_seq;
> >> 
> >>  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
> >>                                            -path =>
> >> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> >> 
> >>  # or after the fact you can change the program_name
> >>  $primer3->program_name('my_superfast_primer3');
> >> 
> >>  unless ($primer3->executable) {
> >>    print STDERR "primer3 can not be found. Is it installed?\n";
> >>    exit(-1)
> >>  }
> >> 
> >>  # set the maximum and minimum Tm of the primer
> >>  $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> >> 
> >>  # Design the primers. This runs primer3 and returns a
> >>  # Bio::Tools::Primer3::result object with the results
> >>  # Primer3 can run in several modes (see explanation for
> >>  # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
> >>  # either call it by its PRIMER_TASK name as in these examples:
> >>  $pcr_primer_results = $primer3->pick_pcr_primers($seq);
> >>  $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
> >>  $check_results = $primer3->check_primers();
> >> 
> >>  # Alternatively, explicitly set the PRIMER_TASK parameter and
> >>  # use the generic 'run' method (this is mainly here for backwards
> >>  # compatibility) :
> >>  $primer3->PRIMER_TASK( 'pick_left_only' );
> >>  $result = $primer3->run( $seq );
> >> 
> >>  # If no task is set and the 'run' method is called, primer3 will default
> >> to
> >>  # pick pcr primers.
> >> 
> >>  # see the Bio::Tools::Primer3Redux POD for
> >>  # things that you can get from this. For example:
> >> 
> >>  print "There were ", $results->num_primer_pairs, " primer pairs\n";
> >> 
> >> 
> >> Can anyone help me with this???
> >> 
> >> 
> >> Best regards,
> >> Kumar
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > 
> > 
> > -- 
> > The Wellcome Trust Sanger Institute is operated by Genome Research 
> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose registered 
> > office is 215 Euston Road, London, NW1 2BE. 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From manju.rawat2 at gmail.com  Fri Sep 16 05:09:25 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:09:25 -0400
Subject: [Bioperl-l] no blast result
In-Reply-To: <1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
Message-ID: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>

Hello Frank,

Yes,u r rite..I tried to run blast in terminal but its not working..
I have installed the latest version of blast and download the database
correctly..

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.
Manju


From manju.rawat2 at gmail.com  Fri Sep 16 05:12:03 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Fri, 16 Sep 2011 01:12:03 -0400
Subject: [Bioperl-l] Command line error in BLAST+
Message-ID: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>

Hi,


I have installed the latest version of blast and download the database
correctly Using this tutorial
http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html

But when i running blastn-help command in terminal it showing me error that
blastn: error while loading shared libraries: libbz2.so.1: cannot open
shared object file: No such file or directory.


and when i am running the blastall command then it showing that
*legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
legacy_blast.pl line 85.
Program failed, try executing the command manually.

While i have set the path of environment variable
PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin

I have checked everything but not able tp fine the error..

Pl help me.

Thanks
Manju


From p.j.a.cock at googlemail.com  Fri Sep 16 08:15:46 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:15:46 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <CAKVJ-_4UF=5oBNc-ZRESAXzO-tC2j+nQGn0Qjh4E51Yrvr2o3A@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:12 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hi,
>
>
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
>
> Thanks
> Manju

You're using the BioPerl wrapper for legacy blast (blastall),
which is not installed. Instead you have the new blast+
suite which includes a wrapper using the perl script
legacy_blast.pl to imitate the old blastall tool (in this
case it calls the new tool blastn).

Fix 1: Edit legacy_blast.pl to use the path to blastn etc
under your home directory

Fix 2: Install BLAST+ at system level

Fix 3: Use the BioPerl wrapper for BLAST+ instead.

I'd go with option 3.

Peter


From p.j.a.cock at googlemail.com  Fri Sep 16 08:17:58 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Fri, 16 Sep 2011 09:17:58 +0100
Subject: [Bioperl-l] no blast result
In-Reply-To: <CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
References: <CAB2c7ypO-cBWbZbwG+MtsLR1Q4hHjgKaLCbmqyGfPbeavb4eLA@mail.gmail.com>
	<CAKWOQSZSFie6=XzHtoA6nitnxuRMQ=0HV+Xaz591ryUsjaa=Cg@mail.gmail.com>
	<CAB2c7yo38O2tJoHMRZi3OP-v=QWRd=GfOc6MruLCYb1ODXt6KQ@mail.gmail.com>
	<CAKWOQSYgRNuZnmfB17qNtKf0aC3t5CsCcXqZTVatL5JnX6KOVQ@mail.gmail.com>
	<CAB2c7yqbw+hBGooWAMr7LA5=i5fTz1UNZe6DG9_XMa+Z=LB94g@mail.gmail.com>
	<CAB2c7yrrT9RsMe6Do02DiobcM22cA0Pn2Td_67=t2xWNLYUvyA@mail.gmail.com>
	<1315835661.3797.563.camel@deskpro15336.internal.sanger.ac.uk>
	<CAKVJ-_6nF6U0PNU2HPew6ra_Jbzd-K51UPgMT=jONMdwK32CcA@mail.gmail.com>
	<CAB2c7yoDagmEpXJ2zjDmXY+SWJ8=UfjhNe=q5kEp79svTeN9uQ@mail.gmail.com>
	<1315926565.3797.587.camel@deskpro15336.internal.sanger.ac.uk>
	<CAB2c7yoTh2hZQYWNOoTZjmYDWvnBc5-YQA1+++vkA+AkCYwUDA@mail.gmail.com>
Message-ID: <CAKVJ-_5Omy7h9qx++7S-46YrxFTxbGoQZu61GDgM12C2FmQJsQ@mail.gmail.com>

On Fri, Sep 16, 2011 at 6:09 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello Frank,
>
> Yes,u r rite..I tried to run blast in terminal but its not working..
> I have installed the latest version of blast and download the database
> correctly..
>
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
>
>
> and when i am running the blastall command then it showing that
> legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out
> Can't exec "/usr/bin/blastn": No such file or directory at
> /usr/bin/legacy_blast.pl line 85.
> Program failed, try executing the command manually.
>
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
>
> I have checked everything but not able tp fine the error..
>
> Pl help me.
> Manju

For the benefit of anyone reading the archives later,
I tried to answer this in Manju's new thread:
http://lists.open-bio.org/pipermail/bioperl-l/2011-September/035696.html

