From jimhu at tamu.edu  Wed Jan  2 14:44:56 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 2 Jan 2013 13:44:56 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
Message-ID: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>

I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.

I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054




From biojiangke at gmail.com  Wed Jan  2 15:20:02 2013
From: biojiangke at gmail.com (Ke Jiang)
Date: Wed, 2 Jan 2013 15:20:02 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>

There is a blast2gff.pl floating around for Gbrowse to visualize blast
results as tracks. Not sure about the blast+. One more reason to stick with
the good old blast!

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Ke

-------------------------------------------
Ke Jiang, Ph.D.
Post-doctoral Fellow
Delbruck Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724

From cjfields at illinois.edu  Wed Jan  2 15:47:52 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 20:47:52 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FD44@CHIMBX5.ad.uillinois.edu>

?except that NCBI no longer supports legacy BLAST.  Caveat emptor.

chris

On Jan 2, 2013, at 2:20 PM, Ke Jiang <biojiangke at gmail.com> wrote:

> There is a blast2gff.pl floating around for Gbrowse to visualize blast
> results as tracks. Not sure about the blast+. One more reason to stick with
> the good old blast!
> 
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> 
> Ke
> 
> -------------------------------------------
> Ke Jiang, Ph.D.
> Post-doctoral Fellow
> Delbruck Laboratory
> Cold Spring Harbor Laboratory
> Cold Spring Harbor, NY 11724
> _______________________________________________
> 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  Wed Jan  2 15:26:22 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 15:26:22 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>

Here's one:

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Another one:

~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl 
#!perl

# Author:      Jason Stajich <jason-at-bioperl-dot-org>
# Description: Turn SearchIO parseable report(s) into a GFF report
#
=head1 NAME

bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report



Brian O.

On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:

> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> 
> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  
> 
> Thanks,
> 
> Jim
> =====================================
> Jim Hu
> Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From scott at scottcain.net  Wed Jan  2 16:32:16 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 2 Jan 2013 16:32:16 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
Message-ID: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>

Hi Brian,

I was going to suggest the same thing--though that script is fairly
old, it's not as old as the blast2gff script in the GBrowse
distribution (which probably should be retired).  I believe it
supports GFF3, though I don't have any sample data with which to test
it to be sure.  I also don't know if it supports BLAST+ input--I
haven't kept up with SearchIO (on which search2gff.pl depends); will
it accept it?

Scott


On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> Here's one:
>
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>
> Another one:
>
> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> #!perl
>
> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> # Description: Turn SearchIO parseable report(s) into a GFF report
> #
> =head1 NAME
>
> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>
>
>
> Brian O.
>
> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>
>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>
>> Thanks,
>>
>> Jim
>> =====================================
>> Jim Hu
>> Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>>
>> _______________________________________________
>> 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



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

From cjfields at illinois.edu  Wed Jan  2 17:26:55 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 22:26:55 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>

It should (I recall using it at one point).  If it doesn't we should fix it so it does.

How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 

chris

On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Brian,
> 
> I was going to suggest the same thing--though that script is fairly
> old, it's not as old as the blast2gff script in the GBrowse
> distribution (which probably should be retired).  I believe it
> supports GFF3, though I don't have any sample data with which to test
> it to be sure.  I also don't know if it supports BLAST+ input--I
> haven't kept up with SearchIO (on which search2gff.pl depends); will
> it accept it?
> 
> Scott
> 
> 
> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>> Here's one:
>> 
>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>> 
>> Another one:
>> 
>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>> #!perl
>> 
>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>> # Description: Turn SearchIO parseable report(s) into a GFF report
>> #
>> =head1 NAME
>> 
>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>> 
>> 
>> 
>> Brian O.
>> 
>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>> 
>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>> 
>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>> 
>>> Thanks,
>>> 
>>> Jim
>>> =====================================
>>> Jim Hu
>>> Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> 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  Wed Jan  2 17:53:50 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 17:53:50 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
Message-ID: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>

Scott and Chris,

I'll test it and see?

Brian O.


On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> 
> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
> 
> chris
> 
> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> 
>> Hi Brian,
>> 
>> I was going to suggest the same thing--though that script is fairly
>> old, it's not as old as the blast2gff script in the GBrowse
>> distribution (which probably should be retired).  I believe it
>> supports GFF3, though I don't have any sample data with which to test
>> it to be sure.  I also don't know if it supports BLAST+ input--I
>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>> it accept it?
>> 
>> Scott
>> 
>> 
>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>> Here's one:
>>> 
>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>> 
>>> Another one:
>>> 
>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>> #!perl
>>> 
>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>> #
>>> =head1 NAME
>>> 
>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>> 
>>> 
>>> 
>>> Brian O.
>>> 
>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>> 
>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>> 
>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>> 
>>>> Thanks,
>>>> 
>>>> Jim
>>>> =====================================
>>>> Jim Hu
>>>> Professor
>>>> Dept. of Biochemistry and Biophysics
>>>> 2128 TAMU
>>>> Texas A&M Univ.
>>>> College Station, TX 77843-2128
>>>> 979-862-4054
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From jimhu at tamu.edu  Fri Jan  4 14:49:51 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 13:49:51 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>

Thanks for the replies, but...

I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.

The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be broken, at least on this page:

	http://www.bioperl.org/wiki/Module:Bio::SearchIO

Jim


On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054




From bosborne11 at verizon.net  Fri Jan  4 14:26:52 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 04 Jan 2013 14:26:52 -0500
Subject: [Bioperl-l] strange error in the beginners howto
In-Reply-To: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
References: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
Message-ID: <BB2BD9EA-3419-4B6C-A659-4D86420CFAE0@verizon.net>

Matthew,

First, let's distinguish "warning" and "error". Errors stop execution of the app or script, what you're seeing is a warning, your script actually completes. Does the warning vanish if you remove "-w"?

Second, seems like this is a Perl version thing:

http://www.sysarchitects.com/bioperl

BIO

On Jan 4, 2013, at 1:55 PM, "Thornton, Matthew" <Matthew.Thornton at med.usc.edu> wrote:

> Hello,
> 
> I am working through the first part of the BioPerl beginners howto and I am getting an error and I was wondering if you could tell me what is wrong.
> 
> I made the seqio.pl script:
> 
> #!/bin/perl -w
> 
> use Bio::Seq;
> 
> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",                        
>                          -display_id => "#12345",                        
>                          -desc => "example 1",                        
>                          -alphabet => "dna" );
> 
> print $seq_obj->seq();
> 
> I execute the script and I get this error:
> 
> gserver at gserver:~/bio$ perl seqio.pl 
> Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251.
> aaaatgggggggggggccccgttgserver at gserver:~/bio$
> 
> Is there something wrong with my installation?
> 
> Any help is greatly appreciated.
> 
> Thanks!
> 
> 
> Matthew E. Thornton
> 
> 
> 
> Laboratory Technician III
> Broad Center for Stem Cell and Regenerative Medicine
> University of Southern California
> 1501 San Pablo St. ZNI
> Los Angeles, CA 90089-2821
> ph.:323-442-1688
> fx.:323-442-4040
> matthew.thornton at med.usc.edu
> 

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



From MEC at stowers.org  Fri Jan  4 15:20:17 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 14:20:17 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>

Jim,

Getting to your original question:

> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.

Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??

If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'

I would guess not because neither of them have 'subfeatures'.

If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.


~Malcolm


 .-----Original Message-----
 .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .Sent: Friday, January 04, 2013 1:50 PM
 .To: Brian Osborne
 .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Thanks for the replies, but...
 .
 .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
 .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .
 .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .broken, at least on this page:
 .
 .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .
 .Jim
 .
 .
 .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .
 .> Scott and Chris,
 .>
 .> I'll test it and see...
 .>
 .> Brian O.
 .>
 .>
 .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .>
 .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .>>
 .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .>>
 .>> chris
 .>>
 .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .>>
 .>>> Hi Brian,
 .>>>
 .>>> I was going to suggest the same thing--though that script is fairly
 .>>> old, it's not as old as the blast2gff script in the GBrowse
 .>>> distribution (which probably should be retired).  I believe it
 .>>> supports GFF3, though I don't have any sample data with which to test
 .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .>>> it accept it?
 .>>>
 .>>> Scott
 .>>>
 .>>>
 .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .>>>> Here's one:
 .>>>>
 .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .>>>>
 .>>>> Another one:
 .>>>>
 .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .>>>> #!perl
 .>>>>
 .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .>>>> #
 .>>>> =head1 NAME
 .>>>>
 .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .>>>>
 .>>>>
 .>>>>
 .>>>> Brian O.
 .>>>>
 .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .>>>>
 .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .>>>>>
 .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .create gff with appropriate subfeatures.
 .>>>>>
 .>>>>> Thanks,
 .>>>>>
 .>>>>> Jim
 .>>>>> =====================================
 .>>>>> Jim Hu
 .>>>>> Professor
 .>>>>> Dept. of Biochemistry and Biophysics
 .>>>>> 2128 TAMU
 .>>>>> Texas A&M Univ.
 .>>>>> College Station, TX 77843-2128
 .>>>>> 979-862-4054
 .>>>>>
 .>>>>>
 .>>>>>
 .>>>>> _______________________________________________
 .>>>>> 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
 .>>>
 .>>>
 .>>>
 .>>> --
 .>>> ------------------------------------------------------------------------
 .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .>>> Ontario Institute for Cancer Research
 .>>> _______________________________________________
 .>>> Bioperl-l mailing list
 .>>> Bioperl-l at lists.open-bio.org
 .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .>>
 .>
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .
 .
 .
 ._______________________________________________
 .Bioperl-l mailing list
 .Bioperl-l at lists.open-bio.org
 .http://lists.open-bio.org/mailman/listinfo/bioperl-l


From jimhu at tamu.edu  Fri Jan  4 16:57:38 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 15:57:38 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
Message-ID: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>

Malcolm,

Thanks, I should have reread the GFF3 spec before posting!

In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see how the final output could be done in different ways, but I'm still stuck on how to get there.  

I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a transposable element, for example.

Excerpting from blastp -help

 *** Formatting options
 -outfmt <String>
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1) 

Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute OR the multi-line match features OR a combination from one of these output formats. 

I'm probably missing something very, very obvious.

Best,

Jim


On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:

> Jim,
> 
> Getting to your original question:
> 
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.
> 
> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
> 
> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'
> 
> I would guess not because neither of them have 'subfeatures'.
> 
> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.
> 
> 
> ~Malcolm
> 
> 
> .-----Original Message-----
> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
> .Sent: Friday, January 04, 2013 1:50 PM
> .To: Brian Osborne
> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
> .
> .Thanks for the replies, but...
> .
> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
> .
> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
> .broken, at least on this page:
> .
> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
> .
> .Jim
> .
> .
> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
> .
> .> Scott and Chris,
> .>
> .> I'll test it and see...
> .>
> .> Brian O.
> .>
> .>
> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> .>
> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> .>>
> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
> .>>
> .>> chris
> .>>
> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> .>>
> .>>> Hi Brian,
> .>>>
> .>>> I was going to suggest the same thing--though that script is fairly
> .>>> old, it's not as old as the blast2gff script in the GBrowse
> .>>> distribution (which probably should be retired).  I believe it
> .>>> supports GFF3, though I don't have any sample data with which to test
> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
> .>>> it accept it?
> .>>>
> .>>> Scott
> .>>>
> .>>>
> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> .>>>> Here's one:
> .>>>>
> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> .>>>>
> .>>>> Another one:
> .>>>>
> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> .>>>> #!perl
> .>>>>
> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
> .>>>> #
> .>>>> =head1 NAME
> .>>>>
> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
> .>>>>
> .>>>>
> .>>>>
> .>>>> Brian O.
> .>>>>
> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
> .>>>>
> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> .>>>>>
> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
> .create gff with appropriate subfeatures.
> .>>>>>
> .>>>>> Thanks,
> .>>>>>
> .>>>>> Jim
> .>>>>> =====================================
> .>>>>> Jim Hu
> .>>>>> Professor
> .>>>>> Dept. of Biochemistry and Biophysics
> .>>>>> 2128 TAMU
> .>>>>> Texas A&M Univ.
> .>>>>> College Station, TX 77843-2128
> .>>>>> 979-862-4054
> .>>>>>
> .>>>>>
> .>>>>>
> .>>>>> _______________________________________________
> .>>>>> 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
> .>>>
> .>>>
> .>>>
> .>>> --
> .>>> ------------------------------------------------------------------------
> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> .>>> Ontario Institute for Cancer Research
> .>>> _______________________________________________
> .>>> Bioperl-l mailing list
> .>>> Bioperl-l at lists.open-bio.org
> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> .>>
> .>
> .
> .=====================================
> .Jim Hu
> .Professor
> .Dept. of Biochemistry and Biophysics
> .2128 TAMU
> .Texas A&M Univ.
> .College Station, TX 77843-2128
> .979-862-4054
> .
> .
> .
> ._______________________________________________
> .Bioperl-l mailing list
> .Bioperl-l at lists.open-bio.org
> .http://lists.open-bio.org/mailman/listinfo/bioperl-l

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054




From MEC at stowers.org  Fri Jan  4 18:33:04 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 17:33:04 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
	<2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE7CB@EXCHMB-02.stowers-institute.org>

Jim,

To get a working example for further discussion....

Assuming you have bioperl and blast+ installed....

This command gets a known transcript from ncbi and blasts it back at ncbi into fly genome:

> bp_download_query_genbank.pl --query 'NM_001259364' | blastn -remote -db refseq_genomic  -entrez_query 'melanogaster[Taxid]'  -outfmt 6  > test.blast.tab

Take a look at the results (see below, or run it yourself).

First line output looks like this:

	NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928

Old GFF did not have parent-child.  Depending on where you are going with this, you MIGHT want to use this strategy: http://gmod.org/wiki/GFF#Alignments

Where the ID in column 9 serves to group the features.  There is an 'implicit' parent.

I think this would be respected by both GBrowse and UCSC genome browser (but I'm not positive).

If so, converting blast output would yield one line output per each line input.

You would need to assign a strand, swap sstart and send where sstart>send, and some slight re-formatting

First line of GFF might look like:

	NT_033778.3 est EST_match 9330023	9327897  . + . ID=Match1;Name= NM_001259364;Target= NM_001259364 1869	3995

Is this along the lines of what you need?

~Malcolm

Complete example blast+ output looks like this:

NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	1019	0	0	3995	5013	9327834	9326816	0.0	1882
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	374	0	0	345	718	9332643	9332270	0.0	 691
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	300	0	0	1	300	9337978	9337679	1e-154	 555
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	270	0	0	717	986	9332201	9331932	5e-138	 499
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	243	0	0	1434	1676	9331200	9330958	5e-123	 449
NM_001259364	gi|116010442|ref|NT_033778.3|	99.55	223	0	1	1154	1376	9331611	9331390	1e-109	 405
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	196	0	0	1675	1870	9330634	9330439	7e-97	 363
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	169	0	0	986	1154	9331847	9331679	7e-82	 313
NM_001259364	gi|116010442|ref|NT_033778.3|	97.26	73	2	0	1372	1444	9331322	9331250	3e-25	 124
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	44	0	0	301	344	9333095	9333052	2e-12	82.4
NM_001259364	gi|195586644|ref|NT_167067.1|	96.52	2127	74	0	1869	3995	7777827	7775701	0.0	3518
NM_001259364	gi|195586644|ref|NT_167067.1|	97.03	404	7	3	4004	4402	7775629	7775226	0.0	 675
NM_001259364	gi|195586644|ref|NT_167067.1|	93.58	374	24	0	345	718	7780392	7780019	8e-156	 558
NM_001259364	gi|195586644|ref|NT_167067.1|	94.37	302	15	1	1	300	7786262	7785961	6e-127	 462
NM_001259364	gi|195586644|ref|NT_167067.1|	96.25	267	10	0	720	986	7779949	7779683	1e-119	 438
NM_001259364	gi|195586644|ref|NT_167067.1|	95.00	240	12	0	1434	1673	7778959	7778720	2e-101	 377
NM_001259364	gi|195586644|ref|NT_167067.1|	96.86	223	6	1	1154	1376	7779370	7779149	1e-99	 372
NM_001259364	gi|195586644|ref|NT_167067.1|	93.88	196	12	0	1675	1870	7778384	7778189	7e-77	 296
NM_001259364	gi|195586644|ref|NT_167067.1|	95.19	187	5	4	4827	5013	7774635	7774453	9e-76	 292
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	168	12	0	987	1154	7779598	7779431	3e-61	 244
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	70	5	0	1374	1443	7779079	7779010	2e-18	 102
NM_001259364	gi|195586644|ref|NT_167067.1|	100.00	44	0	0	301	344	7780833	7780790	2e-12	82.4
NM_001259364	gi|195489961|ref|NT_167063.1|	92.43	2127	161	0	1869	3995	7628910	7631036	0.0	3037
NM_001259364	gi|195489961|ref|NT_167063.1|	91.94	1030	38	20	3995	5013	7631102	7632097	0.0	1400
NM_001259364	gi|195489961|ref|NT_167063.1|	88.56	376	39	4	345	718	7626215	7626588	4e-124	 453
NM_001259364	gi|195489961|ref|NT_167063.1|	93.67	300	18	1	1	300	7620777	7621075	2e-122	 448
NM_001259364	gi|195489961|ref|NT_167063.1|	95.41	196	9	0	1675	1870	7628263	7628458	7e-82	 313
NM_001259364	gi|195489961|ref|NT_167063.1|	91.93	223	17	1	1154	1376	7627224	7627445	2e-81	 311
NM_001259364	gi|195489961|ref|NT_167063.1|	86.42	265	31	3	720	983	7626653	7626913	1e-73	 285
NM_001259364	gi|195489961|ref|NT_167063.1|	86.18	246	25	4	1434	1673	7627635	7627877	3e-65	 257
NM_001259364	gi|195489961|ref|NT_167063.1|	88.27	162	19	0	993	1154	7626999	7627160	3e-46	 195
NM_001259364	gi|195489961|ref|NT_167063.1|	93.06	72	5	0	1372	1443	7627513	7627584	1e-19	 106
NM_001259364	gi|195489961|ref|NT_167063.1|	100.00	44	0	0	301	344	7625770	7625813	2e-12	82.4


~Malcolm


 .-----Original Message-----
 .From: Jim Hu [mailto:jimhu at tamu.edu]
 .Sent: Friday, January 04, 2013 3:58 PM
 .To: Cook, Malcolm
 .Cc: 'Brian Osborne'; 'Fields, Christopher J'; 'Scott Cain'; 'bioperl-l at bioperl.org'
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Malcolm,
 .
 .Thanks, I should have reread the GFF3 spec before posting!
 .
 .In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking
 .of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see
 .how the final output could be done in different ways, but I'm still stuck on how to get there.
 .
 .I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get
 .to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are
 .gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other
 .work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a
 .transposable element, for example.
 .
 .Excerpting from blastp -help
 .
 . *** Formatting options
 . -outfmt <String>
 .   alignment view options:
 .     0 = pairwise,
 .     1 = query-anchored showing identities,
 .     2 = query-anchored no identities,
 .     3 = flat query-anchored, show identities,
 .     4 = flat query-anchored, no identities,
 .     5 = XML Blast output,
 .     6 = tabular,
 .     7 = tabular with comment lines,
 .     8 = Text ASN.1,
 .     9 = Binary ASN.1,
 .    10 = Comma-separated values,
 .    11 = BLAST archive format (ASN.1)
 .
 .Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than
 .suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute
 .OR the multi-line match features OR a combination from one of these output formats.
 .
 .I'm probably missing something very, very obvious.
 .
 .Best,
 .
 .Jim
 .
 .
 .On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:
 .
 .> Jim,
 .>
 .> Getting to your original question:
 .>
 .>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create
 .gff with appropriate subfeatures.
 .>
 .> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
 .>
 .> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE
 .GAP ATTRIBUTE' or as in 'ALIGNMENTS'
 .>
 .> I would guess not because neither of them have 'subfeatures'.
 .>
 .> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have
 .a better idea of what options might suit your needs.
 .>
 .>
 .> ~Malcolm
 .>
 .>
 .> .-----Original Message-----
 .> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .> .Sent: Friday, January 04, 2013 1:50 PM
 .> .To: Brian Osborne
 .> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .> .
 .> .Thanks for the replies, but...
 .> .
 .> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback.
 .Putting
 .> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .> .
 .> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .> .broken, at least on this page:
 .> .
 .> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .> .
 .> .Jim
 .> .
 .> .
 .> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .> .
 .> .> Scott and Chris,
 .> .>
 .> .> I'll test it and see...
 .> .>
 .> .> Brian O.
 .> .>
 .> .>
 .> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .> .>
 .> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .> .>>
 .> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .> .>>
 .> .>> chris
 .> .>>
 .> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .> .>>
 .> .>>> Hi Brian,
 .> .>>>
 .> .>>> I was going to suggest the same thing--though that script is fairly
 .> .>>> old, it's not as old as the blast2gff script in the GBrowse
 .> .>>> distribution (which probably should be retired).  I believe it
 .> .>>> supports GFF3, though I don't have any sample data with which to test
 .> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .> .>>> it accept it?
 .> .>>>
 .> .>>> Scott
 .> .>>>
 .> .>>>
 .> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .> .>>>> Here's one:
 .> .>>>>
 .> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .> .>>>>
 .> .>>>> Another one:
 .> .>>>>
 .> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .> .>>>> #!perl
 .> .>>>>
 .> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .> .>>>> #
 .> .>>>> =head1 NAME
 .> .>>>>
 .> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .> .>>>>
 .> .>>>>
 .> .>>>>
 .> .>>>> Brian O.
 .> .>>>>
 .> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .> .>>>>
 .> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .> .>>>>>
 .> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .> .create gff with appropriate subfeatures.
 .> .>>>>>
 .> .>>>>> Thanks,
 .> .>>>>>
 .> .>>>>> Jim
 .> .>>>>> =====================================
 .> .>>>>> Jim Hu
 .> .>>>>> Professor
 .> .>>>>> Dept. of Biochemistry and Biophysics
 .> .>>>>> 2128 TAMU
 .> .>>>>> Texas A&M Univ.
 .> .>>>>> College Station, TX 77843-2128
 .> .>>>>> 979-862-4054
 .> .>>>>>
 .> .>>>>>
 .> .>>>>>
 .> .>>>>> _______________________________________________
 .> .>>>>> 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
 .> .>>>
 .> .>>>
 .> .>>>
 .> .>>> --
 .> .>>> ------------------------------------------------------------------------
 .> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .> .>>> Ontario Institute for Cancer Research
 .> .>>> _______________________________________________
 .> .>>> Bioperl-l mailing list
 .> .>>> Bioperl-l at lists.open-bio.org
 .> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .> .>>
 .> .>
 .> .
 .> .=====================================
 .> .Jim Hu
 .> .Professor
 .> .Dept. of Biochemistry and Biophysics
 .> .2128 TAMU
 .> .Texas A&M Univ.
 .> .College Station, TX 77843-2128
 .> .979-862-4054
 .> .
 .> .
 .> .
 .> ._______________________________________________
 .> .Bioperl-l mailing list
 .> .Bioperl-l at lists.open-bio.org
 .> .http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .



From bosborne11 at verizon.net  Sat Jan  5 17:25:37 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Sat, 05 Jan 2013 17:25:37 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>

All,

The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.

Brian O.


On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> 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 jason.stajich at gmail.com  Mon Jan  7 04:35:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 7 Jan 2013 01:35:23 -0800
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
Message-ID: <D0FEE7D0-A855-478C-8BA1-08F56FEAD7A7@gmail.com>

with bp_search2gff  I included a cmdline options so you decide what is the reference (seqid column) and what is the target (9th column) since in some cases (BLASTX vs TBLASTN) you may want to be displaying one or the other as the reference. this is the -t option.

You can also have the -m option when you run which will build the grouping match term for a parent and then the sub-children will be HSPs that have that parent per Malcom's description of the parent child info.

Have you tried this with your output - it should work fine with regular vanilla text blast+ output or the -outfmt 6 option (tell bp_search2gff the format is blasttable)  or you can use -outfmt 5 and tell it you are using blastxml format.

 
Jason

On Jan 5, 2013, at 2:25 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> All,
> 
> The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> 
>> Scott and Chris,
>> 
>> I'll test it and see?
>> 
>> Brian O.
>> 
>> 
>> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
>> 
>>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>>> 
>>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>>> 
>>> chris
>>> 
>>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>>> 
>>>> Hi Brian,
>>>> 
>>>> I was going to suggest the same thing--though that script is fairly
>>>> old, it's not as old as the blast2gff script in the GBrowse
>>>> distribution (which probably should be retired).  I believe it
>>>> supports GFF3, though I don't have any sample data with which to test
>>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>>> it accept it?
>>>> 
>>>> Scott
>>>> 
>>>> 
>>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>>> Here's one:
>>>>> 
>>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>>> 
>>>>> Another one:
>>>>> 
>>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>>> #!perl
>>>>> 
>>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>>> #
>>>>> =head1 NAME
>>>>> 
>>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>>> 
>>>>> 
>>>>> 
>>>>> Brian O.
>>>>> 
>>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>>> 
>>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>>> 
>>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Jim
>>>>>> =====================================
>>>>>> Jim Hu
>>>>>> Professor
>>>>>> Dept. of Biochemistry and Biophysics
>>>>>> 2128 TAMU
>>>>>> Texas A&M Univ.
>>>>>> College Station, TX 77843-2128
>>>>>> 979-862-4054
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> _______________________________________________
>>>> 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
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org



From pengyu.ut at gmail.com  Thu Jan  3 17:41:37 2013
From: pengyu.ut at gmail.com (Peng Yu)
Date: Thu, 3 Jan 2013 14:41:37 -0800 (PST)
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file from
	Pfam
Message-ID: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>

Hi,

I tried the following code on the Pfam stockholm file (downloaded at
ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
But it gives me the following error. Is it a bug in bioperl or it is
an error in the Pfam-A.full.gz file?

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;

#use FindBin;
#use lib "$FindBin::Bin/.";

use Bio::AlignIO;
use Data::Dumper;

my $in = Bio::AlignIO->new(
  -format => 'stockholm',
  -file   => '/dev/stdin'
);

while(my $aln=$in->next_aln) {
  print $aln->accession, "\n";
}

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
#!/usr/bin/env bash

zcat ~/db/Pfam-A.full.gz | ./main.pl

~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh

...

------------- EXCEPTION -------------
MSG: '1985D' is not an integer.

STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
Range.pm:227
STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
lib/Bio/Annotation/Target.pm:81
STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:293
STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:73
STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
STACK toplevel ./main.pl:17
-------------------------------------

From thomas.girke at gmail.com  Wed Jan  9 15:59:08 2013
From: thomas.girke at gmail.com (Thomas Girke)
Date: Wed, 9 Jan 2013 12:59:08 -0800 (PST)
Subject: [Bioperl-l] Bioinformatics Position Opening
Message-ID: <9a99afb9-4a67-4d20-89ce-4d416fa7a46b@googlegroups.com>

Dear List,

Below is an announcement for a Ph.D. level bioinformatics position at
UCR. It is a long-term position with a competitive salary in a vibrant
research environment with cutting edge high-performance compute and
genomics facilities. Application instructions are given in the
announcement. Potential candidates are welcome to email me their
questions about this position directly, e.g.  prior or after submitting
a formal application. 

Best,

Thomas

--
Thomas Girke
Associate Professor of Bioinformatics
Institute for Integrative Genome Biology (IIGB)
1207F Genomics Building
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Ph: 951-905-5232
Fax: 951-827-5155


POSITION ANNOUNCEMENT

POSITION
The Institute for Integrative Genome Biology (IIGB) at the University of
California, Riverside is seeking a Ph.D. level bioinformatician to
manage its bioinformatics research activities and computing facility.  

TITLE/RANK
Bioinformatics Facility Director. Salary will be competitive and
commensurate with accomplishments.

LOCATION
University of California, Riverside. 

BACKGROUND
Successful candidates will join an innovative and multidisciplinary
Institute for Integrative Genome Biology (IIGB) that connects
theoretical and experimental researchers from different departments in
Life, Physical and Mathematical Sciences, Medicine, Engineering and
various campus based Centers. The IIGB is organized around a 10,000
sq.ft. suite of Instrumentation Facilities that serve as a centralized,
shared-use resource for faculty, staff and students, offering advanced
tools in bioinformatics, microscopy, proteomics and genomics. Its
bioinformatic component is equipped with an extensive high-performance
compute (HPC) infrastructure. 

QUALIFICATIONS
Applicants must have a Ph.D. from a recognized university in
bioinformatics; or combined degrees in computer science and a biological
science; or a degree in either computer science combined with relevant
experience in biological science; or a degree in a biological science
combined with relevant experience in computer science. The successful
candidate will have at least 2 years of professional hands-on experience
with next generation sequence data analysis, scientific data programming
and high-performance computing. A strong publication record of
bioinformatics research in collaboration with experimental biologists is
expected. Another requirement is several years of professional
experience with common programming languages/environments. This includes
at least one statistical programming environment (preferentially R), one
or more general-purpose scripting languages (e.g. Python, Perl or Ruby),
experience with web development frameworks and relational database
design. Several years of computational research experience using HPC
systems will be beneficial.  The incumbent should also have experience
with the analysis of modern biological data sets, such as microarrays,
next generation sequence data (e.g. genotyping, RNA profiling, de novo
assemblies), phylogenetics and/or molecular dynamics simulations.

RESPONSIBILITIES
The Bioinformatics Facility Director manages IIGB's computational
infrastructure jointly with its bioinformatics staff, including an
HPC/Linux systems administrator, one or more programmers and students
workers. The incumbent will be required to provide data analysis support
to collaborative research activities and make available findings through
presentations and contribute as team member to scientific publications
as well as participate in the preparation of joint grant applications
and reports. The teaching expectations include the development of a
state-of-the-art workshop program on large-scale data analysis and
programming. Participation in collaborative equipment grants will be
another core responsibility to secure future growth of the facility?s
computing resources. 

TO APPLY
Review of applications will continue until the position is filled.
Interested individuals should: (1) submit a curriculum vitae, (2)
provide a statement of research interests, and (3) arrange to have three
letters of reference sent on their behalf. All information should be
emailed to: thomas.girke at ucr.edu

WEBSITE
http://facility.bioinformatics.ucr.edu/position-opening



From frej.tulin at gmail.com  Thu Jan 10 21:53:16 2013
From: frej.tulin at gmail.com (Frej Tulin)
Date: Thu, 10 Jan 2013 21:53:16 -0500
Subject: [Bioperl-l] stand alone blast plus problem
Message-ID: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>

Hi

I have been trying for a long time to control my blast searches with the
Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was
a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing
seems to help.
When I build a database using the makeblastdb directly from the command
line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







-- 
Frej Tulin
Fred Cross lab
Rockefeller University

From cjfields at illinois.edu  Fri Jan 11 00:04:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 11 Jan 2013 05:04:12 +0000
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file
 from	Pfam
In-Reply-To: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
References: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF6A00B@CHIMBX5.ad.uillinois.edu>

I haven't used the '/dev/stdin' file like this, I typically do:

> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -fh   => \*STDIN
> );


but if it works?

That does look like a bug in the parser.  Would you know the Pfam alignmet accessions that triggered it, or maybe ones just prior to the fail?

chris

On Jan 3, 2013, at 4:41 PM, Peng Yu <pengyu.ut at gmail.com> wrote:

> Hi,
> 
> I tried the following code on the Pfam stockholm file (downloaded at
> ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
> But it gives me the following error. Is it a bug in bioperl or it is
> an error in the Pfam-A.full.gz file?
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> 
> #use FindBin;
> #use lib "$FindBin::Bin/.";
> 
> use Bio::AlignIO;
> use Data::Dumper;
> 
> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -file   => '/dev/stdin'
> );
> 
> while(my $aln=$in->next_aln) {
>  print $aln->accession, "\n";
> }
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
> #!/usr/bin/env bash
> 
> zcat ~/db/Pfam-A.full.gz | ./main.pl
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh
> 
> ...
> 
> ------------- EXCEPTION -------------
> MSG: '1985D' is not an integer.
> 
> STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
> Range.pm:227
> STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
> lib/Bio/Annotation/Target.pm:81
> STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
> Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:293
> STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
> py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:73
> STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
> ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
> STACK toplevel ./main.pl:17
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From Russell.Smithies at agresearch.co.nz  Sun Jan 13 17:25:16 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 14 Jan 2013 11:25:16 +1300
Subject: [Bioperl-l] stand alone blast plus problem
In-Reply-To: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
References: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF372E99EE4C1@exchsth.agresearch.co.nz>

Hi Frej,
Here's a few things to try:
Is it possible you need to escape the special chars in your IDs? i.e. the pipes and colons?
Have you tried it with simpler IDs?
Is your BioPerl sequence object collection created correctly?
Can you create the database by just passing it the fasta file?

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_name => 'mydb',
  -db_data => 'myseqs.fas',
  -create => 1
);

--Russell 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Frej Tulin
Sent: Friday, 11 January 2013 3:53 p.m.
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] stand alone blast plus problem

Hi

I have been trying for a long time to control my blast searches with the Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing seems to help.
When I build a database using the makeblastdb directly from the command line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







--
Frej Tulin
Fred Cross lab
Rockefeller University
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

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From awitney at sgul.ac.uk  Thu Jan 17 06:45:40 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 11:45:40 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
Message-ID: <50F7E464.3090906@sgul.ac.uk>

Hi,

I would like to produces graphics as shown in this section (cross 
linking between genome tracks) [scroll down a little to see the pictures]:

http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211

but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, 
but this works within a web browser, I would like to generate these 
diagrams from a stand alone script. If not does anyone know any perl 
libraries that can be used to show genome comparisons?

Thanks

Adam

From cjfields at illinois.edu  Thu Jan 17 08:37:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 13:37:04 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F7E464.3090906@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>

Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.

chris

On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> Hi,
> 
> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
> 
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
> 
> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
> 
> Thanks
> 
> Adam
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From awitney at sgul.ac.uk  Thu Jan 17 12:33:42 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 17:33:42 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
Message-ID: <50F835F6.5090603@sgul.ac.uk>


Thanks Chris. I hadn't seen SynBrowse before, looks good.

But I would like to do this without all the database/webserver overhead, 
I have a perl script that can interact with a gbrowse_syn database to 
generate images ie no webserver, I just need to separate out the 
database stuff now.

Thanks again

Adam

On 17/01/2013 13:37, Fields, Christopher J wrote:
> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>
> chris
>
> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>
>> Hi,
>>
>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>
>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>
>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>
>> Thanks
>>
>> Adam
>> _______________________________________________
>> 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  Thu Jan 17 12:41:47 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 17:41:47 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F835F6.5090603@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
	<50F835F6.5090603@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFD4BA@CITESMBX5.ad.uillinois.edu>

Let us know if this can be of use to the community, I'm sure others would find it useful as well.

chris

On Jan 17, 2013, at 11:33 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> 
> Thanks Chris. I hadn't seen SynBrowse before, looks good.
> 
> But I would like to do this without all the database/webserver overhead, I have a perl script that can interact with a gbrowse_syn database to generate images ie no webserver, I just need to separate out the database stuff now.
> 
> Thanks again
> 
> Adam
> 
> On 17/01/2013 13:37, Fields, Christopher J wrote:
>> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>> 
>> chris
>> 
>> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>> 
>>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>> 
>>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>> 
>>> Thanks
>>> 
>>> Adam
>>> _______________________________________________
>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From buschj at hhu.de  Sat Jan 19 11:12:54 2013
From: buschj at hhu.de (jobu)
Date: Sat, 19 Jan 2013 17:12:54 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking .."
Message-ID: <50FAC606.2060800@hhu.de>

Dear List,

I've got quite a lot of  hits from blasting against nt-database that state:

"Features flanking this part of subject sequence: "

where the subject-accession only will give information about complete
genomic sequences,
the detailed information inside the "Features flanking" section of the
HSP about annotations of upstream and downstream elements would be what
I need.

Is there any elegant way to make Bio::SearchIO do this job for me?

greetings
Jochen

From saladi1 at illinois.edu  Tue Jan 22 16:45:23 2013
From: saladi1 at illinois.edu (Shyam Saladi)
Date: Tue, 22 Jan 2013 13:45:23 -0800
Subject: [Bioperl-l] Bio::DB::Taxonomy example
Message-ID: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>

Hi,

There is an example on how to use Bio::DB::Taxonomy at
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy

I tried the script but could not get it to work properly. After looking
through the documentation it seems that

my @extant_children = grep { $_->rank eq 'species' }
$node->get_all_Descendents;

should instead be

my @extant_children = grep { $_->rank eq 'species' }
$db->get_all_Descendents($node)

I found this solves the problem for me. If my fix is in fact correct, an
admin may want to change the example script online.

Thanks,
Shyam
**

From cjfields at illinois.edu  Tue Jan 22 18:40:05 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 22 Jan 2013 23:40:05 +0000
Subject: [Bioperl-l] Bio::DB::Taxonomy example
In-Reply-To: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
References: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CDFE139@CITESMBX5.ad.uillinois.edu>

Done.  Thanks for pointing that out!

chris

On Jan 23, 2013, at 5:45 AM, Shyam Saladi <saladi1 at illinois.edu>
 wrote:

> Hi,
> 
> There is an example on how to use Bio::DB::Taxonomy at
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> 
> I tried the script but could not get it to work properly. After looking
> through the documentation it seems that
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $node->get_all_Descendents;
> 
> should instead be
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $db->get_all_Descendents($node)
> 
> I found this solves the problem for me. If my fix is in fact correct, an
> admin may want to change the example script online.
> 
> Thanks,
> Shyam
> **
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From buschj at hhu.de  Fri Jan 25 05:20:22 2013
From: buschj at hhu.de (jobu)
Date: Fri, 25 Jan 2013 11:20:22 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
Message-ID: <51025C66.6060008@hhu.de>

Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
> What upstream and downstream elements are you interested in?


I've got a huge pile of short RNA reads.
Part of the question now is whether those RNA fragments originate from
siRNA events,
or may represent miRNAs / parts of pre-miRNAs.

So I did an online  blast search against database nt.
The resulting report quite often just gives subject information like this:

-----
> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
Length=23459830
-----

Now I would like to get the hit's neighbouring regions  for further
analysis.
Preferably I would like to do that  in an automized way, but the only
possible action with this kind of subject gi | description would be to
fetch the entire chromosomal  sequence I guess ?

However,
right below the line above, the report states more precisely:

------
 Features flanking this part of subject sequence:
   8872 bp at 5' side: cytochrome P450 90B1
   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
------

Still I would like to have the possibility to automatically fetch the
subject's sequence(s),
as of now I think  parsing the report with SearchIO won't let me aquire
that information, because SearchIO does not recognize report sections
like those.

I hope I did not miss any of SearchIOs capabilities, but I could not
find any method covering my wish?!

Right now maybe the only way to get the information I want is to
construct my own parser and write it out into a separate file, which in
turn again  I could read into a hash before processing the Blast-Report
with SearchIO to combine both data for further automized work.

I am aware though that even successfully getting the flanking features
would leave me with the more or less wide  intergenic gap my hsp is
located in.

However I'm in need of a way to get the flanking features including
their annotation and the region spanning between them.
But I hope I do not have to get complete sequences to accomplish that,
as this would be kind of an overkill.

with kind regards
Jochen




From afonsomduarte at gmail.com  Mon Jan 14 05:09:48 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 14 Jan 2013 02:09:48 -0800 (PST)
Subject: [Bioperl-l] Parsing Blast results for different genus
Message-ID: <217cf8ac-5323-48f5-8a81-aba032cba68b@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


PS sorry if this message appears twice ... as i was having some trouble 
posting the first time.

From afonsomduarte at gmail.com  Sun Jan 13 14:17:19 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Sun, 13 Jan 2013 11:17:19 -0800 (PST)
Subject: [Bioperl-l] Split blast result by genus. How to parse it ?
Message-ID: <83857a34-14a0-43e2-a2b3-5ca538d41bcd@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best

From afonsomduarte at gmail.com  Mon Jan 21 04:03:44 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 21 Jan 2013 01:03:44 -0800 (PST)
Subject: [Bioperl-l] spliting genbank file into smaller ones via organism
Message-ID: <f8a60619-c086-4a29-8541-13b136b716f3@googlegroups.com>



Dear List,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best

From jason.stajich at gmail.com  Tue Jan 29 14:00:16 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Tue, 29 Jan 2013 11:00:16 -0800
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <51025C66.6060008@hhu.de>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
	<51025C66.6060008@hhu.de>
Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D@gmail.com>

We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.

However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.

basically:
- download the genome and GFF for arabidopsis
- align your sRNA to the genome with a short read aligner - bowtie, bwa, others
- convert your sam to bam file with SAMtools or picard
- compare the location of features with the reads to get expression summaries or individuals reads with BEDTools


On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:

> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>> What upstream and downstream elements are you interested in?
> 
> 
> I've got a huge pile of short RNA reads.
> Part of the question now is whether those RNA fragments originate from
> siRNA events,
> or may represent miRNAs / parts of pre-miRNAs.
> 
> So I did an online  blast search against database nt.
> The resulting report quite often just gives subject information like this:
> 
> -----
>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
> Length=23459830
> -----
> 
> Now I would like to get the hit's neighbouring regions  for further
> analysis.
> Preferably I would like to do that  in an automized way, but the only
> possible action with this kind of subject gi | description would be to
> fetch the entire chromosomal  sequence I guess ?
> 
> However,
> right below the line above, the report states more precisely:
> 
> ------
> Features flanking this part of subject sequence:
>   8872 bp at 5' side: cytochrome P450 90B1
>   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
> ------
> 
> Still I would like to have the possibility to automatically fetch the
> subject's sequence(s),
> as of now I think  parsing the report with SearchIO won't let me aquire
> that information, because SearchIO does not recognize report sections
> like those.
> 
> I hope I did not miss any of SearchIOs capabilities, but I could not
> find any method covering my wish?!
> 
> Right now maybe the only way to get the information I want is to
> construct my own parser and write it out into a separate file, which in
> turn again  I could read into a hash before processing the Blast-Report
> with SearchIO to combine both data for further automized work.
> 
> I am aware though that even successfully getting the flanking features
> would leave me with the more or less wide  intergenic gap my hsp is
> located in.
> 
> However I'm in need of a way to get the flanking features including
> their annotation and the region spanning between them.
> But I hope I do not have to get complete sequences to accomplish that,
> as this would be kind of an overkill.
> 
> with kind regards
> Jochen
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org



From dr_kilburn59 at yahoo.com  Wed Jan 30 16:40:26 2013
From: dr_kilburn59 at yahoo.com (Dan kilburn)
Date: Wed, 30 Jan 2013 16:40:26 -0500
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
Message-ID: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>

Hi Jason,

Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.