Peter


From fs5 at sanger.ac.uk  Fri Sep 16 08:36:37 2011
From: fs5 at sanger.ac.uk (Frank Schwach)
Date: Fri, 16 Sep 2011 09:36:37 +0100
Subject: [Bioperl-l] Command line error in BLAST+
In-Reply-To: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
References: <CAB2c7yoTdVK981R3cR_cEmTHJ4oTAM9h4xKE=9in=eohhTGLVA@mail.gmail.com>
Message-ID: <1316162197.3797.721.camel@deskpro15336.internal.sanger.ac.uk>

Hi Manju,

Are you on Ubuntu? I think I've seen problems with this bzip library on
Ubuntu before. It's not a problem with BLAST in any case. 
Should be possible to install the missing files through your package
manager. I'm sure Google will know what to do :)
Not sure what went wrong with your blast installation. What happens if
you run blastall directly (without the legacy_blast.pl script)? In any
case, it might be better to ask the NCBI people for help with the BLAST
installation as this is not a BioPerl problem.

cheers,

Frank


On Fri, 2011-09-16 at 01:12 -0400, Manju Rawat wrote:
> Hi,
> 
> 
> I have installed the latest version of blast and download the database
> correctly Using this tutorial
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html
> 
> But when i running blastn-help command in terminal it showing me error that
> blastn: error while loading shared libraries: libbz2.so.1: cannot open
> shared object file: No such file or directory.
> 
> 
> and when i am running the blastall command then it showing that
> *legacy_blast.pl blastall -p blastn -i amino.fa -d nr -o blast.out*
> Can't exec "/usr/bin/blastn": No such file or directory at /usr/bin/
> legacy_blast.pl line 85.
> Program failed, try executing the command manually.
> 
> While i have set the path of environment variable
> PATH=$PATH:/home/abc/ncbi-blast-2.2.25+/bin
> 
> I have checked everything but not able tp fine the error..
> 
> Pl help me.
> 
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From ross at cuhk.edu.hk  Fri Sep 16 08:51:38 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Fri, 16 Sep 2011 16:51:38 +0800
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
Message-ID: <085501cc744d$d90b4500$8b21cf00$@edu.hk>

I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!

 




From cjfields at illinois.edu  Fri Sep 16 13:22:07 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 16 Sep 2011 13:22:07 +0000
Subject: [Bioperl-l] use blast to extract similar sequences
In-Reply-To: <085501cc744d$d90b4500$8b21cf00$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
Message-ID: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>

That seems like a pretty straightforward thing to do; there isn't an all-in-one way of doing this, but that's a good thing (it's a separation of concerns).

1) Run and parse BLAST results and grab seqID and coordinates for each hit (or each HSP for each hit) (Bio::SearchIO)
2) Pull the right subsequence +/- 20bp using above from the indexed flat file of your reference (Bio::DB::Fasta)

You can get revcomped sequence from Bio::DB::Fasta directly by flipping coordinates:
  
  # raw sequence
  my $seq      = $db->seq('CHROMOSOME_I',4_000_000 => 4_100_000);
  my $revseq   = $db->seq('CHROMOSOME_I',4_100_000 => 4_000_000);

chris


On Sep 16, 2011, at 3:51 AM, Ross KK Leung wrote:

> I wonder whether bioperl has any built-in modules that extracts sequences based on blast results. For example, a short query sequence of length 1000 is to blast against a reference genome of 3M. The homologous sequence of 1000 +/-  20 is extracted. Why is +/- 20 needed? Because we can't guarantee there must have a good match. Frequent blast users may be well aware that then there can be coverage, split-up due to local alignments, etc and that's why I would like to know if anybody has already developed a module to handle this kind of problem. Thanks in advance!
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From wsavigne at yahoo.com  Fri Sep 16 20:45:12 2011
From: wsavigne at yahoo.com (Willy Savigne)
Date: Fri, 16 Sep 2011 13:45:12 -0700 (PDT)
Subject: [Bioperl-l] question Bioperl installation
Message-ID: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>

my name is william how do download Bioperl i tried other site but NOTHING? i would like to know info in downloading? bioperl .This is my first? time into knowing? bioinformatic i? just got? a book developing bioinformatic and begginning perl bioinformatic. I do alot Dna and RNA sequencing?? and more.
?
Thank u willy


From ross at cuhk.edu.hk  Sun Sep 18 10:51:05 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Sun, 18 Sep 2011 18:51:05 +0800
Subject: [Bioperl-l] snp/frameshift identification
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <08a901cc75f0$dd463b30$97d2b190$@edu.hk>

Dear Bioperl-users,

Following Fields, Christopher J's advice on sequence extraction, I manage to
proceed to the last stage of non-synonymous SNP identification. Now what I
have in hand is thousands of reliable multiple sequence alignment files,
e.g.

>seq1
ATGACAGACACGACGTTGCCGTAG
>seq2
ATGACAGACACGACGTAGCCGTAG
>seq3
ATGACAGACACGACGTTGCCGTAG

Seq2 has a T->A mutation and that leads to a stop codon generation. I wonder
if Bioperl has handled this kind of SNP or frameshift or non-sense mutations
that lead to change of amino acid in the translated protein product.

Thanks again to the community that helps me a great deal so I can catch up
progress during this Sat/Sun!!



From rondonbio at yahoo.com.br  Mon Sep 19 13:46:36 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Mon, 19 Sep 2011 06:46:36 -0700 (PDT)
Subject: [Bioperl-l] help-> SearchIO
Message-ID: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>

Hi guys! I need your help in a loop that I have in SearchIO.
I need to check the nucleotide coverage of querys using BLAST. I'm using the script below. It's open the alignment, create arrays for each query with zeros in each nucleotide position but, when I adds values to the coverage of each nucleotide, the script does it once and passes to another query.
Can you hek me?
Thank you very much,

Rondon
a Brazilian friend.


use Bio::SearchIO;
?
my $alignment = new Bio::SearchIO ( -format => 'blastXML',
? ? ? ? ? ? ? ? ? ? ? ? ?? ? -file ? => $alignment_file );

my %positions;
while (my $result = $alignment->next_result) {
while (my $hit = $result->next_hit) {
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
my @pos = $hsp->seq_inds('query','identical');
for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
foreach my $num (@pos) {
${$positions{$query_name}}[$num -1]++; ? ?#This loop is where I believe that is an error.
}
}
}
}

foreach my $key (keys %positions){
print "$key\t@{$positions{$key}}\n";
}

exit;



From roy.chaudhuri at gmail.com  Mon Sep 19 16:29:41 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:29:41 +0100
Subject: [Bioperl-l] help-> SearchIO
In-Reply-To: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
References: <1316439996.6247.YahooMailNeo@web130220.mail.mud.yahoo.com>
Message-ID: <4E776DF5.6040504@gmail.com>

Hi Rondon,

The line where you populate your arrayref with 0 (starting "for 
(0..$tam)") is within the HSP loop, so the data from every successive 
HSP will overwrite the previous one in your hash. You will therefore 
only see the data for the last HSP from each query. If you move that 
line to execute once per result (i.e. just after the line starting 
"while (my result ="), then I think it should work as you intended.