--Dan
Sent from my iPhone

On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:

> Send Bioperl-l mailing list submissions to
>    bioperl-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>    http://lists.open-bio.org/mailman/listinfo/bioperl-l
> or, via email, send a message with subject or body 'help' to
>    bioperl-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
>    bioperl-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
> 
> 
> Today's Topics:
> 
>   1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>      (Jason Stajich)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 29 Jan 2013 11:00:16 -0800
> From: Jason Stajich <jason.stajich at gmail.com>
> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>    flanking    .."
> To: buschj at hhu.de
> Cc: bioperl-l at lists.open-bio.org
> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
> Content-Type: text/plain;    charset=us-ascii
> 
> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
> 
> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
> 
> basically:
> - download the genome and GFF for arabidopsis
> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
> - convert your sam to bam file with SAMtools or picard
> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
> 
> 
> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
> 
>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>> What upstream and downstream elements are you interested in?
>> 
>> 
>> I've got a huge pile of short RNA reads.
>> Part of the question now is whether those RNA fragments originate from
>> siRNA events,
>> or may represent miRNAs / parts of pre-miRNAs.
>> 
>> So I did an online  blast search against database nt.
>> The resulting report quite often just gives subject information like this:
>> 
>> -----
>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>> Length=23459830
>> -----
>> 
>> Now I would like to get the hit's neighbouring regions  for further
>> analysis.
>> Preferably I would like to do that  in an automized way, but the only
>> possible action with this kind of subject gi | description would be to
>> fetch the entire chromosomal  sequence I guess ?
>> 
>> However,
>> right below the line above, the report states more precisely:
>> 
>> ------
>> Features flanking this part of subject sequence:
>>  8872 bp at 5' side: cytochrome P450 90B1
>>  402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>> ------
>> 
>> Still I would like to have the possibility to automatically fetch the
>> subject's sequence(s),
>> as of now I think  parsing the report with SearchIO won't let me aquire
>> that information, because SearchIO does not recognize report sections
>> like those.
>> 
>> I hope I did not miss any of SearchIOs capabilities, but I could not
>> find any method covering my wish?!
>> 
>> Right now maybe the only way to get the information I want is to
>> construct my own parser and write it out into a separate file, which in
>> turn again  I could read into a hash before processing the Blast-Report
>> with SearchIO to combine both data for further automized work.
>> 
>> I am aware though that even successfully getting the flanking features
>> would leave me with the more or less wide  intergenic gap my hsp is
>> located in.
>> 
>> However I'm in need of a way to get the flanking features including
>> their annotation and the region spanning between them.
>> But I hope I do not have to get complete sequences to accomplish that,
>> as this would be kind of an overkill.
>> 
>> with kind regards
>> Jochen
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> End of Bioperl-l Digest, Vol 117, Issue 13
> ******************************************


From cjfields at illinois.edu  Wed Jan 30 18:13:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 30 Jan 2013 23:13:49 +0000
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
	<575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CE1175C@CHIMBX5.ad.uillinois.edu>

We certainly accept support for updates to the code.  In fact, if you are familiar with git/github the process is fairly straightforward:

1) Fork the code to your github account
2) Make and commit changes
3) Submit a pull request
4) Post something to the list just in case.

We also accept code patches; the best way to submit these is as a bug report to the redmine repository (doesn't hurt to post here as well):

https://redmine.open-bio.org/

chris

On Jan 30, 2013, at 3:40 PM, Dan kilburn <dr_kilburn59 at yahoo.com> wrote:

> Hi Jason,
> 
> Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.
> 
> --Dan
> Sent from my iPhone
> 
> On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:
> 
>> Send Bioperl-l mailing list submissions to
>>   bioperl-l at lists.open-bio.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>>   http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> or, via email, send a message with subject or body 'help' to
>>   bioperl-l-request at lists.open-bio.org
>> 
>> You can reach the person managing the list at
>>   bioperl-l-owner at lists.open-bio.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Bioperl-l digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>>     (Jason Stajich)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Tue, 29 Jan 2013 11:00:16 -0800
>> From: Jason Stajich <jason.stajich at gmail.com>
>> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>>   flanking    .."
>> To: buschj at hhu.de
>> Cc: bioperl-l at lists.open-bio.org
>> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
>> Content-Type: text/plain;    charset=us-ascii
>> 
>> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
>> 
>> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
>> 
>> basically:
>> - download the genome and GFF for arabidopsis
>> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
>> - convert your sam to bam file with SAMtools or picard
>> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
>> 
>> 
>> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
>> 
>>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>>> What upstream and downstream elements are you interested in?
>>> 
>>> 
>>> I've got a huge pile of short RNA reads.
>>> Part of the question now is whether those RNA fragments originate from
>>> siRNA events,
>>> or may represent miRNAs / parts of pre-miRNAs.
>>> 
>>> So I did an online  blast search against database nt.
>>> The resulting report quite often just gives subject information like this:
>>> 
>>> -----
>>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>>> Length=23459830
>>> -----
>>> 
>>> Now I would like to get the hit's neighbouring regions  for further
>>> analysis.
>>> Preferably I would like to do that  in an automized way, but the only
>>> possible action with this kind of subject gi | description would be to
>>> fetch the entire chromosomal  sequence I guess ?
>>> 
>>> However,
>>> right below the line above, the report states more precisely:
>>> 
>>> ------
>>> Features flanking this part of subject sequence:
>>> 8872 bp at 5' side: cytochrome P450 90B1
>>> 402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>>> ------
>>> 
>>> Still I would like to have the possibility to automatically fetch the
>>> subject's sequence(s),
>>> as of now I think  parsing the report with SearchIO won't let me aquire
>>> that information, because SearchIO does not recognize report sections
>>> like those.
>>> 
>>> I hope I did not miss any of SearchIOs capabilities, but I could not
>>> find any method covering my wish?!
>>> 
>>> Right now maybe the only way to get the information I want is to
>>> construct my own parser and write it out into a separate file, which in
>>> turn again  I could read into a hash before processing the Blast-Report
>>> with SearchIO to combine both data for further automized work.
>>> 
>>> I am aware though that even successfully getting the flanking features
>>> would leave me with the more or less wide  intergenic gap my hsp is
>>> located in.
>>> 
>>> However I'm in need of a way to get the flanking features including
>>> their annotation and the region spanning between them.
>>> But I hope I do not have to get complete sequences to accomplish that,
>>> as this would be kind of an overkill.
>>> 
>>> with kind regards
>>> Jochen
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> End of Bioperl-l Digest, Vol 117, Issue 13
>> ******************************************
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From thiago.venancio at gmail.com  Thu Jan 31 12:10:39 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:10:39 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
Message-ID: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>

Hi all,

I am trying to install bioperl-ext and the compilation gives me the error:

/usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
can not be used when making a shared object; recompile with -fPIC
libs/libsw.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
make[1]: Leaving directory 
`/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align'
make: *** [subdirs] Error 2

However, the Makefile says that -fPIC is already being used, which is 
puzzling me.

Any clues ?

Thanks.
Thiago




From thiago.venancio at gmail.com  Thu Jan 31 12:25:12 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:25:12 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
In-Reply-To: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
References: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
Message-ID: <e22d2881-ddd3-42af-9a69-f03503b8fb5a@googlegroups.com>

Solved using the solution posted by jmf here :
https://groups.google.com/forum/?fromgroups=#!searchin/bioperl-l/bioperl-ext/bioperl-l/FgJo_g8UQE8/FB1DEjJkTooJ

Which I found after posting.

T


On Thursday, January 31, 2013 3:10:39 PM UTC-2, Thiago Venancio wrote:
>
> Hi all, 
>
> I am trying to install bioperl-ext and the compilation gives me the error: 
>
> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
> can not be used when making a shared object; recompile with -fPIC 
> libs/libsw.a: could not read symbols: Bad value 
> collect2: ld returned 1 exit status 
> make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 
> make[1]: Leaving directory 
> `/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align' 
> make: *** [subdirs] Error 2 
>
> However, the Makefile says that -fPIC is already being used, which is 
> puzzling me. 
>
> Any clues ? 
>
> Thanks. 
> Thiago 
>
>
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>

From koriege at googlemail.com  Thu Jan 31 21:49:20 2013
From: koriege at googlemail.com (koriege at googlemail.com)
Date: Thu, 31 Jan 2013 18:49:20 -0800 (PST)
Subject: [Bioperl-l] problem with Bio::*::Fasta id_parser
Message-ID: <e9e0c428-0467-4b62-a37d-cfcb91ed818b@googlegroups.com>

Hi,

I tried two methods to create a bioperl FASTA database, but it failes by 
extracting the substring out of my headers.
Can someone explain me why I get the standard header or show me a work 
around? 

thanks in advance.
pyr0

i)
my $objDB = Bio::Index::Fasta->new(-filename => $PATHdbIdx, -write_flag => 
1);
$objDB->id_parser(\&get_id);
$objDB->make_index(glob($objParameter->dbGenome()));

sub get_id {
   my $header = shift;
   $header =~ /^>.*\bsp\|([A-Z]\d{5}\b)/;
   $1;
}

output
Use of uninitialized value $id in concatenation (.) or string at 
/usr/share/perl5/Bio/Index/Abstract.pm line 753, <$FASTA> line 1.
Use of uninitialized value $id in exists at 
/usr/share/perl5/Bio/Index/Abstract.pm line 754, <$FASTA> line 1.
Use of uninitialized value $id in hash element at 
/usr/share/perl5/Bio/Index/Abstract.pm line 757, <$FASTA> line 1.
gi|376282008|ref|NC_016798.1|

ii)
my $PATHdbIdx=catfile($objParameter->DIR,'data','db.idx');
unlink($PATHdbIdx);
my $objDB = Bio::DB::Fasta->new($objParameter->dbGenome(), -makeid => 
\&get_id);
$objDBgenome->set(\$objDB);

output:
Use of uninitialized value $key in pattern match (m//) at 
/usr/share/perl5/Bio/DB/Fasta.pm line 1178.
Use of uninitialized value $id in exists at 
/usr/share/perl5/Bio/DB/Fasta.pm line 617.
gi|376282008|ref|NC_016798.1|

From yuf228 at hotmail.com  Thu Jan 31 23:15:15 2013
From: yuf228 at hotmail.com (Rob)
Date: Fri, 1 Feb 2013 04:15:15 +0000 (UTC)
Subject: [Bioperl-l] Where to get BLASTCLUST or equivalent?
References: <200305311150.h4VBopn2019091@localhost.localdomain>
Message-ID: <loom.20130201T045704-740@post.gmane.org>

Cyril C.C. Chua <bmbcccc <at> bmb.leeds.ac.uk> writes:

> 
> Hi,
> 
> I have some difficulty in sourcing for BLASTCLUST or related 
> programs/mods. Does any1 know exactly how to locate them?
> 
> Regards
> 
> Cyril Chua
> 


Hi Cyril,

I heard of the following programmes that might do similar things (I HAVEN'T 
used any of them yet):

Afree - http://www.vicbioinformatics.com/software.afree.shtml
Uclust - http://drive5.com/uclust/uclust_userguide_2_1.pdf
Usearch - http://www.drive5.com/usearch/
DomClust - http://mbgd.genome.ad.jp/domclust/

or 

Check this: 

http://ppod.princeton.edu/help/help_tech.html

God bless,


Robert



From jimhu at tamu.edu  Wed Jan  2 14:44:56 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 2 Jan 2013 13:44:56 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
Message-ID: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>

I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.

I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From biojiangke at gmail.com  Wed Jan  2 15:20:02 2013
From: biojiangke at gmail.com (Ke Jiang)
Date: Wed, 2 Jan 2013 15:20:02 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>

There is a blast2gff.pl floating around for Gbrowse to visualize blast
results as tracks. Not sure about the blast+. One more reason to stick with
the good old blast!

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Ke

-------------------------------------------
Ke Jiang, Ph.D.
Post-doctoral Fellow
Delbruck Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724


From cjfields at illinois.edu  Wed Jan  2 15:47:52 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 20:47:52 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FD44@CHIMBX5.ad.uillinois.edu>

?except that NCBI no longer supports legacy BLAST.  Caveat emptor.

chris

On Jan 2, 2013, at 2:20 PM, Ke Jiang <biojiangke at gmail.com> wrote:

> There is a blast2gff.pl floating around for Gbrowse to visualize blast
> results as tracks. Not sure about the blast+. One more reason to stick with
> the good old blast!
> 
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> 
> Ke
> 
> -------------------------------------------
> Ke Jiang, Ph.D.
> Post-doctoral Fellow
> Delbruck Laboratory
> Cold Spring Harbor Laboratory
> Cold Spring Harbor, NY 11724
> _______________________________________________
> 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  Wed Jan  2 15:26:22 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 15:26:22 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>

Here's one:

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Another one:

~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl 
#!perl

# Author:      Jason Stajich <jason-at-bioperl-dot-org>
# Description: Turn SearchIO parseable report(s) into a GFF report
#
=head1 NAME

bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report



Brian O.

On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:

> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> 
> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  
> 
> Thanks,
> 
> Jim
> =====================================
> Jim Hu
> Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From scott at scottcain.net  Wed Jan  2 16:32:16 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 2 Jan 2013 16:32:16 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
Message-ID: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>

Hi Brian,

I was going to suggest the same thing--though that script is fairly
old, it's not as old as the blast2gff script in the GBrowse
distribution (which probably should be retired).  I believe it
supports GFF3, though I don't have any sample data with which to test
it to be sure.  I also don't know if it supports BLAST+ input--I
haven't kept up with SearchIO (on which search2gff.pl depends); will
it accept it?

Scott


On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> Here's one:
>
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>
> Another one:
>
> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> #!perl
>
> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> # Description: Turn SearchIO parseable report(s) into a GFF report
> #
> =head1 NAME
>
> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>
>
>
> Brian O.
>
> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>
>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>
>> Thanks,
>>
>> Jim
>> =====================================
>> Jim Hu
>> Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>>
>> _______________________________________________
>> 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



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


From cjfields at illinois.edu  Wed Jan  2 17:26:55 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 22:26:55 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>

It should (I recall using it at one point).  If it doesn't we should fix it so it does.

How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 

chris

On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Brian,
> 
> I was going to suggest the same thing--though that script is fairly
> old, it's not as old as the blast2gff script in the GBrowse
> distribution (which probably should be retired).  I believe it
> supports GFF3, though I don't have any sample data with which to test
> it to be sure.  I also don't know if it supports BLAST+ input--I
> haven't kept up with SearchIO (on which search2gff.pl depends); will
> it accept it?
> 
> Scott
> 
> 
> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>> Here's one:
>> 
>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>> 
>> Another one:
>> 
>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>> #!perl
>> 
>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>> # Description: Turn SearchIO parseable report(s) into a GFF report
>> #
>> =head1 NAME
>> 
>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>> 
>> 
>> 
>> Brian O.
>> 
>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>> 
>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>> 
>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>> 
>>> Thanks,
>>> 
>>> Jim
>>> =====================================
>>> Jim Hu
>>> Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> 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  Wed Jan  2 17:53:50 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 17:53:50 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
Message-ID: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>

Scott and Chris,

I'll test it and see?

Brian O.


On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> 
> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
> 
> chris
> 
> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> 
>> Hi Brian,
>> 
>> I was going to suggest the same thing--though that script is fairly
>> old, it's not as old as the blast2gff script in the GBrowse
>> distribution (which probably should be retired).  I believe it
>> supports GFF3, though I don't have any sample data with which to test
>> it to be sure.  I also don't know if it supports BLAST+ input--I
>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>> it accept it?
>> 
>> Scott
>> 
>> 
>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>> Here's one:
>>> 
>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>> 
>>> Another one:
>>> 
>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>> #!perl
>>> 
>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>> #
>>> =head1 NAME
>>> 
>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>> 
>>> 
>>> 
>>> Brian O.
>>> 
>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>> 
>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>> 
>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>> 
>>>> Thanks,
>>>> 
>>>> Jim
>>>> =====================================
>>>> Jim Hu
>>>> Professor
>>>> Dept. of Biochemistry and Biophysics
>>>> 2128 TAMU
>>>> Texas A&M Univ.
>>>> College Station, TX 77843-2128
>>>> 979-862-4054
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From jimhu at tamu.edu  Fri Jan  4 14:49:51 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 13:49:51 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>

Thanks for the replies, but...

I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.

The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be broken, at least on this page:

	http://www.bioperl.org/wiki/Module:Bio::SearchIO

Jim


On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From bosborne11 at verizon.net  Fri Jan  4 14:26:52 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 04 Jan 2013 14:26:52 -0500
Subject: [Bioperl-l] strange error in the beginners howto
In-Reply-To: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
References: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
Message-ID: <BB2BD9EA-3419-4B6C-A659-4D86420CFAE0@verizon.net>

Matthew,

First, let's distinguish "warning" and "error". Errors stop execution of the app or script, what you're seeing is a warning, your script actually completes. Does the warning vanish if you remove "-w"?

Second, seems like this is a Perl version thing:

http://www.sysarchitects.com/bioperl

BIO

On Jan 4, 2013, at 1:55 PM, "Thornton, Matthew" <Matthew.Thornton at med.usc.edu> wrote:

> Hello,
> 
> I am working through the first part of the BioPerl beginners howto and I am getting an error and I was wondering if you could tell me what is wrong.
> 
> I made the seqio.pl script:
> 
> #!/bin/perl -w
> 
> use Bio::Seq;
> 
> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",                        
>                          -display_id => "#12345",                        
>                          -desc => "example 1",                        
>                          -alphabet => "dna" );
> 
> print $seq_obj->seq();
> 
> I execute the script and I get this error:
> 
> gserver at gserver:~/bio$ perl seqio.pl 
> Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251.
> aaaatgggggggggggccccgttgserver at gserver:~/bio$
> 
> Is there something wrong with my installation?
> 
> Any help is greatly appreciated.
> 
> Thanks!
> 
> 
> Matthew E. Thornton
> 
> 
> 
> Laboratory Technician III
> Broad Center for Stem Cell and Regenerative Medicine
> University of Southern California
> 1501 San Pablo St. ZNI
> Los Angeles, CA 90089-2821
> ph.:323-442-1688
> fx.:323-442-4040
> matthew.thornton at med.usc.edu
> 

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




From MEC at stowers.org  Fri Jan  4 15:20:17 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 14:20:17 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>

Jim,

Getting to your original question:

> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.

Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??

If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'

I would guess not because neither of them have 'subfeatures'.

If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.


~Malcolm


 .-----Original Message-----
 .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .Sent: Friday, January 04, 2013 1:50 PM
 .To: Brian Osborne
 .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Thanks for the replies, but...
 .
 .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
 .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .
 .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .broken, at least on this page:
 .
 .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .
 .Jim
 .
 .
 .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .
 .> Scott and Chris,
 .>
 .> I'll test it and see...
 .>
 .> Brian O.
 .>
 .>
 .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .>
 .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .>>
 .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .>>
 .>> chris
 .>>
 .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .>>
 .>>> Hi Brian,
 .>>>
 .>>> I was going to suggest the same thing--though that script is fairly
 .>>> old, it's not as old as the blast2gff script in the GBrowse
 .>>> distribution (which probably should be retired).  I believe it
 .>>> supports GFF3, though I don't have any sample data with which to test
 .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .>>> it accept it?
 .>>>
 .>>> Scott
 .>>>
 .>>>
 .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .>>>> Here's one:
 .>>>>
 .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .>>>>
 .>>>> Another one:
 .>>>>
 .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .>>>> #!perl
 .>>>>
 .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .>>>> #
 .>>>> =head1 NAME
 .>>>>
 .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .>>>>
 .>>>>
 .>>>>
 .>>>> Brian O.
 .>>>>
 .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .>>>>
 .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .>>>>>
 .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .create gff with appropriate subfeatures.
 .>>>>>
 .>>>>> Thanks,
 .>>>>>
 .>>>>> Jim
 .>>>>> =====================================
 .>>>>> Jim Hu
 .>>>>> Professor
 .>>>>> Dept. of Biochemistry and Biophysics
 .>>>>> 2128 TAMU
 .>>>>> Texas A&M Univ.
 .>>>>> College Station, TX 77843-2128
 .>>>>> 979-862-4054
 .>>>>>
 .>>>>>
 .>>>>>
 .>>>>> _______________________________________________
 .>>>>> 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
 .>>>
 .>>>
 .>>>
 .>>> --
 .>>> ------------------------------------------------------------------------
 .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .>>> Ontario Institute for Cancer Research
 .>>> _______________________________________________
 .>>> Bioperl-l mailing list
 .>>> Bioperl-l at lists.open-bio.org
 .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .>>
 .>
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .
 .
 .
 ._______________________________________________
 .Bioperl-l mailing list
 .Bioperl-l at lists.open-bio.org
 .http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jimhu at tamu.edu  Fri Jan  4 16:57:38 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 15:57:38 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
Message-ID: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>

Malcolm,

Thanks, I should have reread the GFF3 spec before posting!

In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see how the final output could be done in different ways, but I'm still stuck on how to get there.  

I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a transposable element, for example.

Excerpting from blastp -help

 *** Formatting options
 -outfmt <String>
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1) 

Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute OR the multi-line match features OR a combination from one of these output formats. 

I'm probably missing something very, very obvious.