Cheers,
Roy.

On 19/09/2011 14:46, Rondon Neto wrote:
> Hi guys! I need your help in a loop that I have in SearchIO. I need
> to check the nucleotide coverage of querys using BLAST. I'm using the
> script below. It's open the alignment, create arrays for each query
> with zeros in each nucleotide position but, when I adds values to the
> coverage of each nucleotide, the script does it once and passes to
> another query. Can you hek me? Thank you very much,
>
> Rondon a Brazilian friend.
>
> use Bio::SearchIO;
>
> my $alignment = new Bio::SearchIO ( -format =>  'blastXML',
>                               -file   =>  $alignment_file );
>
> my %positions;
> while (my $result = $alignment->next_result) {
> while (my $hit = $result->next_hit) {
> while (my $hsp = $hit->next_hsp) {
> my $query_name = $result->query_name();
> my $tam = $result ->  query_length();
> my @pos = $hsp->seq_inds('query','identical');
> for (0..$tam){ ${$positions{$query_name}}[$_] = 0 } # make arrays for each query and populate with 0 in each position
> foreach my $num (@pos) {
> ${$positions{$query_name}}[$num -1]++;    #This loop is where I believe that is an error.
> }
> }
> }
> }
>
> foreach my $key (keys %positions){
> print "$key\t@{$positions{$key}}\n";
> }
>
> exit;
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From roy.chaudhuri at gmail.com  Mon Sep 19 16:39:40 2011
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Mon, 19 Sep 2011 17:39:40 +0100
Subject: [Bioperl-l] question Bioperl installation
In-Reply-To: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
References: <1316205912.93564.YahooMailClassic@web160515.mail.bf1.yahoo.com>
Message-ID: <4E77704C.20604@gmail.com>

Hi Willy,

There are instructions for downloading and installing BioPerl on the wiki:
http://www.bioperl.org/wiki/Getting_BioPerl
http://www.bioperl.org/wiki/Installing_BioPerl

These are the first two results when you Google for "bioperl download".

Note that the wiki is a little out of date, the latest BioPerl version 
is 1.6.901:
http://search.cpan.org/~cjfields/BioPerl-1.6.901/

Cheers,
Roy.

On 16/09/2011 21:45, Willy Savigne wrote:
> my name is william how do download Bioperl i tried other site but
> NOTHING  i would like to know info in downloading  bioperl .This is
> my first  time into knowing  bioinformatic i  just got  a book
> developing bioinformatic and begginning perl bioinformatic. I do alot
> Dna and RNA sequencing   and more.
>
> Thank u willy
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From bosborne11 at verizon.net  Tue Sep 20 17:01:21 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 13:01:21 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
Message-ID: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>

All,

I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:

..... get the files etc ....

my %alignparams = (
    -seqtype  => 'nucleo',
    -usetree_nowarn => $guidetreefile,
    -in => $tempfile
);
my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);

# $align is a Bio::SimpleAlign object
my $align = $aligner->align($tempfile);

my %treeparams = (
   -data_type => 'nt',
   -model     => 'K80',  # Kimura
   -tree      => 'BIONJ',
   -bootstrap => 1000
);
my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);

#$tree is a Bio::Tree::Tree object
my $tree = $treemaker->run($align);

My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:

$distance = $tree->subtree_length($internal_node)

Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!

Brian O.


From bosborne11 at verizon.net  Tue Sep 20 19:17:13 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 20 Sep 2011 15:17:13 -0400
Subject: [Bioperl-l] Question about a phylogenetic tree
In-Reply-To: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
References: <36D93DC4-135D-408F-8169-AC8D5E59BD90@verizon.net>
Message-ID: <A2EDBACB-963C-4E1C-8E7A-5F769BE89476@verizon.net>

Ah, I see:

my $distances = $tree->distance(-nodes => [$node1,$node2]);

Brian O.


On Sep 20, 2011, at 1:01 PM, Brian Osborne wrote:

> All,
> 
> I have code that starts with a sequence file and makes a tree (Bio::Tree::Tree) using Muscle to align and then Phyml, here's the last part that makes the tree:
> 
> ..... get the files etc ....
> 
> my %alignparams = (
>    -seqtype  => 'nucleo',
>    -usetree_nowarn => $guidetreefile,
>    -in => $tempfile
> );
> my $aligner = Bio::Tools::Run::Alignment::Muscle->new(%alignparams);
> 
> # $align is a Bio::SimpleAlign object
> my $align = $aligner->align($tempfile);
> 
> my %treeparams = (
>   -data_type => 'nt',
>   -model     => 'K80',  # Kimura
>   -tree      => 'BIONJ',
>   -bootstrap => 1000
> );
> my $treemaker = Bio::Tools::Run::Phylo::Phyml->new(%treeparams);
> 
> #$tree is a Bio::Tree::Tree object
> my $tree = $treemaker->run($align);
> 
> My question: do I get the pairwise distance between 2 sequences (based on Kimura here) by doing something like:
> 
> $distance = $tree->subtree_length($internal_node)
> 
> Where $internal_node is the parent of the pair in question? Excuse me if this is obvious, have never made Bioperl trees before!
> 
> Brian O.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From manju.rawat2 at gmail.com  Thu Sep 22 11:07:39 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Thu, 22 Sep 2011 16:37:39 +0530
Subject: [Bioperl-l] database for Bos Touras
Message-ID: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>

Hello To All,

I want to blast my sequence Only in Bos Touras Database Using Local
Blast(Blast+).
But I dnt Know which database I should use for this From this Link.
ftp://ftp.ncbi.nlm.nih.gov/blast/db/

Pl tell me which DB I Should use??

Thanks
Manju


From hrh at fmi.ch  Thu Sep 22 11:44:56 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 13:44:56 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
Message-ID: <4E7B1FB8.8090208@fmi.ch>


assuming you mean 'Bos taurus', it might be easier to get the data from

ucsc:  http://hgdownload.cse.ucsc.edu/downloads.html#cow

or ensembl: ftp://ftp.ensembl.org/pub/release-64/fasta/bos_taurus/dna/



Regards, Hans



On 09/22/2011 01:07 PM, Manju Rawat wrote:
> Hello To All,
>
> I want to blast my sequence Only in Bos Touras Database Using Local
> Blast(Blast+).
> But I dnt Know which database I should use for this From this Link.
> ftp://ftp.ncbi.nlm.nih.gov/blast/db/
>
> Pl tell me which DB I Should use??
>
> Thanks
> Manju
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From hrh at fmi.ch  Thu Sep 22 12:16:00 2011
From: hrh at fmi.ch (Hans-Rudolf Hotz)
Date: Thu, 22 Sep 2011 14:16:00 +0200
Subject: [Bioperl-l] database for Bos Touras
In-Reply-To: <CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
References: <CAB2c7yp49RLNzT2Q0p9AHy_=S7AdbBsA1hbu8Z91KiO5sqpedw@mail.gmail.com>
	<4E7B1FB8.8090208@fmi.ch>
	<CAB2c7yr5_KwrRyrc9bo+x6mgxzr0EMnsKLX4Dt8JGW+VcmMTWQ@mail.gmail.com>
Message-ID: <4E7B2700.8080904@fmi.ch>


Yes, BLAST uses fasta files. You (may need to concatenate the individual 
chromosomes and the you) need to index them with 'makeblastdb' which is 
also part of the blast+ software package.

see: http://www.ncbi.nlm.nih.gov/books/NBK1762/


Hans

On 09/22/2011 01:49 PM, Manju Rawat wrote:
> It will work on Local Blast or not??????


From bosborne11 at verizon.net  Thu Sep 22 16:16:39 2011
From: bosborne11 at verizon.net (Brian Osborne)
Date: Thu, 22 Sep 2011 12:16:39 -0400
Subject: [Bioperl-l] [bioperl-live] genbank_ref_extractor: new script to
 make search on entrez gene and retrieve related sequences (#23)
In-Reply-To: <bioperl/bioperl-live/pull/23@github.com>
References: <bioperl/bioperl-live/pull/23@github.com>
Message-ID: <245C75D5-61EC-4395-B64F-47D8471568F5@verizon.net>

Carne,

This is impressive looking, it is now in scripts/.

Thanks again,

Brian O.

On Sep 21, 2011, at 11:25 AM, Carn? Draug wrote:

> Hi
> 
> I wrote a script with bioperl that I would like to share back. It takes a list of searches for Entrez Gene and attempts to retrieve the related sequences (genomic, transcripts and proteins). It is also possible to obtain extra upstream and downstream bp for genomic sequences and control the naming of the files. In the end it can save all the results in a CSV file.
> 
> Hope you find it up to your coding standards. Suggestions for improvements are welcome, including for a better name.
> 
> Carn?
> 
> You can merge this Pull Request by running:
> 
>  git pull https://github.com/carandraug/bioperl-live bp_genbank_ref_extractor
> 
> Or you can view, comment on it, or merge it online at:
> 
>  https://github.com/bioperl/bioperl-live/pull/23
> 
> -- Commit Summary --
> 
> * genbank_ref_extractor: new script to make search on entrez gene and retrieve related sequences
> 
> -- File Changes --
> 
> A scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl (1064)
> 
> -- Patch Links --
> 
>  https://github.com/bioperl/bioperl-live/pull/23.patch
>  https://github.com/bioperl/bioperl-live/pull/23.diff
> 
> -- 
> Reply to this email directly or view it on GitHub:
> https://github.com/bioperl/bioperl-live/pull/23




From bluecurio at gmail.com  Thu Sep 22 19:32:07 2011
From: bluecurio at gmail.com (Daniel Renfro)
Date: Thu, 22 Sep 2011 14:32:07 -0500
Subject: [Bioperl-l] Download RefSeq revision history programmatically
Message-ID: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>

I am working on a project to find historical differences in GenBank/RefSeq files. I would like to download all the old revisions of a file (for example NC_000913 [http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2?report=girevhist]) using any technology available. I wrote a page-scraper in Perl, but I can't get NCBI to return plaintext, only HTML (which does nobody any good.) 

Does anyone know of a way to get all the "revisions" (not just "versions") of a GenBank/RefSeq file?

-Daniel 
--
http://ecoliwiki.net/User:DanielRenfro
Hu Lab Research Associate
979-862-4055



From ross at cuhk.edu.hk  Tue Sep 27 14:16:14 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Tue, 27 Sep 2011 22:16:14 +0800
Subject: [Bioperl-l]  obtain a distance matrix from tree
In-Reply-To: <AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
Message-ID: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>

After using MEGA to generate a newick tree file (phylogram), I wonder if
Bioperl has any convenient functions to derive the (n x n) distance (by NJ,
MP etc) matrix. Thanks for your advice in advance!




From thomas.sharpton at gmail.com  Tue Sep 27 20:02:44 2011
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Tue, 27 Sep 2011 13:02:44 -0700
Subject: [Bioperl-l] obtain a distance matrix from tree
In-Reply-To: <014201cc7d20$03abd4c0$0b037e40$@edu.hk>
References: <048a01cc6f84$60c41090$224c31b0$@edu.hk>
	<CA+08rdT=0peiw_QfUneFLLvCXbDrV6Lvpd3pfcC2AuGc-Ko=sQ@mail.gmail.com>
	<04a601cc700e$4f051d10$ed0f5730$@edu.hk>
	<CA+08rdTDRsB9=R7PBRYnECJ=tdsRgZ8qg1wzYYSdz8218WqQKg@mail.gmail.com>
	<085501cc744d$d90b4500$8b21cf00$@edu.hk>
	<AA33EFA7-B861-4A13-BA3C-9675111B3D84@illinois.edu>
	<014201cc7d20$03abd4c0$0b037e40$@edu.hk>
Message-ID: <C2ED3ADC-B089-4481-BD63-8D5FDFB51CFA@gmail.com>

Hi Ross,

For very large trees, I found it to be more efficient to do this in R  
using the ape package. I have a script listed in my github repo that  
will convert a tree to a distance matrix via in R at the link below:

https://github.com/sharpton/PhylOTU/blob/master/tree_to_matrix.R

That said, I've also done this in Bioperl using something like the  
following:

use Bio::TreeIO;

my $treein = Bio::TreeIO->new( -fh => "input_tree.nwk", -format =>  
'newick' );
while( my $tree = $treein->next_tree ){
	my %dist_matrix = ();
	my @leaves = $tree->get_leaf_nodes;
	foreach my $leaf1( @leaves ){
		my $id1 = $leaf1->id;	
		foreach my $leaf2( @leaves ){
			my $id2 = $leaf2->id;
			next if $id1 eq $id2;
			next if( defined( $dist_matrix{$id1}->{$id2} ) || defined  
( $dist_matrix{$id2}->{$id1} ) );
			my $distance = $tree->distance( -nodes => [$leaf1, $leaf2] );
			$dist_matrix{$id1}->{$id2} = $distance;
		}
	}
}
#print distance matrix here....