Best,

Jim


On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:

> Jim,
> 
> Getting to your original question:
> 
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.
> 
> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
> 
> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'
> 
> I would guess not because neither of them have 'subfeatures'.
> 
> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.
> 
> 
> ~Malcolm
> 
> 
> .-----Original Message-----
> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
> .Sent: Friday, January 04, 2013 1:50 PM
> .To: Brian Osborne
> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
> .
> .Thanks for the replies, but...
> .
> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
> .
> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
> .broken, at least on this page:
> .
> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
> .
> .Jim
> .
> .
> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
> .
> .> Scott and Chris,
> .>
> .> I'll test it and see...
> .>
> .> Brian O.
> .>
> .>
> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> .>
> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> .>>
> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
> .>>
> .>> chris
> .>>
> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> .>>
> .>>> Hi Brian,
> .>>>
> .>>> I was going to suggest the same thing--though that script is fairly
> .>>> old, it's not as old as the blast2gff script in the GBrowse
> .>>> distribution (which probably should be retired).  I believe it
> .>>> supports GFF3, though I don't have any sample data with which to test
> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
> .>>> it accept it?
> .>>>
> .>>> Scott
> .>>>
> .>>>
> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> .>>>> Here's one:
> .>>>>
> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> .>>>>
> .>>>> Another one:
> .>>>>
> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> .>>>> #!perl
> .>>>>
> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
> .>>>> #
> .>>>> =head1 NAME
> .>>>>
> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
> .>>>>
> .>>>>
> .>>>>
> .>>>> Brian O.
> .>>>>
> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
> .>>>>
> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> .>>>>>
> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
> .create gff with appropriate subfeatures.
> .>>>>>
> .>>>>> Thanks,
> .>>>>>
> .>>>>> Jim
> .>>>>> =====================================
> .>>>>> Jim Hu
> .>>>>> Professor
> .>>>>> Dept. of Biochemistry and Biophysics
> .>>>>> 2128 TAMU
> .>>>>> Texas A&M Univ.
> .>>>>> College Station, TX 77843-2128
> .>>>>> 979-862-4054
> .>>>>>
> .>>>>>
> .>>>>>
> .>>>>> _______________________________________________
> .>>>>> 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
> .>>>
> .>>>
> .>>>
> .>>> --
> .>>> ------------------------------------------------------------------------
> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> .>>> Ontario Institute for Cancer Research
> .>>> _______________________________________________
> .>>> Bioperl-l mailing list
> .>>> Bioperl-l at lists.open-bio.org
> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> .>>
> .>
> .
> .=====================================
> .Jim Hu
> .Professor
> .Dept. of Biochemistry and Biophysics
> .2128 TAMU
> .Texas A&M Univ.
> .College Station, TX 77843-2128
> .979-862-4054
> .
> .
> .
> ._______________________________________________
> .Bioperl-l mailing list
> .Bioperl-l at lists.open-bio.org
> .http://lists.open-bio.org/mailman/listinfo/bioperl-l

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From MEC at stowers.org  Fri Jan  4 18:33:04 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 17:33:04 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
	<2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE7CB@EXCHMB-02.stowers-institute.org>

Jim,

To get a working example for further discussion....

Assuming you have bioperl and blast+ installed....

This command gets a known transcript from ncbi and blasts it back at ncbi into fly genome:

> bp_download_query_genbank.pl --query 'NM_001259364' | blastn -remote -db refseq_genomic  -entrez_query 'melanogaster[Taxid]'  -outfmt 6  > test.blast.tab

Take a look at the results (see below, or run it yourself).

First line output looks like this:

	NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928

Old GFF did not have parent-child.  Depending on where you are going with this, you MIGHT want to use this strategy: http://gmod.org/wiki/GFF#Alignments

Where the ID in column 9 serves to group the features.  There is an 'implicit' parent.

I think this would be respected by both GBrowse and UCSC genome browser (but I'm not positive).

If so, converting blast output would yield one line output per each line input.

You would need to assign a strand, swap sstart and send where sstart>send, and some slight re-formatting

First line of GFF might look like:

	NT_033778.3 est EST_match 9330023	9327897  . + . ID=Match1;Name= NM_001259364;Target= NM_001259364 1869	3995

Is this along the lines of what you need?

~Malcolm

Complete example blast+ output looks like this:

NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	1019	0	0	3995	5013	9327834	9326816	0.0	1882
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	374	0	0	345	718	9332643	9332270	0.0	 691
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	300	0	0	1	300	9337978	9337679	1e-154	 555
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	270	0	0	717	986	9332201	9331932	5e-138	 499
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	243	0	0	1434	1676	9331200	9330958	5e-123	 449
NM_001259364	gi|116010442|ref|NT_033778.3|	99.55	223	0	1	1154	1376	9331611	9331390	1e-109	 405
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	196	0	0	1675	1870	9330634	9330439	7e-97	 363
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	169	0	0	986	1154	9331847	9331679	7e-82	 313
NM_001259364	gi|116010442|ref|NT_033778.3|	97.26	73	2	0	1372	1444	9331322	9331250	3e-25	 124
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	44	0	0	301	344	9333095	9333052	2e-12	82.4
NM_001259364	gi|195586644|ref|NT_167067.1|	96.52	2127	74	0	1869	3995	7777827	7775701	0.0	3518
NM_001259364	gi|195586644|ref|NT_167067.1|	97.03	404	7	3	4004	4402	7775629	7775226	0.0	 675
NM_001259364	gi|195586644|ref|NT_167067.1|	93.58	374	24	0	345	718	7780392	7780019	8e-156	 558
NM_001259364	gi|195586644|ref|NT_167067.1|	94.37	302	15	1	1	300	7786262	7785961	6e-127	 462
NM_001259364	gi|195586644|ref|NT_167067.1|	96.25	267	10	0	720	986	7779949	7779683	1e-119	 438
NM_001259364	gi|195586644|ref|NT_167067.1|	95.00	240	12	0	1434	1673	7778959	7778720	2e-101	 377
NM_001259364	gi|195586644|ref|NT_167067.1|	96.86	223	6	1	1154	1376	7779370	7779149	1e-99	 372
NM_001259364	gi|195586644|ref|NT_167067.1|	93.88	196	12	0	1675	1870	7778384	7778189	7e-77	 296
NM_001259364	gi|195586644|ref|NT_167067.1|	95.19	187	5	4	4827	5013	7774635	7774453	9e-76	 292
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	168	12	0	987	1154	7779598	7779431	3e-61	 244
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	70	5	0	1374	1443	7779079	7779010	2e-18	 102
NM_001259364	gi|195586644|ref|NT_167067.1|	100.00	44	0	0	301	344	7780833	7780790	2e-12	82.4
NM_001259364	gi|195489961|ref|NT_167063.1|	92.43	2127	161	0	1869	3995	7628910	7631036	0.0	3037
NM_001259364	gi|195489961|ref|NT_167063.1|	91.94	1030	38	20	3995	5013	7631102	7632097	0.0	1400
NM_001259364	gi|195489961|ref|NT_167063.1|	88.56	376	39	4	345	718	7626215	7626588	4e-124	 453
NM_001259364	gi|195489961|ref|NT_167063.1|	93.67	300	18	1	1	300	7620777	7621075	2e-122	 448
NM_001259364	gi|195489961|ref|NT_167063.1|	95.41	196	9	0	1675	1870	7628263	7628458	7e-82	 313
NM_001259364	gi|195489961|ref|NT_167063.1|	91.93	223	17	1	1154	1376	7627224	7627445	2e-81	 311
NM_001259364	gi|195489961|ref|NT_167063.1|	86.42	265	31	3	720	983	7626653	7626913	1e-73	 285
NM_001259364	gi|195489961|ref|NT_167063.1|	86.18	246	25	4	1434	1673	7627635	7627877	3e-65	 257
NM_001259364	gi|195489961|ref|NT_167063.1|	88.27	162	19	0	993	1154	7626999	7627160	3e-46	 195
NM_001259364	gi|195489961|ref|NT_167063.1|	93.06	72	5	0	1372	1443	7627513	7627584	1e-19	 106
NM_001259364	gi|195489961|ref|NT_167063.1|	100.00	44	0	0	301	344	7625770	7625813	2e-12	82.4


~Malcolm


 .-----Original Message-----
 .From: Jim Hu [mailto:jimhu at tamu.edu]
 .Sent: Friday, January 04, 2013 3:58 PM
 .To: Cook, Malcolm
 .Cc: 'Brian Osborne'; 'Fields, Christopher J'; 'Scott Cain'; 'bioperl-l at bioperl.org'
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Malcolm,
 .
 .Thanks, I should have reread the GFF3 spec before posting!
 .
 .In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking
 .of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see
 .how the final output could be done in different ways, but I'm still stuck on how to get there.
 .
 .I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get
 .to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are
 .gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other
 .work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a
 .transposable element, for example.
 .
 .Excerpting from blastp -help
 .
 . *** Formatting options
 . -outfmt <String>
 .   alignment view options:
 .     0 = pairwise,
 .     1 = query-anchored showing identities,
 .     2 = query-anchored no identities,
 .     3 = flat query-anchored, show identities,
 .     4 = flat query-anchored, no identities,
 .     5 = XML Blast output,
 .     6 = tabular,
 .     7 = tabular with comment lines,
 .     8 = Text ASN.1,
 .     9 = Binary ASN.1,
 .    10 = Comma-separated values,
 .    11 = BLAST archive format (ASN.1)
 .
 .Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than
 .suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute
 .OR the multi-line match features OR a combination from one of these output formats.
 .
 .I'm probably missing something very, very obvious.
 .
 .Best,
 .
 .Jim
 .
 .
 .On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:
 .
 .> Jim,
 .>
 .> Getting to your original question:
 .>
 .>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create
 .gff with appropriate subfeatures.
 .>
 .> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
 .>
 .> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE
 .GAP ATTRIBUTE' or as in 'ALIGNMENTS'
 .>
 .> I would guess not because neither of them have 'subfeatures'.
 .>
 .> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have
 .a better idea of what options might suit your needs.
 .>
 .>
 .> ~Malcolm
 .>
 .>
 .> .-----Original Message-----
 .> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .> .Sent: Friday, January 04, 2013 1:50 PM
 .> .To: Brian Osborne
 .> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .> .
 .> .Thanks for the replies, but...
 .> .
 .> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback.
 .Putting
 .> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .> .
 .> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .> .broken, at least on this page:
 .> .
 .> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .> .
 .> .Jim
 .> .
 .> .
 .> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .> .
 .> .> Scott and Chris,
 .> .>
 .> .> I'll test it and see...
 .> .>
 .> .> Brian O.
 .> .>
 .> .>
 .> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .> .>
 .> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .> .>>
 .> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .> .>>
 .> .>> chris
 .> .>>
 .> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .> .>>
 .> .>>> Hi Brian,
 .> .>>>
 .> .>>> I was going to suggest the same thing--though that script is fairly
 .> .>>> old, it's not as old as the blast2gff script in the GBrowse
 .> .>>> distribution (which probably should be retired).  I believe it
 .> .>>> supports GFF3, though I don't have any sample data with which to test
 .> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .> .>>> it accept it?
 .> .>>>
 .> .>>> Scott
 .> .>>>
 .> .>>>
 .> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .> .>>>> Here's one:
 .> .>>>>
 .> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .> .>>>>
 .> .>>>> Another one:
 .> .>>>>
 .> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .> .>>>> #!perl
 .> .>>>>
 .> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .> .>>>> #
 .> .>>>> =head1 NAME
 .> .>>>>
 .> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .> .>>>>
 .> .>>>>
 .> .>>>>
 .> .>>>> Brian O.
 .> .>>>>
 .> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .> .>>>>
 .> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .> .>>>>>
 .> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .> .create gff with appropriate subfeatures.
 .> .>>>>>
 .> .>>>>> Thanks,
 .> .>>>>>
 .> .>>>>> Jim
 .> .>>>>> =====================================
 .> .>>>>> Jim Hu
 .> .>>>>> Professor
 .> .>>>>> Dept. of Biochemistry and Biophysics
 .> .>>>>> 2128 TAMU
 .> .>>>>> Texas A&M Univ.
 .> .>>>>> College Station, TX 77843-2128
 .> .>>>>> 979-862-4054
 .> .>>>>>
 .> .>>>>>
 .> .>>>>>
 .> .>>>>> _______________________________________________
 .> .>>>>> 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
 .> .>>>
 .> .>>>
 .> .>>>
 .> .>>> --
 .> .>>> ------------------------------------------------------------------------
 .> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .> .>>> Ontario Institute for Cancer Research
 .> .>>> _______________________________________________
 .> .>>> Bioperl-l mailing list
 .> .>>> Bioperl-l at lists.open-bio.org
 .> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .> .>>
 .> .>
 .> .
 .> .=====================================
 .> .Jim Hu
 .> .Professor
 .> .Dept. of Biochemistry and Biophysics
 .> .2128 TAMU
 .> .Texas A&M Univ.
 .> .College Station, TX 77843-2128
 .> .979-862-4054
 .> .
 .> .
 .> .
 .> ._______________________________________________
 .> .Bioperl-l mailing list
 .> .Bioperl-l at lists.open-bio.org
 .> .http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .




From bosborne11 at verizon.net  Sat Jan  5 17:25:37 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Sat, 05 Jan 2013 17:25:37 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>

All,

The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.

Brian O.


On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> 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 jason.stajich at gmail.com  Mon Jan  7 04:35:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 7 Jan 2013 01:35:23 -0800
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
Message-ID: <D0FEE7D0-A855-478C-8BA1-08F56FEAD7A7@gmail.com>

with bp_search2gff  I included a cmdline options so you decide what is the reference (seqid column) and what is the target (9th column) since in some cases (BLASTX vs TBLASTN) you may want to be displaying one or the other as the reference. this is the -t option.

You can also have the -m option when you run which will build the grouping match term for a parent and then the sub-children will be HSPs that have that parent per Malcom's description of the parent child info.

Have you tried this with your output - it should work fine with regular vanilla text blast+ output or the -outfmt 6 option (tell bp_search2gff the format is blasttable)  or you can use -outfmt 5 and tell it you are using blastxml format.

 
Jason

On Jan 5, 2013, at 2:25 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> All,
> 
> The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> 
>> Scott and Chris,
>> 
>> I'll test it and see?
>> 
>> Brian O.
>> 
>> 
>> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
>> 
>>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>>> 
>>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>>> 
>>> chris
>>> 
>>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>>> 
>>>> Hi Brian,
>>>> 
>>>> I was going to suggest the same thing--though that script is fairly
>>>> old, it's not as old as the blast2gff script in the GBrowse
>>>> distribution (which probably should be retired).  I believe it
>>>> supports GFF3, though I don't have any sample data with which to test
>>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>>> it accept it?
>>>> 
>>>> Scott
>>>> 
>>>> 
>>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>>> Here's one:
>>>>> 
>>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>>> 
>>>>> Another one:
>>>>> 
>>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>>> #!perl
>>>>> 
>>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>>> #
>>>>> =head1 NAME
>>>>> 
>>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>>> 
>>>>> 
>>>>> 
>>>>> Brian O.
>>>>> 
>>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>>> 
>>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>>> 
>>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Jim
>>>>>> =====================================
>>>>>> Jim Hu
>>>>>> Professor
>>>>>> Dept. of Biochemistry and Biophysics
>>>>>> 2128 TAMU
>>>>>> Texas A&M Univ.
>>>>>> College Station, TX 77843-2128
>>>>>> 979-862-4054
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> _______________________________________________
>>>> 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
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From pengyu.ut at gmail.com  Thu Jan  3 17:41:37 2013
From: pengyu.ut at gmail.com (Peng Yu)
Date: Thu, 3 Jan 2013 14:41:37 -0800 (PST)
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file from
	Pfam
Message-ID: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>

Hi,

I tried the following code on the Pfam stockholm file (downloaded at
ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
But it gives me the following error. Is it a bug in bioperl or it is
an error in the Pfam-A.full.gz file?

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;

#use FindBin;
#use lib "$FindBin::Bin/.";

use Bio::AlignIO;
use Data::Dumper;

my $in = Bio::AlignIO->new(
  -format => 'stockholm',
  -file   => '/dev/stdin'
);

while(my $aln=$in->next_aln) {
  print $aln->accession, "\n";
}

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
#!/usr/bin/env bash

zcat ~/db/Pfam-A.full.gz | ./main.pl

~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh

...

------------- EXCEPTION -------------
MSG: '1985D' is not an integer.

STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
Range.pm:227
STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
lib/Bio/Annotation/Target.pm:81
STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:293
STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:73
STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
STACK toplevel ./main.pl:17
-------------------------------------


From thomas.girke at gmail.com  Wed Jan  9 15:59:08 2013
From: thomas.girke at gmail.com (Thomas Girke)
Date: Wed, 9 Jan 2013 12:59:08 -0800 (PST)
Subject: [Bioperl-l] Bioinformatics Position Opening
Message-ID: <9a99afb9-4a67-4d20-89ce-4d416fa7a46b@googlegroups.com>

Dear List,

Below is an announcement for a Ph.D. level bioinformatics position at
UCR. It is a long-term position with a competitive salary in a vibrant
research environment with cutting edge high-performance compute and
genomics facilities. Application instructions are given in the
announcement. Potential candidates are welcome to email me their
questions about this position directly, e.g.  prior or after submitting
a formal application. 

Best,

Thomas

--
Thomas Girke
Associate Professor of Bioinformatics
Institute for Integrative Genome Biology (IIGB)
1207F Genomics Building
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Ph: 951-905-5232
Fax: 951-827-5155


POSITION ANNOUNCEMENT

POSITION
The Institute for Integrative Genome Biology (IIGB) at the University of
California, Riverside is seeking a Ph.D. level bioinformatician to
manage its bioinformatics research activities and computing facility.  

TITLE/RANK
Bioinformatics Facility Director. Salary will be competitive and
commensurate with accomplishments.

LOCATION
University of California, Riverside. 

BACKGROUND
Successful candidates will join an innovative and multidisciplinary
Institute for Integrative Genome Biology (IIGB) that connects
theoretical and experimental researchers from different departments in
Life, Physical and Mathematical Sciences, Medicine, Engineering and
various campus based Centers. The IIGB is organized around a 10,000
sq.ft. suite of Instrumentation Facilities that serve as a centralized,
shared-use resource for faculty, staff and students, offering advanced
tools in bioinformatics, microscopy, proteomics and genomics. Its
bioinformatic component is equipped with an extensive high-performance
compute (HPC) infrastructure. 

QUALIFICATIONS
Applicants must have a Ph.D. from a recognized university in
bioinformatics; or combined degrees in computer science and a biological
science; or a degree in either computer science combined with relevant
experience in biological science; or a degree in a biological science
combined with relevant experience in computer science. The successful
candidate will have at least 2 years of professional hands-on experience
with next generation sequence data analysis, scientific data programming
and high-performance computing. A strong publication record of
bioinformatics research in collaboration with experimental biologists is
expected. Another requirement is several years of professional
experience with common programming languages/environments. This includes
at least one statistical programming environment (preferentially R), one
or more general-purpose scripting languages (e.g. Python, Perl or Ruby),
experience with web development frameworks and relational database
design. Several years of computational research experience using HPC
systems will be beneficial.  The incumbent should also have experience
with the analysis of modern biological data sets, such as microarrays,
next generation sequence data (e.g. genotyping, RNA profiling, de novo
assemblies), phylogenetics and/or molecular dynamics simulations.

RESPONSIBILITIES
The Bioinformatics Facility Director manages IIGB's computational
infrastructure jointly with its bioinformatics staff, including an
HPC/Linux systems administrator, one or more programmers and students
workers. The incumbent will be required to provide data analysis support
to collaborative research activities and make available findings through
presentations and contribute as team member to scientific publications
as well as participate in the preparation of joint grant applications
and reports. The teaching expectations include the development of a
state-of-the-art workshop program on large-scale data analysis and
programming. Participation in collaborative equipment grants will be
another core responsibility to secure future growth of the facility?s
computing resources. 

TO APPLY
Review of applications will continue until the position is filled.
Interested individuals should: (1) submit a curriculum vitae, (2)
provide a statement of research interests, and (3) arrange to have three
letters of reference sent on their behalf. All information should be
emailed to: thomas.girke at ucr.edu

WEBSITE
http://facility.bioinformatics.ucr.edu/position-opening




From frej.tulin at gmail.com  Thu Jan 10 21:53:16 2013
From: frej.tulin at gmail.com (Frej Tulin)
Date: Thu, 10 Jan 2013 21:53:16 -0500
Subject: [Bioperl-l] stand alone blast plus problem
Message-ID: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>

Hi

I have been trying for a long time to control my blast searches with the
Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was
a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing
seems to help.
When I build a database using the makeblastdb directly from the command
line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







-- 
Frej Tulin
Fred Cross lab
Rockefeller University


From cjfields at illinois.edu  Fri Jan 11 00:04:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 11 Jan 2013 05:04:12 +0000
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file
 from	Pfam
In-Reply-To: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
References: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF6A00B@CHIMBX5.ad.uillinois.edu>

I haven't used the '/dev/stdin' file like this, I typically do:

> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -fh   => \*STDIN
> );


but if it works?

That does look like a bug in the parser.  Would you know the Pfam alignmet accessions that triggered it, or maybe ones just prior to the fail?

chris

On Jan 3, 2013, at 4:41 PM, Peng Yu <pengyu.ut at gmail.com> wrote:

> Hi,
> 
> I tried the following code on the Pfam stockholm file (downloaded at
> ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
> But it gives me the following error. Is it a bug in bioperl or it is
> an error in the Pfam-A.full.gz file?
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> 
> #use FindBin;
> #use lib "$FindBin::Bin/.";
> 
> use Bio::AlignIO;
> use Data::Dumper;
> 
> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -file   => '/dev/stdin'
> );
> 
> while(my $aln=$in->next_aln) {
>  print $aln->accession, "\n";
> }
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
> #!/usr/bin/env bash
> 
> zcat ~/db/Pfam-A.full.gz | ./main.pl
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh
> 
> ...
> 
> ------------- EXCEPTION -------------
> MSG: '1985D' is not an integer.
> 
> STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
> Range.pm:227
> STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
> lib/Bio/Annotation/Target.pm:81
> STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
> Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:293
> STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
> py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:73
> STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
> ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
> STACK toplevel ./main.pl:17
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Russell.Smithies at agresearch.co.nz  Sun Jan 13 17:25:16 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 14 Jan 2013 11:25:16 +1300
Subject: [Bioperl-l] stand alone blast plus problem
In-Reply-To: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
References: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF372E99EE4C1@exchsth.agresearch.co.nz>

Hi Frej,
Here's a few things to try:
Is it possible you need to escape the special chars in your IDs? i.e. the pipes and colons?
Have you tried it with simpler IDs?
Is your BioPerl sequence object collection created correctly?
Can you create the database by just passing it the fasta file?