This will put the information you need to create either a full or a  
upper triangle distance matrix into the hash %dist_matrix. I didn't  
test the above, so hopefully there are no bugs....

Someone else may have a more elegant solution.

Best,
Tom

PS: Sorry if you get this twice.

On Sep 27, 2011, at 7:16 AM, Ross KK Leung wrote:

> After using MEGA to generate a newick tree file (phylogram), I  
> wonder if
> Bioperl has any convenient functions to derive the (n x n) distance  
> (by NJ,
> MP etc) matrix. Thanks for your advice in advance!
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From member at linkedin.com  Tue Sep 27 23:45:10 2011
From: member at linkedin.com (Razi Khaja via LinkedIn)
Date: Tue, 27 Sep 2011 23:45:10 +0000 (UTC)
Subject: [Bioperl-l] Invitation to connect on LinkedIn
Message-ID: <1856085440.8574001.1317167110185.JavaMail.app@ela4-bed82.prod>

LinkedIn
------------




    Razi Khaja requested to add you as a connection on LinkedIn:
  
------------------------------------------

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Accept invitation from Razi Khaja
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------------------------------------------



From ross at cuhk.edu.hk  Wed Sep 28 03:57:52 2011
From: ross at cuhk.edu.hk (Ross KK Leung)
Date: Wed, 28 Sep 2011 11:57:52 +0800
Subject: [Bioperl-l]  ancestral state derived from Tree
In-Reply-To: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
References: <29B78DBCEBCA42B5A99461FE1E9BC33F@gmail.com>
Message-ID: <017701cc7d92$cba88d20$62f9a760$@edu.hk>


By using Tom's advice, I'm able to obtain the distance matrix for the
following tree by Bioperl TreeIO. 

((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.000
00000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00
000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(
L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0
.00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,
(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000
):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.000000
00);

For the last few nodes T, U and V, they should be monophyletic but U and V
should be more closely related. Although I can use TreeIO methods like
is_monophyletic or is_paraphyletic to test in this case, the problem becomes
more tricky for nodes A, B, C, D because D actually makes no difference from
the common ancestor of nodes A, B, C and D. Since is_monophyletic does not
take into account for this case, is there any workaround? I have to pay
attention to such a detail in order to make a better guess for the ancestral
state(s) at various points of this tree.

Thanks again for the TreeIO developers for making tree analysis easier for
us biologists!



From manju.rawat2 at gmail.com  Wed Sep 28 09:54:07 2011
From: manju.rawat2 at gmail.com (Manju Rawat)
Date: Wed, 28 Sep 2011 15:24:07 +0530
Subject: [Bioperl-l] how to blast a seq against multiple dbase
Message-ID: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>

Hello,

I have downloaded all the chromosome of Bos Taurus and i'd changed them in
blast format using makeblastdb..and now i want to localy blast my sequence
against these all chromosome..
now i have 29 database.Is there any method by which can i blast my sequence
against all 29 database in my program..


whta should i write in database????

@params = ('database' => '????????', 'outfile' => 'blast2.out',
        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');



Thanks
Manju Rawat


From p.j.a.cock at googlemail.com  Wed Sep 28 10:02:07 2011
From: p.j.a.cock at googlemail.com (Peter Cock)
Date: Wed, 28 Sep 2011 11:02:07 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <CAKVJ-_7HCbvfm=mgcXEmL_9AH6A3rttnLrW86rs1ecNB0L7=XQ@mail.gmail.com>

On Wed, Sep 28, 2011 at 10:54 AM, Manju Rawat <manju.rawat2 at gmail.com> wrote:
> Hello,
>
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
>
>
> whta should i write in database????
>
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
> ? ? ? ?'_READMETHOD' => 'Blast', 'prog'=> 'blastn');
>

The simple answer is make a combined database. This
works internally with alias files, have a look at the NR
and NT databases for example - they act like singe
databases but are actually a collection of chunks.

Even simpler would be to combine your Bos taurus
sequence files into a single multi-entry FASTA file,
and make that into a single BLAST database.

Peter



From awitney at sgul.ac.uk  Wed Sep 28 10:42:39 2011
From: awitney at sgul.ac.uk (Adam Witney)
Date: Wed, 28 Sep 2011 11:42:39 +0100
Subject: [Bioperl-l] how to blast a seq against multiple dbase
In-Reply-To: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
References: <CAB2c7yrcNmzCwQkv_QhZLVNOaazEhoAojNzmOtRpWEgY0q9y0w@mail.gmail.com>
Message-ID: <B2F15B1E-24EB-41B5-8BC4-07A2EF4C8286@sgul.ac.uk>


I think if you want to keep the databases separate you would need to create a factory for each database, something like this

foreach my $db ( @databases ) {
	my $factory = Bio::Tools::Run::StandAloneBlastPlus->new( -db_data => $db ,  < ? any other params ? > );

	? do blast stuff?
}

or as Peter says in another email you could combine your databases and run one query then filter them out in the results.

regards

adam

On 28 Sep 2011, at 10:54, Manju Rawat wrote:

> Hello,
> 
> I have downloaded all the chromosome of Bos Taurus and i'd changed them in
> blast format using makeblastdb..and now i want to localy blast my sequence
> against these all chromosome..
> now i have 29 database.Is there any method by which can i blast my sequence
> against all 29 database in my program..
> 
> 
> whta should i write in database????
> 
> @params = ('database' => '????????', 'outfile' => 'blast2.out',
>        '_READMETHOD' => 'Blast', 'prog'=> 'blastn');
> 
> 
> 
> Thanks
> Manju Rawat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Wed Sep 28 11:43:02 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 12:43:02 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
Message-ID: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>

Hi everyone,

is there a recommended way to get the version of a script that is part
of bioperl (the ones in the scripts directory)? Rather than hard
coding the version of the script independent of bioperl, I thought on
using the bioperl version itself. How can this be done?

Thanks in advance,
Carn?



From carandraug+dev at gmail.com  Wed Sep 28 15:00:34 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 16:00:34 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
Message-ID: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>

2011/9/28 longbow leo <longbow0 at gmail.com>:
> Hi, Carn?,
>
> Do you mean this:
>
> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>
> In my machine, the output is

Thank you. Yes this is what I was looking for. I looked down how that
variable comes up and so I think I'll use

use Bio::Root::Version;
say $Bio::Root::Version::VERSION;

Carn?



From pcantalupo at gmail.com  Wed Sep 28 16:54:19 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 28 Sep 2011 12:54:19 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
Message-ID: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>

Hello,

I'm using the most recent copy of bioperl-live (pulled yesterday). I
have a BLASTN (from blast+) output file for 3 query sequences
(https://gist.github.com/1248342). I used this script,
https://gist.github.com/1248338, to print the query id, algorithm and
algorithm_version for each result. When I run the script, I get the
following output:

GFAVMM201BADC0 ?BLASTN ?2.2.25+
GFAVMM201A1JOH ?BLASTN
GFAVMM201D933Z ?BLASTN

Algorithm_version outputs the correct version for the first result but
outputs the empty string for the 2nd and 3rd query. Why? This
functionality worked about a month ago. What has changed to cause this
to happen?

Thank you,

Paul



From rondonbio at yahoo.com.br  Wed Sep 28 19:47:45 2011
From: rondonbio at yahoo.com.br (Rondon Neto)
Date: Wed, 28 Sep 2011 12:47:45 -0700 (PDT)
Subject: [Bioperl-l] best Hit
Message-ID: <1317239265.98674.YahooMailNeo@web130214.mail.mud.yahoo.com>

Hi guys.?

I have this subroutine that returns a hash with nucleotide's coverage of each query from a blast alignment.
So, I want to compute uniq hits. If a hit has already been aligned with a query, it must be eliminated from my experiment.
Can anyone check if it's right or can fix it to me? Is there a way to do that directly in blast?

Thank you

Rondon Neto


sub nucleotide_coverage{
#Bio::SearchIO dependent
#This subroutine return a Hash and a file with nucleotide coverage?
#for each query in an blast alignment xlm file. The input is the
#alignment file.

my ($alignment_file) = @_;

my $alignment = new Bio::SearchIO ( -format => 'blastXML',
 ? ?-file ? => $alignment_file );my %positions;my @used_reads;
while (my $result = $alignment->next_result) {
my $query_name = $result->query_name();
my $tam = $result -> query_length();
for (0..$tam-1){ ${$positions{$query_name}}[$_] = 0 }?
while (my $hit = $result->next_hit) {
my $hit_name = $hit->name;
# Here is my best hit parser. Is it ok?
foreach my $read (@used_reads) {
if ( $read eq $hit_name ) {
next;
}
}
while (my $hsp = $hit->next_hsp) {
my $query_name = $result->query_name();
my @pos = $hsp->seq_inds('query','identical');
foreach my $num (@pos) {
${$positions{$query_name}}[$num-1]++;
}
}
push (@used_reads, $hit_name);
}
}

my $outfile = "nucleotide_coverage.txt";
open OUT, ">$outfile" or die $!;foreach my $key (keys %positions){print OUT "$key\t@{$positions{$key}}\n";
}

close OUT;

return \%positions;

}


From shalabh.sharma7 at gmail.com  Wed Sep 28 19:53:07 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Wed, 28 Sep 2011 15:53:07 -0400
Subject: [Bioperl-l] Getting taxa from gi
Message-ID: <CAA7rn9dYGfeCS-qVccDcdwVenj8KFQs4i89EoT8_63gQk5b42g@mail.gmail.com>

Hi All,
        I know this has been discussed before, but this is kind of a new
problem that i am facing.
I want to get taxonomy (full linage) information from the huge list of GI's.
I am using Bio::DB:Genbak for this with perl-5.12.3.
Here is my small script.

#! /usr/local/perl-5.12.3/bin/perl -w
use strict;
use warnings;
use Bio::DB::GenBank;

my @ids = qw( CP000490 );
my $gbh = Bio::DB::GenBank->new();

foreach my $id( @ids ) {
# say "* ID: $id";
 my $seq = $gbh->get_Seq_by_acc( $id );
 my $org = $seq->species;
 #print "$org\n";
 my $class = join'-', $org->classification;
 print "$class\n";
}

The output is: Paracoccus denitrificans
PD1222-Paracoccus-Rhodobacteraceae-Rhodobacterales-Alphaproteobacteria-Proteobacteria-Bacteria
which is fine but i also want to get the taxa id, and if possible taxa ids
for all the linage classification.

ideally i would like to get something like this: 318586 - - - - - - - 1224 -
2

I would really appreciate your help.

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Wed Sep 28 21:36:37 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:36:37 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
Message-ID: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>

On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:

> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>> Hi, Carn?,
>> 
>> Do you mean this:
>> 
>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>> 
>> In my machine, the output is
> 
> Thank you. Yes this is what I was looking for. I looked down how that
> variable comes up and so I think I'll use
> 
> use Bio::Root::Version;
> say $Bio::Root::Version::VERSION;
> 
> Carn?

Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

chris


From cjfields at illinois.edu  Wed Sep 28 21:40:48 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 28 Sep 2011 21:40:48 +0000
Subject: [Bioperl-l] algorithm_version not working in multi-result
	blast	output
In-Reply-To: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
Message-ID: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>

Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.  

This should be an easy enough fix, but can you submit it as a bug so we can track it?

chris

On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:

> Hello,
> 
> I'm using the most recent copy of bioperl-live (pulled yesterday). I
> have a BLASTN (from blast+) output file for 3 query sequences
> (https://gist.github.com/1248342). I used this script,
> https://gist.github.com/1248338, to print the query id, algorithm and
> algorithm_version for each result. When I run the script, I get the
> following output:
> 
> GFAVMM201BADC0  BLASTN  2.2.25+
> GFAVMM201A1JOH  BLASTN
> GFAVMM201D933Z  BLASTN
> 
> Algorithm_version outputs the correct version for the first result but
> outputs the empty string for the 2nd and 3rd query. Why? This
> functionality worked about a month ago. What has changed to cause this
> to happen?
> 
> Thank you,
> 
> Paul
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From carandraug+dev at gmail.com  Wed Sep 28 22:07:53 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Wed, 28 Sep 2011 23:07:53 +0100
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
Message-ID: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>

2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>
>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>> Hi, Carn?,
>>>
>>> Do you mean this:
>>>
>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>
>>> In my machine, the output is
>>
>> Thank you. Yes this is what I was looking for. I looked down how that
>> variable comes up and so I think I'll use
>>
>> use Bio::Root::Version;
>> say $Bio::Root::Version::VERSION;
>>
>> Carn?
>
> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).