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_name => 'mydb',
  -db_data => 'myseqs.fas',
  -create => 1
);

--Russell 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Frej Tulin
Sent: Friday, 11 January 2013 3:53 p.m.
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] stand alone blast plus problem

Hi

I have been trying for a long time to control my blast searches with the Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing seems to help.
When I build a database using the makeblastdb directly from the command line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







--
Frej Tulin
Fred Cross lab
Rockefeller University
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

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From awitney at sgul.ac.uk  Thu Jan 17 06:45:40 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 11:45:40 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
Message-ID: <50F7E464.3090906@sgul.ac.uk>

Hi,

I would like to produces graphics as shown in this section (cross 
linking between genome tracks) [scroll down a little to see the pictures]:

http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211

but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, 
but this works within a web browser, I would like to generate these 
diagrams from a stand alone script. If not does anyone know any perl 
libraries that can be used to show genome comparisons?

Thanks

Adam


From cjfields at illinois.edu  Thu Jan 17 08:37:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 13:37:04 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F7E464.3090906@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>

Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.

chris

On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> Hi,
> 
> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
> 
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
> 
> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
> 
> Thanks
> 
> Adam
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From awitney at sgul.ac.uk  Thu Jan 17 12:33:42 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 17:33:42 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
Message-ID: <50F835F6.5090603@sgul.ac.uk>


Thanks Chris. I hadn't seen SynBrowse before, looks good.

But I would like to do this without all the database/webserver overhead, 
I have a perl script that can interact with a gbrowse_syn database to 
generate images ie no webserver, I just need to separate out the 
database stuff now.

Thanks again

Adam

On 17/01/2013 13:37, Fields, Christopher J wrote:
> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>
> chris
>
> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>
>> Hi,
>>
>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>
>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>
>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>
>> Thanks
>>
>> Adam
>> _______________________________________________
>> 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  Thu Jan 17 12:41:47 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 17:41:47 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F835F6.5090603@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
	<50F835F6.5090603@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFD4BA@CITESMBX5.ad.uillinois.edu>

Let us know if this can be of use to the community, I'm sure others would find it useful as well.

chris

On Jan 17, 2013, at 11:33 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> 
> Thanks Chris. I hadn't seen SynBrowse before, looks good.
> 
> But I would like to do this without all the database/webserver overhead, I have a perl script that can interact with a gbrowse_syn database to generate images ie no webserver, I just need to separate out the database stuff now.
> 
> Thanks again
> 
> Adam
> 
> On 17/01/2013 13:37, Fields, Christopher J wrote:
>> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>> 
>> chris
>> 
>> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>> 
>>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>> 
>>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>> 
>>> Thanks
>>> 
>>> Adam
>>> _______________________________________________
>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From buschj at hhu.de  Sat Jan 19 11:12:54 2013
From: buschj at hhu.de (jobu)
Date: Sat, 19 Jan 2013 17:12:54 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking .."
Message-ID: <50FAC606.2060800@hhu.de>

Dear List,

I've got quite a lot of  hits from blasting against nt-database that state:

"Features flanking this part of subject sequence: "

where the subject-accession only will give information about complete
genomic sequences,
the detailed information inside the "Features flanking" section of the
HSP about annotations of upstream and downstream elements would be what
I need.

Is there any elegant way to make Bio::SearchIO do this job for me?

greetings
Jochen


From saladi1 at illinois.edu  Tue Jan 22 16:45:23 2013
From: saladi1 at illinois.edu (Shyam Saladi)
Date: Tue, 22 Jan 2013 13:45:23 -0800
Subject: [Bioperl-l] Bio::DB::Taxonomy example
Message-ID: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>

Hi,

There is an example on how to use Bio::DB::Taxonomy at
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy

I tried the script but could not get it to work properly. After looking
through the documentation it seems that

my @extant_children = grep { $_->rank eq 'species' }
$node->get_all_Descendents;

should instead be

my @extant_children = grep { $_->rank eq 'species' }
$db->get_all_Descendents($node)

I found this solves the problem for me. If my fix is in fact correct, an
admin may want to change the example script online.

Thanks,
Shyam
**


From cjfields at illinois.edu  Tue Jan 22 18:40:05 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 22 Jan 2013 23:40:05 +0000
Subject: [Bioperl-l] Bio::DB::Taxonomy example
In-Reply-To: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
References: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CDFE139@CITESMBX5.ad.uillinois.edu>

Done.  Thanks for pointing that out!

chris

On Jan 23, 2013, at 5:45 AM, Shyam Saladi <saladi1 at illinois.edu>
 wrote:

> Hi,
> 
> There is an example on how to use Bio::DB::Taxonomy at
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> 
> I tried the script but could not get it to work properly. After looking
> through the documentation it seems that
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $node->get_all_Descendents;
> 
> should instead be
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $db->get_all_Descendents($node)
> 
> I found this solves the problem for me. If my fix is in fact correct, an
> admin may want to change the example script online.
> 
> Thanks,
> Shyam
> **
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From buschj at hhu.de  Fri Jan 25 05:20:22 2013
From: buschj at hhu.de (jobu)
Date: Fri, 25 Jan 2013 11:20:22 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
Message-ID: <51025C66.6060008@hhu.de>

Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
> What upstream and downstream elements are you interested in?


I've got a huge pile of short RNA reads.
Part of the question now is whether those RNA fragments originate from
siRNA events,
or may represent miRNAs / parts of pre-miRNAs.

So I did an online  blast search against database nt.
The resulting report quite often just gives subject information like this:

-----
> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
Length=23459830
-----

Now I would like to get the hit's neighbouring regions  for further
analysis.
Preferably I would like to do that  in an automized way, but the only
possible action with this kind of subject gi | description would be to
fetch the entire chromosomal  sequence I guess ?

However,
right below the line above, the report states more precisely:

------
 Features flanking this part of subject sequence:
   8872 bp at 5' side: cytochrome P450 90B1
   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
------

Still I would like to have the possibility to automatically fetch the
subject's sequence(s),
as of now I think  parsing the report with SearchIO won't let me aquire
that information, because SearchIO does not recognize report sections
like those.

I hope I did not miss any of SearchIOs capabilities, but I could not
find any method covering my wish?!

Right now maybe the only way to get the information I want is to
construct my own parser and write it out into a separate file, which in
turn again  I could read into a hash before processing the Blast-Report
with SearchIO to combine both data for further automized work.

I am aware though that even successfully getting the flanking features
would leave me with the more or less wide  intergenic gap my hsp is
located in.

However I'm in need of a way to get the flanking features including
their annotation and the region spanning between them.
But I hope I do not have to get complete sequences to accomplish that,
as this would be kind of an overkill.

with kind regards
Jochen





From afonsomduarte at gmail.com  Mon Jan 14 05:09:48 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 14 Jan 2013 02:09:48 -0800 (PST)
Subject: [Bioperl-l] Parsing Blast results for different genus
Message-ID: <217cf8ac-5323-48f5-8a81-aba032cba68b@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


PS sorry if this message appears twice ... as i was having some trouble 
posting the first time.


From afonsomduarte at gmail.com  Sun Jan 13 14:17:19 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Sun, 13 Jan 2013 11:17:19 -0800 (PST)
Subject: [Bioperl-l] Split blast result by genus. How to parse it ?
Message-ID: <83857a34-14a0-43e2-a2b3-5ca538d41bcd@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


From afonsomduarte at gmail.com  Mon Jan 21 04:03:44 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 21 Jan 2013 01:03:44 -0800 (PST)
Subject: [Bioperl-l] spliting genbank file into smaller ones via organism
Message-ID: <f8a60619-c086-4a29-8541-13b136b716f3@googlegroups.com>



Dear List,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


From jason.stajich at gmail.com  Tue Jan 29 14:00:16 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Tue, 29 Jan 2013 11:00:16 -0800
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <51025C66.6060008@hhu.de>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
	<51025C66.6060008@hhu.de>
Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D@gmail.com>

We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.

However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.

basically:
- download the genome and GFF for arabidopsis
- align your sRNA to the genome with a short read aligner - bowtie, bwa, others
- convert your sam to bam file with SAMtools or picard
- compare the location of features with the reads to get expression summaries or individuals reads with BEDTools


On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:

> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>> What upstream and downstream elements are you interested in?
> 
> 
> I've got a huge pile of short RNA reads.
> Part of the question now is whether those RNA fragments originate from
> siRNA events,
> or may represent miRNAs / parts of pre-miRNAs.
> 
> So I did an online  blast search against database nt.
> The resulting report quite often just gives subject information like this:
> 
> -----
>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
> Length=23459830
> -----
> 
> Now I would like to get the hit's neighbouring regions  for further
> analysis.
> Preferably I would like to do that  in an automized way, but the only
> possible action with this kind of subject gi | description would be to
> fetch the entire chromosomal  sequence I guess ?
> 
> However,
> right below the line above, the report states more precisely:
> 
> ------
> Features flanking this part of subject sequence:
>   8872 bp at 5' side: cytochrome P450 90B1
>   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
> ------
> 
> Still I would like to have the possibility to automatically fetch the
> subject's sequence(s),
> as of now I think  parsing the report with SearchIO won't let me aquire
> that information, because SearchIO does not recognize report sections
> like those.
> 
> I hope I did not miss any of SearchIOs capabilities, but I could not
> find any method covering my wish?!
> 
> Right now maybe the only way to get the information I want is to
> construct my own parser and write it out into a separate file, which in
> turn again  I could read into a hash before processing the Blast-Report
> with SearchIO to combine both data for further automized work.
> 
> I am aware though that even successfully getting the flanking features
> would leave me with the more or less wide  intergenic gap my hsp is
> located in.
> 
> However I'm in need of a way to get the flanking features including
> their annotation and the region spanning between them.
> But I hope I do not have to get complete sequences to accomplish that,
> as this would be kind of an overkill.
> 
> with kind regards
> Jochen
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From dr_kilburn59 at yahoo.com  Wed Jan 30 16:40:26 2013
From: dr_kilburn59 at yahoo.com (Dan kilburn)
Date: Wed, 30 Jan 2013 16:40:26 -0500
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
Message-ID: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>

Hi Jason,

Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.

--Dan
Sent from my iPhone

On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:

> Send Bioperl-l mailing list submissions to
>    bioperl-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>    http://lists.open-bio.org/mailman/listinfo/bioperl-l
> or, via email, send a message with subject or body 'help' to
>    bioperl-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
>    bioperl-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
> 
> 
> Today's Topics:
> 
>   1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>      (Jason Stajich)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 29 Jan 2013 11:00:16 -0800
> From: Jason Stajich <jason.stajich at gmail.com>
> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>    flanking    .."
> To: buschj at hhu.de
> Cc: bioperl-l at lists.open-bio.org
> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
> Content-Type: text/plain;    charset=us-ascii
> 
> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
> 
> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
> 
> basically:
> - download the genome and GFF for arabidopsis
> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
> - convert your sam to bam file with SAMtools or picard
> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
> 
> 
> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
> 
>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>> What upstream and downstream elements are you interested in?
>> 
>> 
>> I've got a huge pile of short RNA reads.
>> Part of the question now is whether those RNA fragments originate from
>> siRNA events,
>> or may represent miRNAs / parts of pre-miRNAs.
>> 
>> So I did an online  blast search against database nt.
>> The resulting report quite often just gives subject information like this:
>> 
>> -----
>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>> Length=23459830
>> -----
>> 
>> Now I would like to get the hit's neighbouring regions  for further
>> analysis.
>> Preferably I would like to do that  in an automized way, but the only
>> possible action with this kind of subject gi | description would be to
>> fetch the entire chromosomal  sequence I guess ?
>> 
>> However,
>> right below the line above, the report states more precisely:
>> 
>> ------
>> Features flanking this part of subject sequence:
>>  8872 bp at 5' side: cytochrome P450 90B1
>>  402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>> ------
>> 
>> Still I would like to have the possibility to automatically fetch the
>> subject's sequence(s),
>> as of now I think  parsing the report with SearchIO won't let me aquire
>> that information, because SearchIO does not recognize report sections
>> like those.
>> 
>> I hope I did not miss any of SearchIOs capabilities, but I could not
>> find any method covering my wish?!
>> 
>> Right now maybe the only way to get the information I want is to
>> construct my own parser and write it out into a separate file, which in
>> turn again  I could read into a hash before processing the Blast-Report
>> with SearchIO to combine both data for further automized work.
>> 
>> I am aware though that even successfully getting the flanking features
>> would leave me with the more or less wide  intergenic gap my hsp is
>> located in.
>> 
>> However I'm in need of a way to get the flanking features including
>> their annotation and the region spanning between them.
>> But I hope I do not have to get complete sequences to accomplish that,
>> as this would be kind of an overkill.
>> 
>> with kind regards
>> Jochen
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> End of Bioperl-l Digest, Vol 117, Issue 13
> ******************************************



From cjfields at illinois.edu  Wed Jan 30 18:13:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 30 Jan 2013 23:13:49 +0000
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
	<575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CE1175C@CHIMBX5.ad.uillinois.edu>

We certainly accept support for updates to the code.  In fact, if you are familiar with git/github the process is fairly straightforward:

1) Fork the code to your github account
2) Make and commit changes
3) Submit a pull request
4) Post something to the list just in case.

We also accept code patches; the best way to submit these is as a bug report to the redmine repository (doesn't hurt to post here as well):

https://redmine.open-bio.org/

chris

On Jan 30, 2013, at 3:40 PM, Dan kilburn <dr_kilburn59 at yahoo.com> wrote:

> Hi Jason,
> 
> Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.
> 
> --Dan
> Sent from my iPhone
> 
> On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:
> 
>> Send Bioperl-l mailing list submissions to
>>   bioperl-l at lists.open-bio.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>>   http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> or, via email, send a message with subject or body 'help' to
>>   bioperl-l-request at lists.open-bio.org
>> 
>> You can reach the person managing the list at
>>   bioperl-l-owner at lists.open-bio.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Bioperl-l digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>>     (Jason Stajich)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Tue, 29 Jan 2013 11:00:16 -0800
>> From: Jason Stajich <jason.stajich at gmail.com>
>> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>>   flanking    .."
>> To: buschj at hhu.de
>> Cc: bioperl-l at lists.open-bio.org
>> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
>> Content-Type: text/plain;    charset=us-ascii
>> 
>> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
>> 
>> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
>> 
>> basically:
>> - download the genome and GFF for arabidopsis
>> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
>> - convert your sam to bam file with SAMtools or picard
>> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
>> 
>> 
>> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
>> 
>>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>>> What upstream and downstream elements are you interested in?
>>> 
>>> 
>>> I've got a huge pile of short RNA reads.
>>> Part of the question now is whether those RNA fragments originate from
>>> siRNA events,
>>> or may represent miRNAs / parts of pre-miRNAs.
>>> 
>>> So I did an online  blast search against database nt.
>>> The resulting report quite often just gives subject information like this:
>>> 
>>> -----
>>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>>> Length=23459830
>>> -----
>>> 
>>> Now I would like to get the hit's neighbouring regions  for further
>>> analysis.
>>> Preferably I would like to do that  in an automized way, but the only
>>> possible action with this kind of subject gi | description would be to
>>> fetch the entire chromosomal  sequence I guess ?
>>> 
>>> However,
>>> right below the line above, the report states more precisely:
>>> 
>>> ------
>>> Features flanking this part of subject sequence:
>>> 8872 bp at 5' side: cytochrome P450 90B1
>>> 402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>>> ------
>>> 
>>> Still I would like to have the possibility to automatically fetch the
>>> subject's sequence(s),
>>> as of now I think  parsing the report with SearchIO won't let me aquire
>>> that information, because SearchIO does not recognize report sections
>>> like those.
>>> 
>>> I hope I did not miss any of SearchIOs capabilities, but I could not
>>> find any method covering my wish?!
>>> 
>>> Right now maybe the only way to get the information I want is to
>>> construct my own parser and write it out into a separate file, which in
>>> turn again  I could read into a hash before processing the Blast-Report
>>> with SearchIO to combine both data for further automized work.
>>> 
>>> I am aware though that even successfully getting the flanking features
>>> would leave me with the more or less wide  intergenic gap my hsp is
>>> located in.
>>> 
>>> However I'm in need of a way to get the flanking features including
>>> their annotation and the region spanning between them.
>>> But I hope I do not have to get complete sequences to accomplish that,
>>> as this would be kind of an overkill.
>>> 
>>> with kind regards
>>> Jochen
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> End of Bioperl-l Digest, Vol 117, Issue 13
>> ******************************************
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From thiago.venancio at gmail.com  Thu Jan 31 12:10:39 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:10:39 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
Message-ID: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>

Hi all,

I am trying to install bioperl-ext and the compilation gives me the error:

/usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
can not be used when making a shared object; recompile with -fPIC
libs/libsw.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
make[1]: Leaving directory 
`/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align'
make: *** [subdirs] Error 2

However, the Makefile says that -fPIC is already being used, which is 
puzzling me.

Any clues ?

Thanks.
Thiago





From thiago.venancio at gmail.com  Thu Jan 31 12:25:12 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:25:12 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
In-Reply-To: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
References: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
Message-ID: <e22d2881-ddd3-42af-9a69-f03503b8fb5a@googlegroups.com>

Solved using the solution posted by jmf here :
https://groups.google.com/forum/?fromgroups=#!searchin/bioperl-l/bioperl-ext/bioperl-l/FgJo_g8UQE8/FB1DEjJkTooJ

Which I found after posting.

T


On Thursday, January 31, 2013 3:10:39 PM UTC-2, Thiago Venancio wrote:
>
> Hi all, 
>
> I am trying to install bioperl-ext and the compilation gives me the error: 
>
> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
> can not be used when making a shared object; recompile with -fPIC 
> libs/libsw.a: could not read symbols: Bad value 
> collect2: ld returned 1 exit status 
> make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 
> make[1]: Leaving directory 
> `/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align' 
> make: *** [subdirs] Error 2 
>
> However, the Makefile says that -fPIC is already being used, which is 
> puzzling me. 
>
> Any clues ? 
>
> Thanks. 
> Thiago 
>
>
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From koriege at googlemail.com  Thu Jan 31 21:49:20 2013
From: koriege at googlemail.com (koriege at googlemail.com)
Date: Thu, 31 Jan 2013 18:49:20 -0800 (PST)
Subject: [Bioperl-l] problem with Bio::*::Fasta id_parser
Message-ID: <e9e0c428-0467-4b62-a37d-cfcb91ed818b@googlegroups.com>

Hi,

I tried two methods to create a bioperl FASTA database, but it failes by 
extracting the substring out of my headers.
Can someone explain me why I get the standard header or show me a work 
around? 

thanks in advance.
pyr0

i)
my $objDB = Bio::Index::Fasta->new(-filename => $PATHdbIdx, -write_flag => 
1);
$objDB->id_parser(\&get_id);
$objDB->make_index(glob($objParameter->dbGenome()));

sub get_id {
   my $header = shift;
   $header =~ /^>.*\bsp\|([A-Z]\d{5}\b)/;
   $1;
}

output
Use of uninitialized value $id in concatenation (.) or string at 
/usr/share/perl5/Bio/Index/Abstract.pm line 753, <$FASTA> line 1.
Use of uninitialized value $id in exists at 
/usr/share/perl5/Bio/Index/Abstract.pm line 754, <$FASTA> line 1.
Use of uninitialized value $id in hash element at 
/usr/share/perl5/Bio/Index/Abstract.pm line 757, <$FASTA> line 1.
gi|376282008|ref|NC_016798.1|

ii)
my $PATHdbIdx=catfile($objParameter->DIR,'data','db.idx');
unlink($PATHdbIdx);
my $objDB = Bio::DB::Fasta->new($objParameter->dbGenome(), -makeid => 
\&get_id);
$objDBgenome->set(\$objDB);

output:
Use of uninitialized value $key in pattern match (m//) at 
/usr/share/perl5/Bio/DB/Fasta.pm line 1178.
Use of uninitialized value $id in exists at 
/usr/share/perl5/Bio/DB/Fasta.pm line 617.
gi|376282008|ref|NC_016798.1|


From yuf228 at hotmail.com  Thu Jan 31 23:15:15 2013
From: yuf228 at hotmail.com (Rob)
Date: Fri, 1 Feb 2013 04:15:15 +0000 (UTC)
Subject: [Bioperl-l] Where to get BLASTCLUST or equivalent?
References: <200305311150.h4VBopn2019091@localhost.localdomain>
Message-ID: <loom.20130201T045704-740@post.gmane.org>

Cyril C.C. Chua <bmbcccc <at> bmb.leeds.ac.uk> writes:

> 
> Hi,
> 
> I have some difficulty in sourcing for BLASTCLUST or related 
> programs/mods. Does any1 know exactly how to locate them?
> 
> Regards
> 
> Cyril Chua
> 


Hi Cyril,

I heard of the following programmes that might do similar things (I HAVEN'T 
used any of them yet):

Afree - http://www.vicbioinformatics.com/software.afree.shtml
Uclust - http://drive5.com/uclust/uclust_userguide_2_1.pdf
Usearch - http://www.drive5.com/usearch/
DomClust - http://mbgd.genome.ad.jp/domclust/

or 

Check this: 

http://ppod.princeton.edu/help/help_tech.html

God bless,


Robert




From jimhu at tamu.edu  Wed Jan  2 14:44:56 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 2 Jan 2013 13:44:56 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
Message-ID: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>

I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.

I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From biojiangke at gmail.com  Wed Jan  2 15:20:02 2013
From: biojiangke at gmail.com (Ke Jiang)
Date: Wed, 2 Jan 2013 15:20:02 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>

There is a blast2gff.pl floating around for Gbrowse to visualize blast
results as tracks. Not sure about the blast+. One more reason to stick with
the good old blast!