Where will the scripts end up after this restructuration? What I want
is to create a version of the script (not of bioperl). Since the
script is released with bioperl, they are the same. I actually already
made the commit that makes this, just haven't bothered with the pull
request yet.

Also, will there be a release before this change?

Carn?



From shalabh.sharma7 at gmail.com  Thu Sep 29 14:37:53 2011
From: shalabh.sharma7 at gmail.com (shalabh sharma)
Date: Thu, 29 Sep 2011 10:37:53 -0400
Subject: [Bioperl-l] GFF to GTF
Message-ID: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>

Hi,
    Is there any module to convert GFF file to GTF?

Thanks
Shalabh


-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


From cjfields at illinois.edu  Thu Sep 29 15:07:27 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 29 Sep 2011 15:07:27 +0000
Subject: [Bioperl-l] retrieving bioperl version for scripts
In-Reply-To: <CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
References: <CAPOrs_1nugM_2kRNEhfb-KA4uvjMHp8q8zP4mAnNAmKnF+7jHQ@mail.gmail.com>
	<CAKPXXkc1UKDDYaAh9cGB7WKytb7v0cKDQ8J+m3QPxR5R_Pr64g@mail.gmail.com>
	<CAPOrs_3Qk8fUySQPgRPF_5wm2kUsQpeH1Y3C8hkrGmyXhEBa0g@mail.gmail.com>
	<E801F02F-D3E8-44CF-8015-0F9D0E1493EE@illinois.edu>
	<CAPOrs_2Q-NpKVHX=phiy_3=KZzEHC8D4d79E7cwSQmgAqBuLbQ@mail.gmail.com>
Message-ID: <46733E36-5795-4EB6-9C2B-C978000FFD46@illinois.edu>

On Sep 28, 2011, at 5:07 PM, Carn? Draug wrote:

> 2011/9/28 Fields, Christopher J <cjfields at illinois.edu>:
>> On Sep 28, 2011, at 10:00 AM, Carn? Draug wrote:
>> 
>>> 2011/9/28 longbow leo <longbow0 at gmail.com>:
>>>> Hi, Carn?,
>>>> 
>>>> Do you mean this:
>>>> 
>>>> perl -MBio::SeqIO -e 'print $Bio::SeqIO::VERSION'
>>>> 
>>>> In my machine, the output is
>>> 
>>> Thank you. Yes this is what I was looking for. I looked down how that
>>> variable comes up and so I think I'll use
>>> 
>>> use Bio::Root::Version;
>>> say $Bio::Root::Version::VERSION;
>>> 
>>> Carn?
>> 
>> Just a warning on this: we're shortly to announce a major restructuring effort with BioPerl that will dramatically affect core versioning, mainly from the point of view that modularizing BioPerl into more manageable sub-distributions will require that each sub-distribution have it's own version (not necessarily a bad thing).
> 
> Where will the scripts end up after this restructuration? What I want
> is to create a version of the script (not of bioperl). Since the
> script is released with bioperl, they are the same. I actually already
> made the commit that makes this, just haven't bothered with the pull
> request yet.
> 
> Also, will there be a release before this change?
> 
> Carn?

Scripts will likely go with the distribution that they most closely are tied to, but that's still an area for debate (some may equally fall within one distribution or another, which will be tricky).  

For more on the release aspects see the (currently being revised and thus not complete) wiki page:

http://www.bioperl.org/wiki/BioPerl_Modularization

chris


From pcantalupo at gmail.com  Thu Sep 29 16:13:05 2011
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 29 Sep 2011 12:13:05 -0400
Subject: [Bioperl-l] algorithm_version not working in multi-result blast
	output
In-Reply-To: <4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
References: <CAJqbkv5iKA74mn4vhcbVOrbLga=CDAnZDKPL+WQCFOA2w33bSQ@mail.gmail.com>
	<4240A221-7BF7-4723-A7A1-30C806CE3DC6@illinois.edu>
Message-ID: <CAJqbkv6Cgf8V4x2DDrzJjc7yKyF8j-kMFNz6JGpnhn9QQTZEQg@mail.gmail.com>

Bug submitted: https://redmine.open-bio.org/issues/3298





On Wed, Sep 28, 2011 at 5:40 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Not sure, but I would hazard a guess that only the 'Query=' line is present in concatenated BLAST reports past the initial report, and the version isn't carried over (I recall this being a problem with the algorithm() as well, but that was fixed a while ago.
>
> This should be an easy enough fix, but can you submit it as a bug so we can track it?
>
> chris
>
> On Sep 28, 2011, at 11:54 AM, Paul Cantalupo wrote:
>
>> Hello,
>>
>> I'm using the most recent copy of bioperl-live (pulled yesterday). I
>> have a BLASTN (from blast+) output file for 3 query sequences
>> (https://gist.github.com/1248342). I used this script,
>> https://gist.github.com/1248338, to print the query id, algorithm and
>> algorithm_version for each result. When I run the script, I get the
>> following output:
>>
>> GFAVMM201BADC0 ?BLASTN ?2.2.25+
>> GFAVMM201A1JOH ?BLASTN
>> GFAVMM201D933Z ?BLASTN
>>
>> Algorithm_version outputs the correct version for the first result but
>> outputs the empty string for the 2nd and 3rd query. Why? This
>> functionality worked about a month ago. What has changed to cause this
>> to happen?
>>
>> Thank you,
>>
>> Paul
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



From jluis.lavin at unavarra.es  Fri Sep 30 08:23:19 2011
From: jluis.lavin at unavarra.es (jluis.lavin at unavarra.es)
Date: Fri, 30 Sep 2011 10:23:19 +0200
Subject: [Bioperl-l] Bio-Graphics module
Message-ID: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>


Dear All,

I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
windows machine.

I read about the Bio-Graphics module and it'd be wonderful to install it,
but seems like it is  only available for Perl 5.8...
Is there any other Perl and/or Bioperl module to do the same kind of
genomic and Blast report representation currently available?