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Ke

-------------------------------------------
Ke Jiang, Ph.D.
Post-doctoral Fellow
Delbruck Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724


From cjfields at illinois.edu  Wed Jan  2 15:47:52 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 20:47:52 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FD44@CHIMBX5.ad.uillinois.edu>

?except that NCBI no longer supports legacy BLAST.  Caveat emptor.

chris

On Jan 2, 2013, at 2:20 PM, Ke Jiang <biojiangke at gmail.com> wrote:

> There is a blast2gff.pl floating around for Gbrowse to visualize blast
> results as tracks. Not sure about the blast+. One more reason to stick with
> the good old blast!
> 
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> 
> Ke
> 
> -------------------------------------------
> Ke Jiang, Ph.D.
> Post-doctoral Fellow
> Delbruck Laboratory
> Cold Spring Harbor Laboratory
> Cold Spring Harbor, NY 11724
> _______________________________________________
> 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  Wed Jan  2 15:26:22 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 15:26:22 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>

Here's one:

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Another one:

~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl 
#!perl

# Author:      Jason Stajich <jason-at-bioperl-dot-org>
# Description: Turn SearchIO parseable report(s) into a GFF report
#
=head1 NAME

bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report



Brian O.

On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:

> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> 
> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  
> 
> Thanks,
> 
> Jim
> =====================================
> Jim Hu
> Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From scott at scottcain.net  Wed Jan  2 16:32:16 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 2 Jan 2013 16:32:16 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
Message-ID: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>

Hi Brian,

I was going to suggest the same thing--though that script is fairly
old, it's not as old as the blast2gff script in the GBrowse
distribution (which probably should be retired).  I believe it
supports GFF3, though I don't have any sample data with which to test
it to be sure.  I also don't know if it supports BLAST+ input--I
haven't kept up with SearchIO (on which search2gff.pl depends); will
it accept it?

Scott


On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> Here's one:
>
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>
> Another one:
>
> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> #!perl
>
> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> # Description: Turn SearchIO parseable report(s) into a GFF report
> #
> =head1 NAME
>
> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>
>
>
> Brian O.
>
> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>
>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>
>> Thanks,
>>
>> Jim
>> =====================================
>> Jim Hu
>> Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>>
>> _______________________________________________
>> 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



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


From cjfields at illinois.edu  Wed Jan  2 17:26:55 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 22:26:55 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>

It should (I recall using it at one point).  If it doesn't we should fix it so it does.

How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 

chris

On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Brian,
> 
> I was going to suggest the same thing--though that script is fairly
> old, it's not as old as the blast2gff script in the GBrowse
> distribution (which probably should be retired).  I believe it
> supports GFF3, though I don't have any sample data with which to test
> it to be sure.  I also don't know if it supports BLAST+ input--I
> haven't kept up with SearchIO (on which search2gff.pl depends); will
> it accept it?
> 
> Scott
> 
> 
> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>> Here's one:
>> 
>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>> 
>> Another one:
>> 
>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>> #!perl
>> 
>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>> # Description: Turn SearchIO parseable report(s) into a GFF report
>> #
>> =head1 NAME
>> 
>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>> 
>> 
>> 
>> Brian O.
>> 
>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>> 
>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>> 
>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>> 
>>> Thanks,
>>> 
>>> Jim
>>> =====================================
>>> Jim Hu
>>> Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> 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  Wed Jan  2 17:53:50 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 17:53:50 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
Message-ID: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>

Scott and Chris,

I'll test it and see?

Brian O.


On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> 
> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
> 
> chris
> 
> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> 
>> Hi Brian,
>> 
>> I was going to suggest the same thing--though that script is fairly
>> old, it's not as old as the blast2gff script in the GBrowse
>> distribution (which probably should be retired).  I believe it
>> supports GFF3, though I don't have any sample data with which to test
>> it to be sure.  I also don't know if it supports BLAST+ input--I
>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>> it accept it?
>> 
>> Scott
>> 
>> 
>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>> Here's one:
>>> 
>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>> 
>>> Another one:
>>> 
>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>> #!perl
>>> 
>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>> #
>>> =head1 NAME
>>> 
>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>> 
>>> 
>>> 
>>> Brian O.
>>> 
>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>> 
>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>> 
>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>> 
>>>> Thanks,
>>>> 
>>>> Jim
>>>> =====================================
>>>> Jim Hu
>>>> Professor
>>>> Dept. of Biochemistry and Biophysics
>>>> 2128 TAMU
>>>> Texas A&M Univ.
>>>> College Station, TX 77843-2128
>>>> 979-862-4054
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From jimhu at tamu.edu  Fri Jan  4 14:49:51 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 13:49:51 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>

Thanks for the replies, but...

I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.

The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be broken, at least on this page:

	http://www.bioperl.org/wiki/Module:Bio::SearchIO

Jim


On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From bosborne11 at verizon.net  Fri Jan  4 14:26:52 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 04 Jan 2013 14:26:52 -0500
Subject: [Bioperl-l] strange error in the beginners howto
In-Reply-To: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
References: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
Message-ID: <BB2BD9EA-3419-4B6C-A659-4D86420CFAE0@verizon.net>

Matthew,

First, let's distinguish "warning" and "error". Errors stop execution of the app or script, what you're seeing is a warning, your script actually completes. Does the warning vanish if you remove "-w"?

Second, seems like this is a Perl version thing:

http://www.sysarchitects.com/bioperl

BIO

On Jan 4, 2013, at 1:55 PM, "Thornton, Matthew" <Matthew.Thornton at med.usc.edu> wrote:

> Hello,
> 
> I am working through the first part of the BioPerl beginners howto and I am getting an error and I was wondering if you could tell me what is wrong.
> 
> I made the seqio.pl script:
> 
> #!/bin/perl -w
> 
> use Bio::Seq;
> 
> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",                        
>                          -display_id => "#12345",                        
>                          -desc => "example 1",                        
>                          -alphabet => "dna" );
> 
> print $seq_obj->seq();
> 
> I execute the script and I get this error:
> 
> gserver at gserver:~/bio$ perl seqio.pl 
> Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251.
> aaaatgggggggggggccccgttgserver at gserver:~/bio$
> 
> Is there something wrong with my installation?
> 
> Any help is greatly appreciated.
> 
> Thanks!
> 
> 
> Matthew E. Thornton
> 
> 
> 
> Laboratory Technician III
> Broad Center for Stem Cell and Regenerative Medicine
> University of Southern California
> 1501 San Pablo St. ZNI
> Los Angeles, CA 90089-2821
> ph.:323-442-1688
> fx.:323-442-4040
> matthew.thornton at med.usc.edu
> 

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




From MEC at stowers.org  Fri Jan  4 15:20:17 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 14:20:17 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>

Jim,

Getting to your original question:

> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.

Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??

If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'

I would guess not because neither of them have 'subfeatures'.

If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.


~Malcolm


 .-----Original Message-----
 .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .Sent: Friday, January 04, 2013 1:50 PM
 .To: Brian Osborne
 .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Thanks for the replies, but...
 .
 .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
 .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .
 .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .broken, at least on this page:
 .
 .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .
 .Jim
 .
 .
 .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .
 .> Scott and Chris,
 .>
 .> I'll test it and see...
 .>
 .> Brian O.
 .>
 .>
 .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .>
 .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .>>
 .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .>>
 .>> chris
 .>>
 .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .>>
 .>>> Hi Brian,
 .>>>
 .>>> I was going to suggest the same thing--though that script is fairly
 .>>> old, it's not as old as the blast2gff script in the GBrowse
 .>>> distribution (which probably should be retired).  I believe it
 .>>> supports GFF3, though I don't have any sample data with which to test
 .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .>>> it accept it?
 .>>>
 .>>> Scott
 .>>>
 .>>>
 .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .>>>> Here's one:
 .>>>>
 .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .>>>>
 .>>>> Another one:
 .>>>>
 .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .>>>> #!perl
 .>>>>
 .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .>>>> #
 .>>>> =head1 NAME
 .>>>>
 .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .>>>>
 .>>>>
 .>>>>
 .>>>> Brian O.
 .>>>>
 .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .>>>>
 .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .>>>>>
 .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .create gff with appropriate subfeatures.
 .>>>>>
 .>>>>> Thanks,
 .>>>>>
 .>>>>> Jim
 .>>>>> =====================================
 .>>>>> Jim Hu
 .>>>>> Professor
 .>>>>> Dept. of Biochemistry and Biophysics
 .>>>>> 2128 TAMU
 .>>>>> Texas A&M Univ.
 .>>>>> College Station, TX 77843-2128
 .>>>>> 979-862-4054
 .>>>>>
 .>>>>>
 .>>>>>
 .>>>>> _______________________________________________
 .>>>>> 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
 .>>>
 .>>>
 .>>>
 .>>> --
 .>>> ------------------------------------------------------------------------
 .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .>>> Ontario Institute for Cancer Research
 .>>> _______________________________________________
 .>>> Bioperl-l mailing list
 .>>> Bioperl-l at lists.open-bio.org
 .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .>>
 .>
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .
 .
 .
 ._______________________________________________
 .Bioperl-l mailing list
 .Bioperl-l at lists.open-bio.org
 .http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jimhu at tamu.edu  Fri Jan  4 16:57:38 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 15:57:38 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
Message-ID: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>

Malcolm,

Thanks, I should have reread the GFF3 spec before posting!

In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see how the final output could be done in different ways, but I'm still stuck on how to get there.  

I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a transposable element, for example.

Excerpting from blastp -help

 *** Formatting options
 -outfmt <String>
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1) 

Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute OR the multi-line match features OR a combination from one of these output formats. 

I'm probably missing something very, very obvious.

Best,

Jim


On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:

> Jim,
> 
> Getting to your original question:
> 
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.
> 
> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
> 
> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'
> 
> I would guess not because neither of them have 'subfeatures'.
> 
> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.
> 
> 
> ~Malcolm
> 
> 
> .-----Original Message-----
> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
> .Sent: Friday, January 04, 2013 1:50 PM
> .To: Brian Osborne
> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
> .
> .Thanks for the replies, but...
> .
> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
> .
> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
> .broken, at least on this page:
> .
> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
> .
> .Jim
> .
> .
> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
> .
> .> Scott and Chris,
> .>
> .> I'll test it and see...
> .>
> .> Brian O.
> .>
> .>
> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> .>
> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> .>>
> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
> .>>
> .>> chris
> .>>
> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> .>>
> .>>> Hi Brian,
> .>>>
> .>>> I was going to suggest the same thing--though that script is fairly
> .>>> old, it's not as old as the blast2gff script in the GBrowse
> .>>> distribution (which probably should be retired).  I believe it
> .>>> supports GFF3, though I don't have any sample data with which to test
> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
> .>>> it accept it?
> .>>>
> .>>> Scott
> .>>>
> .>>>
> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> .>>>> Here's one:
> .>>>>
> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> .>>>>
> .>>>> Another one:
> .>>>>
> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> .>>>> #!perl
> .>>>>
> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
> .>>>> #
> .>>>> =head1 NAME
> .>>>>
> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
> .>>>>
> .>>>>
> .>>>>
> .>>>> Brian O.
> .>>>>
> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
> .>>>>
> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> .>>>>>
> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
> .create gff with appropriate subfeatures.
> .>>>>>
> .>>>>> Thanks,
> .>>>>>
> .>>>>> Jim
> .>>>>> =====================================
> .>>>>> Jim Hu
> .>>>>> Professor
> .>>>>> Dept. of Biochemistry and Biophysics
> .>>>>> 2128 TAMU
> .>>>>> Texas A&M Univ.
> .>>>>> College Station, TX 77843-2128
> .>>>>> 979-862-4054
> .>>>>>
> .>>>>>
> .>>>>>
> .>>>>> _______________________________________________
> .>>>>> 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
> .>>>
> .>>>
> .>>>
> .>>> --
> .>>> ------------------------------------------------------------------------
> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> .>>> Ontario Institute for Cancer Research
> .>>> _______________________________________________
> .>>> Bioperl-l mailing list
> .>>> Bioperl-l at lists.open-bio.org
> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> .>>
> .>
> .
> .=====================================
> .Jim Hu
> .Professor
> .Dept. of Biochemistry and Biophysics
> .2128 TAMU
> .Texas A&M Univ.
> .College Station, TX 77843-2128
> .979-862-4054
> .
> .
> .
> ._______________________________________________
> .Bioperl-l mailing list
> .Bioperl-l at lists.open-bio.org
> .http://lists.open-bio.org/mailman/listinfo/bioperl-l

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From MEC at stowers.org  Fri Jan  4 18:33:04 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 17:33:04 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
	<2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE7CB@EXCHMB-02.stowers-institute.org>

Jim,

To get a working example for further discussion....

Assuming you have bioperl and blast+ installed....

This command gets a known transcript from ncbi and blasts it back at ncbi into fly genome:

> bp_download_query_genbank.pl --query 'NM_001259364' | blastn -remote -db refseq_genomic  -entrez_query 'melanogaster[Taxid]'  -outfmt 6  > test.blast.tab

Take a look at the results (see below, or run it yourself).

First line output looks like this:

	NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928

Old GFF did not have parent-child.  Depending on where you are going with this, you MIGHT want to use this strategy: http://gmod.org/wiki/GFF#Alignments

Where the ID in column 9 serves to group the features.  There is an 'implicit' parent.

I think this would be respected by both GBrowse and UCSC genome browser (but I'm not positive).

If so, converting blast output would yield one line output per each line input.

You would need to assign a strand, swap sstart and send where sstart>send, and some slight re-formatting

First line of GFF might look like:

	NT_033778.3 est EST_match 9330023	9327897  . + . ID=Match1;Name= NM_001259364;Target= NM_001259364 1869	3995

Is this along the lines of what you need?

~Malcolm

Complete example blast+ output looks like this:

NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	1019	0	0	3995	5013	9327834	9326816	0.0	1882
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	374	0	0	345	718	9332643	9332270	0.0	 691
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	300	0	0	1	300	9337978	9337679	1e-154	 555
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	270	0	0	717	986	9332201	9331932	5e-138	 499
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	243	0	0	1434	1676	9331200	9330958	5e-123	 449
NM_001259364	gi|116010442|ref|NT_033778.3|	99.55	223	0	1	1154	1376	9331611	9331390	1e-109	 405
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	196	0	0	1675	1870	9330634	9330439	7e-97	 363
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	169	0	0	986	1154	9331847	9331679	7e-82	 313
NM_001259364	gi|116010442|ref|NT_033778.3|	97.26	73	2	0	1372	1444	9331322	9331250	3e-25	 124
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	44	0	0	301	344	9333095	9333052	2e-12	82.4
NM_001259364	gi|195586644|ref|NT_167067.1|	96.52	2127	74	0	1869	3995	7777827	7775701	0.0	3518
NM_001259364	gi|195586644|ref|NT_167067.1|	97.03	404	7	3	4004	4402	7775629	7775226	0.0	 675
NM_001259364	gi|195586644|ref|NT_167067.1|	93.58	374	24	0	345	718	7780392	7780019	8e-156	 558
NM_001259364	gi|195586644|ref|NT_167067.1|	94.37	302	15	1	1	300	7786262	7785961	6e-127	 462
NM_001259364	gi|195586644|ref|NT_167067.1|	96.25	267	10	0	720	986	7779949	7779683	1e-119	 438
NM_001259364	gi|195586644|ref|NT_167067.1|	95.00	240	12	0	1434	1673	7778959	7778720	2e-101	 377
NM_001259364	gi|195586644|ref|NT_167067.1|	96.86	223	6	1	1154	1376	7779370	7779149	1e-99	 372
NM_001259364	gi|195586644|ref|NT_167067.1|	93.88	196	12	0	1675	1870	7778384	7778189	7e-77	 296
NM_001259364	gi|195586644|ref|NT_167067.1|	95.19	187	5	4	4827	5013	7774635	7774453	9e-76	 292
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	168	12	0	987	1154	7779598	7779431	3e-61	 244
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	70	5	0	1374	1443	7779079	7779010	2e-18	 102
NM_001259364	gi|195586644|ref|NT_167067.1|	100.00	44	0	0	301	344	7780833	7780790	2e-12	82.4
NM_001259364	gi|195489961|ref|NT_167063.1|	92.43	2127	161	0	1869	3995	7628910	7631036	0.0	3037
NM_001259364	gi|195489961|ref|NT_167063.1|	91.94	1030	38	20	3995	5013	7631102	7632097	0.0	1400
NM_001259364	gi|195489961|ref|NT_167063.1|	88.56	376	39	4	345	718	7626215	7626588	4e-124	 453
NM_001259364	gi|195489961|ref|NT_167063.1|	93.67	300	18	1	1	300	7620777	7621075	2e-122	 448
NM_001259364	gi|195489961|ref|NT_167063.1|	95.41	196	9	0	1675	1870	7628263	7628458	7e-82	 313
NM_001259364	gi|195489961|ref|NT_167063.1|	91.93	223	17	1	1154	1376	7627224	7627445	2e-81	 311
NM_001259364	gi|195489961|ref|NT_167063.1|	86.42	265	31	3	720	983	7626653	7626913	1e-73	 285
NM_001259364	gi|195489961|ref|NT_167063.1|	86.18	246	25	4	1434	1673	7627635	7627877	3e-65	 257
NM_001259364	gi|195489961|ref|NT_167063.1|	88.27	162	19	0	993	1154	7626999	7627160	3e-46	 195
NM_001259364	gi|195489961|ref|NT_167063.1|	93.06	72	5	0	1372	1443	7627513	7627584	1e-19	 106
NM_001259364	gi|195489961|ref|NT_167063.1|	100.00	44	0	0	301	344	7625770	7625813	2e-12	82.4


~Malcolm


 .-----Original Message-----
 .From: Jim Hu [mailto:jimhu at tamu.edu]
 .Sent: Friday, January 04, 2013 3:58 PM
 .To: Cook, Malcolm
 .Cc: 'Brian Osborne'; 'Fields, Christopher J'; 'Scott Cain'; 'bioperl-l at bioperl.org'
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Malcolm,
 .
 .Thanks, I should have reread the GFF3 spec before posting!
 .
 .In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking
 .of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see
 .how the final output could be done in different ways, but I'm still stuck on how to get there.
 .
 .I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get
 .to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are
 .gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other
 .work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a
 .transposable element, for example.
 .
 .Excerpting from blastp -help
 .
 . *** Formatting options
 . -outfmt <String>
 .   alignment view options:
 .     0 = pairwise,
 .     1 = query-anchored showing identities,
 .     2 = query-anchored no identities,
 .     3 = flat query-anchored, show identities,
 .     4 = flat query-anchored, no identities,
 .     5 = XML Blast output,
 .     6 = tabular,
 .     7 = tabular with comment lines,
 .     8 = Text ASN.1,
 .     9 = Binary ASN.1,
 .    10 = Comma-separated values,
 .    11 = BLAST archive format (ASN.1)
 .
 .Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than
 .suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute
 .OR the multi-line match features OR a combination from one of these output formats.
 .
 .I'm probably missing something very, very obvious.
 .
 .Best,
 .
 .Jim
 .
 .
 .On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:
 .
 .> Jim,
 .>
 .> Getting to your original question:
 .>
 .>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create
 .gff with appropriate subfeatures.
 .>
 .> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
 .>
 .> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE
 .GAP ATTRIBUTE' or as in 'ALIGNMENTS'
 .>
 .> I would guess not because neither of them have 'subfeatures'.
 .>
 .> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have
 .a better idea of what options might suit your needs.
 .>
 .>
 .> ~Malcolm
 .>
 .>
 .> .-----Original Message-----
 .> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .> .Sent: Friday, January 04, 2013 1:50 PM
 .> .To: Brian Osborne
 .> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .> .
 .> .Thanks for the replies, but...
 .> .
 .> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback.
 .Putting
 .> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .> .
 .> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .> .broken, at least on this page:
 .> .
 .> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .> .
 .> .Jim
 .> .
 .> .
 .> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .> .
 .> .> Scott and Chris,
 .> .>
 .> .> I'll test it and see...
 .> .>
 .> .> Brian O.
 .> .>
 .> .>
 .> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .> .>
 .> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .> .>>
 .> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .> .>>
 .> .>> chris
 .> .>>
 .> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .> .>>
 .> .>>> Hi Brian,
 .> .>>>
 .> .>>> I was going to suggest the same thing--though that script is fairly
 .> .>>> old, it's not as old as the blast2gff script in the GBrowse
 .> .>>> distribution (which probably should be retired).  I believe it
 .> .>>> supports GFF3, though I don't have any sample data with which to test
 .> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .> .>>> it accept it?
 .> .>>>
 .> .>>> Scott
 .> .>>>
 .> .>>>
 .> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .> .>>>> Here's one:
 .> .>>>>
 .> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .> .>>>>
 .> .>>>> Another one:
 .> .>>>>
 .> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .> .>>>> #!perl
 .> .>>>>
 .> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .> .>>>> #
 .> .>>>> =head1 NAME
 .> .>>>>
 .> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .> .>>>>
 .> .>>>>
 .> .>>>>
 .> .>>>> Brian O.
 .> .>>>>
 .> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .> .>>>>
 .> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .> .>>>>>
 .> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .> .create gff with appropriate subfeatures.
 .> .>>>>>
 .> .>>>>> Thanks,
 .> .>>>>>
 .> .>>>>> Jim
 .> .>>>>> =====================================
 .> .>>>>> Jim Hu
 .> .>>>>> Professor
 .> .>>>>> Dept. of Biochemistry and Biophysics
 .> .>>>>> 2128 TAMU
 .> .>>>>> Texas A&M Univ.
 .> .>>>>> College Station, TX 77843-2128
 .> .>>>>> 979-862-4054
 .> .>>>>>
 .> .>>>>>
 .> .>>>>>
 .> .>>>>> _______________________________________________
 .> .>>>>> 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
 .> .>>>
 .> .>>>
 .> .>>>
 .> .>>> --
 .> .>>> ------------------------------------------------------------------------
 .> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .> .>>> Ontario Institute for Cancer Research
 .> .>>> _______________________________________________
 .> .>>> Bioperl-l mailing list
 .> .>>> Bioperl-l at lists.open-bio.org
 .> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .> .>>
 .> .>
 .> .
 .> .=====================================
 .> .Jim Hu
 .> .Professor
 .> .Dept. of Biochemistry and Biophysics
 .> .2128 TAMU
 .> .Texas A&M Univ.
 .> .College Station, TX 77843-2128
 .> .979-862-4054
 .> .
 .> .
 .> .
 .> ._______________________________________________
 .> .Bioperl-l mailing list
 .> .Bioperl-l at lists.open-bio.org
 .> .http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .




From bosborne11 at verizon.net  Sat Jan  5 17:25:37 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Sat, 05 Jan 2013 17:25:37 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>

All,

The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.

Brian O.


On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> 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 jason.stajich at gmail.com  Mon Jan  7 04:35:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 7 Jan 2013 01:35:23 -0800
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
Message-ID: <D0FEE7D0-A855-478C-8BA1-08F56FEAD7A7@gmail.com>

with bp_search2gff  I included a cmdline options so you decide what is the reference (seqid column) and what is the target (9th column) since in some cases (BLASTX vs TBLASTN) you may want to be displaying one or the other as the reference. this is the -t option.

You can also have the -m option when you run which will build the grouping match term for a parent and then the sub-children will be HSPs that have that parent per Malcom's description of the parent child info.

Have you tried this with your output - it should work fine with regular vanilla text blast+ output or the -outfmt 6 option (tell bp_search2gff the format is blasttable)  or you can use -outfmt 5 and tell it you are using blastxml format.

 
Jason

On Jan 5, 2013, at 2:25 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> All,
> 
> The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> 
>> Scott and Chris,
>> 
>> I'll test it and see?
>> 
>> Brian O.
>> 
>> 
>> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
>> 
>>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>>> 
>>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>>> 
>>> chris
>>> 
>>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>>> 
>>>> Hi Brian,
>>>> 
>>>> I was going to suggest the same thing--though that script is fairly
>>>> old, it's not as old as the blast2gff script in the GBrowse
>>>> distribution (which probably should be retired).  I believe it
>>>> supports GFF3, though I don't have any sample data with which to test
>>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>>> it accept it?
>>>> 
>>>> Scott
>>>> 
>>>> 
>>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>>> Here's one:
>>>>> 
>>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>>> 
>>>>> Another one:
>>>>> 
>>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>>> #!perl
>>>>> 
>>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>>> #
>>>>> =head1 NAME
>>>>> 
>>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>>> 
>>>>> 
>>>>> 
>>>>> Brian O.
>>>>> 
>>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>>> 
>>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>>> 
>>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Jim
>>>>>> =====================================
>>>>>> Jim Hu
>>>>>> Professor
>>>>>> Dept. of Biochemistry and Biophysics
>>>>>> 2128 TAMU
>>>>>> Texas A&M Univ.
>>>>>> College Station, TX 77843-2128
>>>>>> 979-862-4054
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> _______________________________________________
>>>> 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
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From pengyu.ut at gmail.com  Thu Jan  3 17:41:37 2013
From: pengyu.ut at gmail.com (Peng Yu)
Date: Thu, 3 Jan 2013 14:41:37 -0800 (PST)
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file from
	Pfam
Message-ID: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>

Hi,

I tried the following code on the Pfam stockholm file (downloaded at
ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
But it gives me the following error. Is it a bug in bioperl or it is
an error in the Pfam-A.full.gz file?

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;

#use FindBin;
#use lib "$FindBin::Bin/.";

use Bio::AlignIO;
use Data::Dumper;

my $in = Bio::AlignIO->new(
  -format => 'stockholm',
  -file   => '/dev/stdin'
);

while(my $aln=$in->next_aln) {
  print $aln->accession, "\n";
}

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
#!/usr/bin/env bash

zcat ~/db/Pfam-A.full.gz | ./main.pl

~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh

...

------------- EXCEPTION -------------
MSG: '1985D' is not an integer.

STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
Range.pm:227
STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
lib/Bio/Annotation/Target.pm:81
STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:293
STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:73
STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
STACK toplevel ./main.pl:17
-------------------------------------


From thomas.girke at gmail.com  Wed Jan  9 15:59:08 2013
From: thomas.girke at gmail.com (Thomas Girke)
Date: Wed, 9 Jan 2013 12:59:08 -0800 (PST)
Subject: [Bioperl-l] Bioinformatics Position Opening
Message-ID: <9a99afb9-4a67-4d20-89ce-4d416fa7a46b@googlegroups.com>

Dear List,

Below is an announcement for a Ph.D. level bioinformatics position at
UCR. It is a long-term position with a competitive salary in a vibrant
research environment with cutting edge high-performance compute and
genomics facilities. Application instructions are given in the
announcement. Potential candidates are welcome to email me their
questions about this position directly, e.g.  prior or after submitting
a formal application. 

Best,

Thomas

--
Thomas Girke
Associate Professor of Bioinformatics
Institute for Integrative Genome Biology (IIGB)
1207F Genomics Building
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Ph: 951-905-5232
Fax: 951-827-5155


POSITION ANNOUNCEMENT

POSITION
The Institute for Integrative Genome Biology (IIGB) at the University of
California, Riverside is seeking a Ph.D. level bioinformatician to
manage its bioinformatics research activities and computing facility.  

TITLE/RANK
Bioinformatics Facility Director. Salary will be competitive and
commensurate with accomplishments.

LOCATION
University of California, Riverside. 

BACKGROUND
Successful candidates will join an innovative and multidisciplinary
Institute for Integrative Genome Biology (IIGB) that connects
theoretical and experimental researchers from different departments in
Life, Physical and Mathematical Sciences, Medicine, Engineering and
various campus based Centers. The IIGB is organized around a 10,000
sq.ft. suite of Instrumentation Facilities that serve as a centralized,
shared-use resource for faculty, staff and students, offering advanced
tools in bioinformatics, microscopy, proteomics and genomics. Its
bioinformatic component is equipped with an extensive high-performance
compute (HPC) infrastructure. 

QUALIFICATIONS
Applicants must have a Ph.D. from a recognized university in
bioinformatics; or combined degrees in computer science and a biological
science; or a degree in either computer science combined with relevant
experience in biological science; or a degree in a biological science
combined with relevant experience in computer science. The successful
candidate will have at least 2 years of professional hands-on experience
with next generation sequence data analysis, scientific data programming
and high-performance computing. A strong publication record of
bioinformatics research in collaboration with experimental biologists is
expected. Another requirement is several years of professional
experience with common programming languages/environments. This includes
at least one statistical programming environment (preferentially R), one
or more general-purpose scripting languages (e.g. Python, Perl or Ruby),
experience with web development frameworks and relational database
design. Several years of computational research experience using HPC
systems will be beneficial.  The incumbent should also have experience
with the analysis of modern biological data sets, such as microarrays,
next generation sequence data (e.g. genotyping, RNA profiling, de novo
assemblies), phylogenetics and/or molecular dynamics simulations.

RESPONSIBILITIES
The Bioinformatics Facility Director manages IIGB's computational
infrastructure jointly with its bioinformatics staff, including an
HPC/Linux systems administrator, one or more programmers and students
workers. The incumbent will be required to provide data analysis support
to collaborative research activities and make available findings through
presentations and contribute as team member to scientific publications
as well as participate in the preparation of joint grant applications
and reports. The teaching expectations include the development of a
state-of-the-art workshop program on large-scale data analysis and
programming. Participation in collaborative equipment grants will be
another core responsibility to secure future growth of the facility?s
computing resources. 

TO APPLY
Review of applications will continue until the position is filled.
Interested individuals should: (1) submit a curriculum vitae, (2)
provide a statement of research interests, and (3) arrange to have three
letters of reference sent on their behalf. All information should be
emailed to: thomas.girke at ucr.edu

WEBSITE
http://facility.bioinformatics.ucr.edu/position-opening




From frej.tulin at gmail.com  Thu Jan 10 21:53:16 2013
From: frej.tulin at gmail.com (Frej Tulin)
Date: Thu, 10 Jan 2013 21:53:16 -0500
Subject: [Bioperl-l] stand alone blast plus problem
Message-ID: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>

Hi

I have been trying for a long time to control my blast searches with the
Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was
a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing
seems to help.
When I build a database using the makeblastdb directly from the command
line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







-- 
Frej Tulin
Fred Cross lab
Rockefeller University


From cjfields at illinois.edu  Fri Jan 11 00:04:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 11 Jan 2013 05:04:12 +0000
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file
 from	Pfam
In-Reply-To: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
References: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF6A00B@CHIMBX5.ad.uillinois.edu>

I haven't used the '/dev/stdin' file like this, I typically do:

> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -fh   => \*STDIN
> );


but if it works?

That does look like a bug in the parser.  Would you know the Pfam alignmet accessions that triggered it, or maybe ones just prior to the fail?

chris

On Jan 3, 2013, at 4:41 PM, Peng Yu <pengyu.ut at gmail.com> wrote:

> Hi,
> 
> I tried the following code on the Pfam stockholm file (downloaded at
> ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
> But it gives me the following error. Is it a bug in bioperl or it is
> an error in the Pfam-A.full.gz file?
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> 
> #use FindBin;
> #use lib "$FindBin::Bin/.";
> 
> use Bio::AlignIO;
> use Data::Dumper;
> 
> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -file   => '/dev/stdin'
> );
> 
> while(my $aln=$in->next_aln) {
>  print $aln->accession, "\n";
> }
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
> #!/usr/bin/env bash
> 
> zcat ~/db/Pfam-A.full.gz | ./main.pl
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh
> 
> ...
> 
> ------------- EXCEPTION -------------
> MSG: '1985D' is not an integer.
> 
> STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
> Range.pm:227
> STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
> lib/Bio/Annotation/Target.pm:81
> STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
> Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:293
> STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
> py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:73
> STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
> ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
> STACK toplevel ./main.pl:17
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Russell.Smithies at agresearch.co.nz  Sun Jan 13 17:25:16 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 14 Jan 2013 11:25:16 +1300
Subject: [Bioperl-l] stand alone blast plus problem
In-Reply-To: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
References: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF372E99EE4C1@exchsth.agresearch.co.nz>

Hi Frej,
Here's a few things to try:
Is it possible you need to escape the special chars in your IDs? i.e. the pipes and colons?
Have you tried it with simpler IDs?
Is your BioPerl sequence object collection created correctly?
Can you create the database by just passing it the fasta file?

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_name => 'mydb',
  -db_data => 'myseqs.fas',
  -create => 1
);

--Russell 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Frej Tulin
Sent: Friday, 11 January 2013 3:53 p.m.
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] stand alone blast plus problem

Hi

I have been trying for a long time to control my blast searches with the Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing seems to help.
When I build a database using the makeblastdb directly from the command line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







--
Frej Tulin
Fred Cross lab
Rockefeller University
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

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From awitney at sgul.ac.uk  Thu Jan 17 06:45:40 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 11:45:40 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
Message-ID: <50F7E464.3090906@sgul.ac.uk>

Hi,

I would like to produces graphics as shown in this section (cross 
linking between genome tracks) [scroll down a little to see the pictures]:

http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211

but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, 
but this works within a web browser, I would like to generate these 
diagrams from a stand alone script. If not does anyone know any perl 
libraries that can be used to show genome comparisons?

Thanks

Adam


From cjfields at illinois.edu  Thu Jan 17 08:37:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 13:37:04 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F7E464.3090906@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>

Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.

chris

On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> Hi,
> 
> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
> 
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
> 
> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
> 
> Thanks
> 
> Adam
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From awitney at sgul.ac.uk  Thu Jan 17 12:33:42 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 17:33:42 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
Message-ID: <50F835F6.5090603@sgul.ac.uk>


Thanks Chris. I hadn't seen SynBrowse before, looks good.

But I would like to do this without all the database/webserver overhead, 
I have a perl script that can interact with a gbrowse_syn database to 
generate images ie no webserver, I just need to separate out the 
database stuff now.

Thanks again

Adam

On 17/01/2013 13:37, Fields, Christopher J wrote:
> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>
> chris
>
> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>
>> Hi,
>>
>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>
>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>
>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>
>> Thanks
>>
>> Adam
>> _______________________________________________
>> 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  Thu Jan 17 12:41:47 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 17:41:47 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F835F6.5090603@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
	<50F835F6.5090603@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFD4BA@CITESMBX5.ad.uillinois.edu>

Let us know if this can be of use to the community, I'm sure others would find it useful as well.

chris

On Jan 17, 2013, at 11:33 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> 
> Thanks Chris. I hadn't seen SynBrowse before, looks good.
> 
> But I would like to do this without all the database/webserver overhead, I have a perl script that can interact with a gbrowse_syn database to generate images ie no webserver, I just need to separate out the database stuff now.
> 
> Thanks again
> 
> Adam
> 
> On 17/01/2013 13:37, Fields, Christopher J wrote:
>> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>> 
>> chris
>> 
>> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>> 
>>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>> 
>>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>> 
>>> Thanks
>>> 
>>> Adam
>>> _______________________________________________
>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From buschj at hhu.de  Sat Jan 19 11:12:54 2013
From: buschj at hhu.de (jobu)
Date: Sat, 19 Jan 2013 17:12:54 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking .."
Message-ID: <50FAC606.2060800@hhu.de>

Dear List,

I've got quite a lot of  hits from blasting against nt-database that state:

"Features flanking this part of subject sequence: "

where the subject-accession only will give information about complete
genomic sequences,
the detailed information inside the "Features flanking" section of the
HSP about annotations of upstream and downstream elements would be what
I need.

Is there any elegant way to make Bio::SearchIO do this job for me?

greetings
Jochen


From saladi1 at illinois.edu  Tue Jan 22 16:45:23 2013
From: saladi1 at illinois.edu (Shyam Saladi)
Date: Tue, 22 Jan 2013 13:45:23 -0800
Subject: [Bioperl-l] Bio::DB::Taxonomy example
Message-ID: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>

Hi,

There is an example on how to use Bio::DB::Taxonomy at
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy

I tried the script but could not get it to work properly. After looking
through the documentation it seems that

my @extant_children = grep { $_->rank eq 'species' }
$node->get_all_Descendents;

should instead be

my @extant_children = grep { $_->rank eq 'species' }
$db->get_all_Descendents($node)

I found this solves the problem for me. If my fix is in fact correct, an
admin may want to change the example script online.

Thanks,
Shyam
**


From cjfields at illinois.edu  Tue Jan 22 18:40:05 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 22 Jan 2013 23:40:05 +0000
Subject: [Bioperl-l] Bio::DB::Taxonomy example
In-Reply-To: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
References: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CDFE139@CITESMBX5.ad.uillinois.edu>

Done.  Thanks for pointing that out!

chris

On Jan 23, 2013, at 5:45 AM, Shyam Saladi <saladi1 at illinois.edu>
 wrote:

> Hi,
> 
> There is an example on how to use Bio::DB::Taxonomy at
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> 
> I tried the script but could not get it to work properly. After looking
> through the documentation it seems that
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $node->get_all_Descendents;
> 
> should instead be
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $db->get_all_Descendents($node)
> 
> I found this solves the problem for me. If my fix is in fact correct, an
> admin may want to change the example script online.
> 
> Thanks,
> Shyam
> **
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From buschj at hhu.de  Fri Jan 25 05:20:22 2013
From: buschj at hhu.de (jobu)
Date: Fri, 25 Jan 2013 11:20:22 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
Message-ID: <51025C66.6060008@hhu.de>

Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
> What upstream and downstream elements are you interested in?


I've got a huge pile of short RNA reads.
Part of the question now is whether those RNA fragments originate from
siRNA events,
or may represent miRNAs / parts of pre-miRNAs.

So I did an online  blast search against database nt.
The resulting report quite often just gives subject information like this:

-----
> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
Length=23459830
-----

Now I would like to get the hit's neighbouring regions  for further
analysis.
Preferably I would like to do that  in an automized way, but the only
possible action with this kind of subject gi | description would be to
fetch the entire chromosomal  sequence I guess ?

However,
right below the line above, the report states more precisely:

------
 Features flanking this part of subject sequence:
   8872 bp at 5' side: cytochrome P450 90B1
   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
------

Still I would like to have the possibility to automatically fetch the
subject's sequence(s),
as of now I think  parsing the report with SearchIO won't let me aquire
that information, because SearchIO does not recognize report sections
like those.

I hope I did not miss any of SearchIOs capabilities, but I could not
find any method covering my wish?!

Right now maybe the only way to get the information I want is to
construct my own parser and write it out into a separate file, which in
turn again  I could read into a hash before processing the Blast-Report
with SearchIO to combine both data for further automized work.

I am aware though that even successfully getting the flanking features
would leave me with the more or less wide  intergenic gap my hsp is
located in.

However I'm in need of a way to get the flanking features including
their annotation and the region spanning between them.
But I hope I do not have to get complete sequences to accomplish that,
as this would be kind of an overkill.

with kind regards
Jochen





From afonsomduarte at gmail.com  Mon Jan 14 05:09:48 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 14 Jan 2013 02:09:48 -0800 (PST)
Subject: [Bioperl-l] Parsing Blast results for different genus
Message-ID: <217cf8ac-5323-48f5-8a81-aba032cba68b@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


PS sorry if this message appears twice ... as i was having some trouble 
posting the first time.


From afonsomduarte at gmail.com  Sun Jan 13 14:17:19 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Sun, 13 Jan 2013 11:17:19 -0800 (PST)
Subject: [Bioperl-l] Split blast result by genus. How to parse it ?
Message-ID: <83857a34-14a0-43e2-a2b3-5ca538d41bcd@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


From afonsomduarte at gmail.com  Mon Jan 21 04:03:44 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 21 Jan 2013 01:03:44 -0800 (PST)
Subject: [Bioperl-l] spliting genbank file into smaller ones via organism
Message-ID: <f8a60619-c086-4a29-8541-13b136b716f3@googlegroups.com>



Dear List,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


From jason.stajich at gmail.com  Tue Jan 29 14:00:16 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Tue, 29 Jan 2013 11:00:16 -0800
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <51025C66.6060008@hhu.de>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
	<51025C66.6060008@hhu.de>
Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D@gmail.com>

We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.

However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.

basically:
- download the genome and GFF for arabidopsis
- align your sRNA to the genome with a short read aligner - bowtie, bwa, others
- convert your sam to bam file with SAMtools or picard
- compare the location of features with the reads to get expression summaries or individuals reads with BEDTools


On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:

> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>> What upstream and downstream elements are you interested in?
> 
> 
> I've got a huge pile of short RNA reads.
> Part of the question now is whether those RNA fragments originate from
> siRNA events,
> or may represent miRNAs / parts of pre-miRNAs.
> 
> So I did an online  blast search against database nt.
> The resulting report quite often just gives subject information like this:
> 
> -----
>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
> Length=23459830
> -----
> 
> Now I would like to get the hit's neighbouring regions  for further
> analysis.
> Preferably I would like to do that  in an automized way, but the only
> possible action with this kind of subject gi | description would be to
> fetch the entire chromosomal  sequence I guess ?
> 
> However,
> right below the line above, the report states more precisely:
> 
> ------
> Features flanking this part of subject sequence:
>   8872 bp at 5' side: cytochrome P450 90B1
>   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
> ------
> 
> Still I would like to have the possibility to automatically fetch the
> subject's sequence(s),
> as of now I think  parsing the report with SearchIO won't let me aquire
> that information, because SearchIO does not recognize report sections
> like those.
> 
> I hope I did not miss any of SearchIOs capabilities, but I could not
> find any method covering my wish?!
> 
> Right now maybe the only way to get the information I want is to
> construct my own parser and write it out into a separate file, which in
> turn again  I could read into a hash before processing the Blast-Report
> with SearchIO to combine both data for further automized work.
> 
> I am aware though that even successfully getting the flanking features
> would leave me with the more or less wide  intergenic gap my hsp is
> located in.
> 
> However I'm in need of a way to get the flanking features including
> their annotation and the region spanning between them.
> But I hope I do not have to get complete sequences to accomplish that,
> as this would be kind of an overkill.
> 
> with kind regards
> Jochen
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From dr_kilburn59 at yahoo.com  Wed Jan 30 16:40:26 2013
From: dr_kilburn59 at yahoo.com (Dan kilburn)
Date: Wed, 30 Jan 2013 16:40:26 -0500
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
Message-ID: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>

Hi Jason,

Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.