Thanks in advance

-- 
Dr. Jos? Luis Lav?n Trueba

Dpto. de Producci?n Agraria
Grupo de Gen?tica y Microbiolog?a
Universidad P?blica de Navarra
31006 Pamplona
Navarra
SPAIN




From cjfields at illinois.edu  Fri Sep 30 12:38:01 2011
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 30 Sep 2011 12:38:01 +0000
Subject: [Bioperl-l] Bio-Graphics module
In-Reply-To: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
References: <52f9bcbb5c40302fe5d1ea274982c24b.squirrel@webmail.unavarra.es>
Message-ID: <B1F1674B-D8DA-46E2-AAAE-DD9DDBC4C51A@illinois.edu>

It's available for all perl versions from 5.8.8 up.  I have it running with perl 5.14.  Now, I recall there being problems with installation on Mac OS X, though I think that was mainly due to GD.pm and libgd.

chris

On Sep 30, 2011, at 3:23 AM, <jluis.lavin at unavarra.es>
 <jluis.lavin at unavarra.es> wrote:

> 
> Dear All,
> 
> I'm currently using Perl 5.10.0 version and Bioperl 1.6.1 running on a
> windows machine.
> 
> I read about the Bio-Graphics module and it'd be wonderful to install it,
> but seems like it is  only available for Perl 5.8...
> Is there any other Perl and/or Bioperl module to do the same kind of
> genomic and Blast report representation currently available?
> 
> Thanks in advance
> 
> -- 
> Dr. Jos? Luis Lav?n Trueba
> 
> Dpto. de Producci?n Agraria
> Grupo de Gen?tica y Microbiolog?a
> Universidad P?blica de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jillianrowe91286 at gmail.com  Wed Sep 28 06:03:32 2011
From: jillianrowe91286 at gmail.com (Jill)
Date: Tue, 27 Sep 2011 23:03:32 -0700 (PDT)
Subject: [Bioperl-l] Gene Type in Entrez gene?
Message-ID: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>

Hi there,

I am using the Bio::DB::Eutilities module to download gene sequences
based on a query.

<code>
while (my $docsum = $summaries->next_DocSum) {
  ## some items in DocSum are also named ChrStart so we pick the
genomic
  ## information item and get the coordinates from it
  my ($genomic_info)  = $docsum->get_Items_by_name('GenomicInfoType');

  ## some entries may have no data on genomic coordinates. This
condition filters then out
  if (!$genomic_info) {
    ## found no genomic coordinates data
    next;
  }

  ## get coordinates of sequence
  ## get_contents_by_name always returns a list
  my ($chr_acc_ver)   = $genomic_info-
>get_contents_by_name("ChrAccVer");
  my ($chr_start)     = $genomic_info-
>get_contents_by_name("ChrStart");
  my ($chr_stop)      = $genomic_info-
>get_contents_by_name("ChrStop");
  my $strand;

  if ($chr_start < $chr_stop) {
    $strand     = 1;
    $chr_start  = $chr_start +1 - $bp5_extra;
    $chr_stop   = $chr_stop  +1 + $bp5_extra;
  } elsif ($chr_start > $chr_stop) {
    $strand     = 2;
    $chr_start  = $chr_start +1 - (-$bp5_extra);
    $chr_stop   = $chr_stop  +1 + (-$bp5_extra);
  } else {
    next;
  }

  while (my $item = $docsum->next_Item('flattened'))  {
	next if ($item->get_name =~ m/NomenclatureName/);
	if($item->get_name =~ m/Description/) {
	  $description = $item->get_content if $item->get_content;
	  $description =~ tr/ /_/;
	  print $description, "\n";}
	if($item->get_name =~ m/Name/) {
	    $name = $item->get_content if $item->get_content;
	    print $name, "\n";
	  }
        printf("%-20s:%s\n",$item->get_name,$item->get_content) if
$item->get_content;
    }
}
</code>

Then I go on to use genbank to download the sequences based on the
chromosome splice. For what I have it works great. But I am trying to
get to the gene type (either protein coding or pseudo) as well. I can
see it in the summary on the Entrez Gene sight, but can't get to it
through bioperl. When I have it print out all the contents of the
summary it doesn't show up there either.

Any help?

Thanks!


From liam.elbourne at mq.edu.au  Thu Sep 29 21:34:04 2011
From: liam.elbourne at mq.edu.au (Liam Elbourne)
Date: Fri, 30 Sep 2011 07:34:04 +1000
Subject: [Bioperl-l] GFF to GTF
In-Reply-To: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
References: <CAA7rn9eXnGt3Yv0VfDD_ia4TukSH4900=avd81MwWDBZNnn+mQ@mail.gmail.com>
Message-ID: <8D027281-44E6-467C-8D22-D2D2F87D04B6@mq.edu.au>

Hi Shalabh,

Not sure about bioperl (I looked a while back and either missed it or it's not there) but there is a program associated with the cufflinks suite called gffread that should convert. 

Regards,
Liam Elbourne. 



On 30/09/2011, at 12:37 AM, shalabh sharma <shalabh.sharma7 at gmail.com> wrote:

> Hi,
>    Is there any module to convert GFF file to GTF?
> 
> Thanks
> Shalabh
> 
> 
> -- 
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From carandraug+dev at gmail.com  Fri Sep 30 13:18:04 2011
From: carandraug+dev at gmail.com (=?ISO-8859-1?Q?Carn=EB_Draug?=)
Date: Fri, 30 Sep 2011 14:18:04 +0100
Subject: [Bioperl-l] Gene Type in Entrez gene?
In-Reply-To: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
References: <ed6a2dd5-a3eb-4549-9be3-0d6e51041c07@dm9g2000vbb.googlegroups.com>
Message-ID: <CAPOrs_2QOMOyPsZ90iYc3fMd8YE9HGnPcVqELGo+rYRRxJu9NQ@mail.gmail.com>

On 28 September 2011 07:03, Jill <jillianrowe91286 at gmail.com> wrote:
> Hi there,
>
> I am using the Bio::DB::Eutilities module to download gene sequences
> based on a query.
>
> <code>
> [...]
> }
> </code>
>
> Then I go on to use genbank to download the sequences based on the
> chromosome splice. For what I have it works great. But I am trying to
> get to the gene type (either protein coding or pseudo) as well. I can
> see it in the summary on the Entrez Gene sight, but can't get to it
> through bioperl. When I have it print out all the contents of the
> summary it doesn't show up there either.
>
> Any help?

Hi Jill,

there's already a script in bioperl that does what you want, it's just
not part of the current stable release. You can get it here

https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl

You can download the script alone, it will work fine in previous
releases of bioperl, no need to write another one.

Carn? Draug