--Dan
Sent from my iPhone

On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:

> Send Bioperl-l mailing list submissions to
>    bioperl-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>    http://lists.open-bio.org/mailman/listinfo/bioperl-l
> or, via email, send a message with subject or body 'help' to
>    bioperl-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
>    bioperl-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
> 
> 
> Today's Topics:
> 
>   1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>      (Jason Stajich)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 29 Jan 2013 11:00:16 -0800
> From: Jason Stajich <jason.stajich at gmail.com>
> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>    flanking    .."
> To: buschj at hhu.de
> Cc: bioperl-l at lists.open-bio.org
> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
> Content-Type: text/plain;    charset=us-ascii
> 
> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
> 
> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
> 
> basically:
> - download the genome and GFF for arabidopsis
> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
> - convert your sam to bam file with SAMtools or picard
> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
> 
> 
> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
> 
>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>> What upstream and downstream elements are you interested in?
>> 
>> 
>> I've got a huge pile of short RNA reads.
>> Part of the question now is whether those RNA fragments originate from
>> siRNA events,
>> or may represent miRNAs / parts of pre-miRNAs.
>> 
>> So I did an online  blast search against database nt.
>> The resulting report quite often just gives subject information like this:
>> 
>> -----
>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>> Length=23459830
>> -----
>> 
>> Now I would like to get the hit's neighbouring regions  for further
>> analysis.
>> Preferably I would like to do that  in an automized way, but the only
>> possible action with this kind of subject gi | description would be to
>> fetch the entire chromosomal  sequence I guess ?
>> 
>> However,
>> right below the line above, the report states more precisely:
>> 
>> ------
>> Features flanking this part of subject sequence:
>>  8872 bp at 5' side: cytochrome P450 90B1
>>  402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>> ------
>> 
>> Still I would like to have the possibility to automatically fetch the
>> subject's sequence(s),
>> as of now I think  parsing the report with SearchIO won't let me aquire
>> that information, because SearchIO does not recognize report sections
>> like those.
>> 
>> I hope I did not miss any of SearchIOs capabilities, but I could not
>> find any method covering my wish?!
>> 
>> Right now maybe the only way to get the information I want is to
>> construct my own parser and write it out into a separate file, which in
>> turn again  I could read into a hash before processing the Blast-Report
>> with SearchIO to combine both data for further automized work.
>> 
>> I am aware though that even successfully getting the flanking features
>> would leave me with the more or less wide  intergenic gap my hsp is
>> located in.
>> 
>> However I'm in need of a way to get the flanking features including
>> their annotation and the region spanning between them.
>> But I hope I do not have to get complete sequences to accomplish that,
>> as this would be kind of an overkill.
>> 
>> with kind regards
>> Jochen
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> End of Bioperl-l Digest, Vol 117, Issue 13
> ******************************************



From cjfields at illinois.edu  Wed Jan 30 18:13:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 30 Jan 2013 23:13:49 +0000
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
	<575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CE1175C@CHIMBX5.ad.uillinois.edu>

We certainly accept support for updates to the code.  In fact, if you are familiar with git/github the process is fairly straightforward:

1) Fork the code to your github account
2) Make and commit changes
3) Submit a pull request
4) Post something to the list just in case.

We also accept code patches; the best way to submit these is as a bug report to the redmine repository (doesn't hurt to post here as well):

https://redmine.open-bio.org/

chris

On Jan 30, 2013, at 3:40 PM, Dan kilburn <dr_kilburn59 at yahoo.com> wrote:

> Hi Jason,
> 
> Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.
> 
> --Dan
> Sent from my iPhone
> 
> On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:
> 
>> Send Bioperl-l mailing list submissions to
>>   bioperl-l at lists.open-bio.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>>   http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> or, via email, send a message with subject or body 'help' to
>>   bioperl-l-request at lists.open-bio.org
>> 
>> You can reach the person managing the list at
>>   bioperl-l-owner at lists.open-bio.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Bioperl-l digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>>     (Jason Stajich)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Tue, 29 Jan 2013 11:00:16 -0800
>> From: Jason Stajich <jason.stajich at gmail.com>
>> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>>   flanking    .."
>> To: buschj at hhu.de
>> Cc: bioperl-l at lists.open-bio.org
>> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
>> Content-Type: text/plain;    charset=us-ascii
>> 
>> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
>> 
>> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
>> 
>> basically:
>> - download the genome and GFF for arabidopsis
>> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
>> - convert your sam to bam file with SAMtools or picard
>> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
>> 
>> 
>> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
>> 
>>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>>> What upstream and downstream elements are you interested in?
>>> 
>>> 
>>> I've got a huge pile of short RNA reads.
>>> Part of the question now is whether those RNA fragments originate from
>>> siRNA events,
>>> or may represent miRNAs / parts of pre-miRNAs.
>>> 
>>> So I did an online  blast search against database nt.
>>> The resulting report quite often just gives subject information like this:
>>> 
>>> -----
>>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>>> Length=23459830
>>> -----
>>> 
>>> Now I would like to get the hit's neighbouring regions  for further
>>> analysis.
>>> Preferably I would like to do that  in an automized way, but the only
>>> possible action with this kind of subject gi | description would be to
>>> fetch the entire chromosomal  sequence I guess ?
>>> 
>>> However,
>>> right below the line above, the report states more precisely:
>>> 
>>> ------
>>> Features flanking this part of subject sequence:
>>> 8872 bp at 5' side: cytochrome P450 90B1
>>> 402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>>> ------
>>> 
>>> Still I would like to have the possibility to automatically fetch the
>>> subject's sequence(s),
>>> as of now I think  parsing the report with SearchIO won't let me aquire
>>> that information, because SearchIO does not recognize report sections
>>> like those.
>>> 
>>> I hope I did not miss any of SearchIOs capabilities, but I could not
>>> find any method covering my wish?!
>>> 
>>> Right now maybe the only way to get the information I want is to
>>> construct my own parser and write it out into a separate file, which in
>>> turn again  I could read into a hash before processing the Blast-Report
>>> with SearchIO to combine both data for further automized work.
>>> 
>>> I am aware though that even successfully getting the flanking features
>>> would leave me with the more or less wide  intergenic gap my hsp is
>>> located in.
>>> 
>>> However I'm in need of a way to get the flanking features including
>>> their annotation and the region spanning between them.
>>> But I hope I do not have to get complete sequences to accomplish that,
>>> as this would be kind of an overkill.
>>> 
>>> with kind regards
>>> Jochen
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> End of Bioperl-l Digest, Vol 117, Issue 13
>> ******************************************
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From thiago.venancio at gmail.com  Thu Jan 31 12:10:39 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:10:39 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
Message-ID: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>

Hi all,

I am trying to install bioperl-ext and the compilation gives me the error:

/usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
can not be used when making a shared object; recompile with -fPIC
libs/libsw.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
make[1]: Leaving directory 
`/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align'
make: *** [subdirs] Error 2

However, the Makefile says that -fPIC is already being used, which is 
puzzling me.

Any clues ?

Thanks.
Thiago





From thiago.venancio at gmail.com  Thu Jan 31 12:25:12 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:25:12 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
In-Reply-To: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
References: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
Message-ID: <e22d2881-ddd3-42af-9a69-f03503b8fb5a@googlegroups.com>

Solved using the solution posted by jmf here :
https://groups.google.com/forum/?fromgroups=#!searchin/bioperl-l/bioperl-ext/bioperl-l/FgJo_g8UQE8/FB1DEjJkTooJ

Which I found after posting.

T


On Thursday, January 31, 2013 3:10:39 PM UTC-2, Thiago Venancio wrote:
>
> Hi all, 
>
> I am trying to install bioperl-ext and the compilation gives me the error: 
>
> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
> can not be used when making a shared object; recompile with -fPIC 
> libs/libsw.a: could not read symbols: Bad value 
> collect2: ld returned 1 exit status 
> make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 
> make[1]: Leaving directory 
> `/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align' 
> make: *** [subdirs] Error 2 
>
> However, the Makefile says that -fPIC is already being used, which is 
> puzzling me. 
>
> Any clues ? 
>
> Thanks. 
> Thiago 
>
>
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>


From koriege at googlemail.com  Thu Jan 31 21:49:20 2013
From: koriege at googlemail.com (koriege at googlemail.com)
Date: Thu, 31 Jan 2013 18:49:20 -0800 (PST)
Subject: [Bioperl-l] problem with Bio::*::Fasta id_parser
Message-ID: <e9e0c428-0467-4b62-a37d-cfcb91ed818b@googlegroups.com>

Hi,

I tried two methods to create a bioperl FASTA database, but it failes by 
extracting the substring out of my headers.
Can someone explain me why I get the standard header or show me a work 
around? 

thanks in advance.
pyr0

i)
my $objDB = Bio::Index::Fasta->new(-filename => $PATHdbIdx, -write_flag => 
1);
$objDB->id_parser(\&get_id);
$objDB->make_index(glob($objParameter->dbGenome()));

sub get_id {
   my $header = shift;
   $header =~ /^>.*\bsp\|([A-Z]\d{5}\b)/;
   $1;
}

output
Use of uninitialized value $id in concatenation (.) or string at 
/usr/share/perl5/Bio/Index/Abstract.pm line 753, <$FASTA> line 1.
Use of uninitialized value $id in exists at 
/usr/share/perl5/Bio/Index/Abstract.pm line 754, <$FASTA> line 1.
Use of uninitialized value $id in hash element at 
/usr/share/perl5/Bio/Index/Abstract.pm line 757, <$FASTA> line 1.
gi|376282008|ref|NC_016798.1|

ii)
my $PATHdbIdx=catfile($objParameter->DIR,'data','db.idx');
unlink($PATHdbIdx);
my $objDB = Bio::DB::Fasta->new($objParameter->dbGenome(), -makeid => 
\&get_id);
$objDBgenome->set(\$objDB);

output:
Use of uninitialized value $key in pattern match (m//) at 
/usr/share/perl5/Bio/DB/Fasta.pm line 1178.
Use of uninitialized value $id in exists at 
/usr/share/perl5/Bio/DB/Fasta.pm line 617.
gi|376282008|ref|NC_016798.1|


From yuf228 at hotmail.com  Thu Jan 31 23:15:15 2013
From: yuf228 at hotmail.com (Rob)
Date: Fri, 1 Feb 2013 04:15:15 +0000 (UTC)
Subject: [Bioperl-l] Where to get BLASTCLUST or equivalent?
References: <200305311150.h4VBopn2019091@localhost.localdomain>
Message-ID: <loom.20130201T045704-740@post.gmane.org>

Cyril C.C. Chua <bmbcccc <at> bmb.leeds.ac.uk> writes:

> 
> Hi,
> 
> I have some difficulty in sourcing for BLASTCLUST or related 
> programs/mods. Does any1 know exactly how to locate them?
> 
> Regards
> 
> Cyril Chua
> 


Hi Cyril,

I heard of the following programmes that might do similar things (I HAVEN'T 
used any of them yet):

Afree - http://www.vicbioinformatics.com/software.afree.shtml
Uclust - http://drive5.com/uclust/uclust_userguide_2_1.pdf
Usearch - http://www.drive5.com/usearch/
DomClust - http://mbgd.genome.ad.jp/domclust/

or 

Check this: 

http://ppod.princeton.edu/help/help_tech.html

God bless,


Robert




From jimhu at tamu.edu  Wed Jan  2 19:44:56 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Wed, 2 Jan 2013 13:44:56 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
Message-ID: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>

I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.

I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  

Thanks,

Jim
=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From biojiangke at gmail.com  Wed Jan  2 20:20:02 2013
From: biojiangke at gmail.com (Ke Jiang)
Date: Wed, 2 Jan 2013 15:20:02 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>

There is a blast2gff.pl floating around for Gbrowse to visualize blast
results as tracks. Not sure about the blast+. One more reason to stick with
the good old blast!

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Ke

-------------------------------------------
Ke Jiang, Ph.D.
Post-doctoral Fellow
Delbruck Laboratory
Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11724


From cjfields at illinois.edu  Wed Jan  2 20:47:52 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 20:47:52 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<CANRaYz34waZXzW795Qnn2wWyTQ3z20Lh+Kr0xZkGNvizyq2AaA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FD44@CHIMBX5.ad.uillinois.edu>

?except that NCBI no longer supports legacy BLAST.  Caveat emptor.

chris

On Jan 2, 2013, at 2:20 PM, Ke Jiang <biojiangke at gmail.com> wrote:

> There is a blast2gff.pl floating around for Gbrowse to visualize blast
> results as tracks. Not sure about the blast+. One more reason to stick with
> the good old blast!
> 
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> 
> Ke
> 
> -------------------------------------------
> Ke Jiang, Ph.D.
> Post-doctoral Fellow
> Delbruck Laboratory
> Cold Spring Harbor Laboratory
> Cold Spring Harbor, NY 11724
> _______________________________________________
> 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  Wed Jan  2 20:26:22 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 15:26:22 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
Message-ID: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>

Here's one:

https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl

Another one:

~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl 
#!perl

# Author:      Jason Stajich <jason-at-bioperl-dot-org>
# Description: Turn SearchIO parseable report(s) into a GFF report
#
=head1 NAME

bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report



Brian O.

On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:

> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> 
> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.  
> 
> Thanks,
> 
> Jim
> =====================================
> Jim Hu
> Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From scott at scottcain.net  Wed Jan  2 21:32:16 2013
From: scott at scottcain.net (Scott Cain)
Date: Wed, 2 Jan 2013 16:32:16 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
Message-ID: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>

Hi Brian,

I was going to suggest the same thing--though that script is fairly
old, it's not as old as the blast2gff script in the GBrowse
distribution (which probably should be retired).  I believe it
supports GFF3, though I don't have any sample data with which to test
it to be sure.  I also don't know if it supports BLAST+ input--I
haven't kept up with SearchIO (on which search2gff.pl depends); will
it accept it?

Scott


On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> Here's one:
>
> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>
> Another one:
>
> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> #!perl
>
> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> # Description: Turn SearchIO parseable report(s) into a GFF report
> #
> =head1 NAME
>
> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>
>
>
> Brian O.
>
> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>
>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>
>> Thanks,
>>
>> Jim
>> =====================================
>> Jim Hu
>> Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>>
>> _______________________________________________
>> 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



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


From cjfields at illinois.edu  Wed Jan  2 22:26:55 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 2 Jan 2013 22:26:55 +0000
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>

It should (I recall using it at one point).  If it doesn't we should fix it so it does.

How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 

chris

On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Brian,
> 
> I was going to suggest the same thing--though that script is fairly
> old, it's not as old as the blast2gff script in the GBrowse
> distribution (which probably should be retired).  I believe it
> supports GFF3, though I don't have any sample data with which to test
> it to be sure.  I also don't know if it supports BLAST+ input--I
> haven't kept up with SearchIO (on which search2gff.pl depends); will
> it accept it?
> 
> Scott
> 
> 
> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>> Here's one:
>> 
>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>> 
>> Another one:
>> 
>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>> #!perl
>> 
>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>> # Description: Turn SearchIO parseable report(s) into a GFF report
>> #
>> =head1 NAME
>> 
>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>> 
>> 
>> 
>> Brian O.
>> 
>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>> 
>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>> 
>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>> 
>>> Thanks,
>>> 
>>> Jim
>>> =====================================
>>> Jim Hu
>>> Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> 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  Wed Jan  2 22:53:50 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Wed, 02 Jan 2013 17:53:50 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
Message-ID: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>

Scott and Chris,

I'll test it and see?

Brian O.


On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> 
> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
> 
> chris
> 
> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> 
>> Hi Brian,
>> 
>> I was going to suggest the same thing--though that script is fairly
>> old, it's not as old as the blast2gff script in the GBrowse
>> distribution (which probably should be retired).  I believe it
>> supports GFF3, though I don't have any sample data with which to test
>> it to be sure.  I also don't know if it supports BLAST+ input--I
>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>> it accept it?
>> 
>> Scott
>> 
>> 
>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>> Here's one:
>>> 
>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>> 
>>> Another one:
>>> 
>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>> #!perl
>>> 
>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>> #
>>> =head1 NAME
>>> 
>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>> 
>>> 
>>> 
>>> Brian O.
>>> 
>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>> 
>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>> 
>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>> 
>>>> Thanks,
>>>> 
>>>> Jim
>>>> =====================================
>>>> Jim Hu
>>>> Professor
>>>> Dept. of Biochemistry and Biophysics
>>>> 2128 TAMU
>>>> Texas A&M Univ.
>>>> College Station, TX 77843-2128
>>>> 979-862-4054
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> 
>> 
>> -- 
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From jimhu at tamu.edu  Fri Jan  4 19:49:51 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 13:49:51 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>

Thanks for the replies, but...

I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.

The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be broken, at least on this page:

	http://www.bioperl.org/wiki/Module:Bio::SearchIO

Jim


On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From bosborne11 at verizon.net  Fri Jan  4 19:26:52 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Fri, 04 Jan 2013 14:26:52 -0500
Subject: [Bioperl-l] strange error in the beginners howto
In-Reply-To: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
References: <AD53D86BA0E3974B908175E10777B27E3EE92A62@MED-MBX1.med.usc.edu>
Message-ID: <BB2BD9EA-3419-4B6C-A659-4D86420CFAE0@verizon.net>

Matthew,

First, let's distinguish "warning" and "error". Errors stop execution of the app or script, what you're seeing is a warning, your script actually completes. Does the warning vanish if you remove "-w"?

Second, seems like this is a Perl version thing:

http://www.sysarchitects.com/bioperl

BIO

On Jan 4, 2013, at 1:55 PM, "Thornton, Matthew" <Matthew.Thornton at med.usc.edu> wrote:

> Hello,
> 
> I am working through the first part of the BioPerl beginners howto and I am getting an error and I was wondering if you could tell me what is wrong.
> 
> I made the seqio.pl script:
> 
> #!/bin/perl -w
> 
> use Bio::Seq;
> 
> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",                        
>                          -display_id => "#12345",                        
>                          -desc => "example 1",                        
>                          -alphabet => "dna" );
> 
> print $seq_obj->seq();
> 
> I execute the script and I get this error:
> 
> gserver at gserver:~/bio$ perl seqio.pl 
> Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251.
> aaaatgggggggggggccccgttgserver at gserver:~/bio$
> 
> Is there something wrong with my installation?
> 
> Any help is greatly appreciated.
> 
> Thanks!
> 
> 
> Matthew E. Thornton
> 
> 
> 
> Laboratory Technician III
> Broad Center for Stem Cell and Regenerative Medicine
> University of Southern California
> 1501 San Pablo St. ZNI
> Los Angeles, CA 90089-2821
> ph.:323-442-1688
> fx.:323-442-4040
> matthew.thornton at med.usc.edu
> 

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




From MEC at stowers.org  Fri Jan  4 20:20:17 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 14:20:17 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>

Jim,

Getting to your original question:

> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.

Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??

If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'

I would guess not because neither of them have 'subfeatures'.

If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.


~Malcolm


 .-----Original Message-----
 .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .Sent: Friday, January 04, 2013 1:50 PM
 .To: Brian Osborne
 .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Thanks for the replies, but...
 .
 .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
 .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .
 .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .broken, at least on this page:
 .
 .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .
 .Jim
 .
 .
 .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .
 .> Scott and Chris,
 .>
 .> I'll test it and see...
 .>
 .> Brian O.
 .>
 .>
 .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .>
 .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .>>
 .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .>>
 .>> chris
 .>>
 .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .>>
 .>>> Hi Brian,
 .>>>
 .>>> I was going to suggest the same thing--though that script is fairly
 .>>> old, it's not as old as the blast2gff script in the GBrowse
 .>>> distribution (which probably should be retired).  I believe it
 .>>> supports GFF3, though I don't have any sample data with which to test
 .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .>>> it accept it?
 .>>>
 .>>> Scott
 .>>>
 .>>>
 .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .>>>> Here's one:
 .>>>>
 .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .>>>>
 .>>>> Another one:
 .>>>>
 .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .>>>> #!perl
 .>>>>
 .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .>>>> #
 .>>>> =head1 NAME
 .>>>>
 .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .>>>>
 .>>>>
 .>>>>
 .>>>> Brian O.
 .>>>>
 .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .>>>>
 .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .>>>>>
 .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .create gff with appropriate subfeatures.
 .>>>>>
 .>>>>> Thanks,
 .>>>>>
 .>>>>> Jim
 .>>>>> =====================================
 .>>>>> Jim Hu
 .>>>>> Professor
 .>>>>> Dept. of Biochemistry and Biophysics
 .>>>>> 2128 TAMU
 .>>>>> Texas A&M Univ.
 .>>>>> College Station, TX 77843-2128
 .>>>>> 979-862-4054
 .>>>>>
 .>>>>>
 .>>>>>
 .>>>>> _______________________________________________
 .>>>>> 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
 .>>>
 .>>>
 .>>>
 .>>> --
 .>>> ------------------------------------------------------------------------
 .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .>>> Ontario Institute for Cancer Research
 .>>> _______________________________________________
 .>>> Bioperl-l mailing list
 .>>> Bioperl-l at lists.open-bio.org
 .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .>>
 .>
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .
 .
 .
 ._______________________________________________
 .Bioperl-l mailing list
 .Bioperl-l at lists.open-bio.org
 .http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jimhu at tamu.edu  Fri Jan  4 21:57:38 2013
From: jimhu at tamu.edu (Jim Hu)
Date: Fri, 4 Jan 2013 15:57:38 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
Message-ID: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>

Malcolm,

Thanks, I should have reread the GFF3 spec before posting!

In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see how the final output could be done in different ways, but I'm still stuck on how to get there.  

I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a transposable element, for example.

Excerpting from blastp -help

 *** Formatting options
 -outfmt <String>
   alignment view options:
     0 = pairwise,
     1 = query-anchored showing identities,
     2 = query-anchored no identities,
     3 = flat query-anchored, show identities,
     4 = flat query-anchored, no identities,
     5 = XML Blast output,
     6 = tabular,
     7 = tabular with comment lines,
     8 = Text ASN.1,
     9 = Binary ASN.1,
    10 = Comma-separated values,
    11 = BLAST archive format (ASN.1) 

Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute OR the multi-line match features OR a combination from one of these output formats. 

I'm probably missing something very, very obvious.

Best,

Jim


On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:

> Jim,
> 
> Getting to your original question:
> 
>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create gff with appropriate subfeatures.
> 
> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
> 
> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE GAP ATTRIBUTE' or as in 'ALIGNMENTS'
> 
> I would guess not because neither of them have 'subfeatures'.
> 
> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have a better idea of what options might suit your needs.
> 
> 
> ~Malcolm
> 
> 
> .-----Original Message-----
> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
> .Sent: Friday, January 04, 2013 1:50 PM
> .To: Brian Osborne
> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
> .
> .Thanks for the replies, but...
> .
> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting
> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
> .
> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
> .broken, at least on this page:
> .
> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
> .
> .Jim
> .
> .
> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
> .
> .> Scott and Chris,
> .>
> .> I'll test it and see...
> .>
> .> Brian O.
> .>
> .>
> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> .>
> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
> .>>
> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
> .>>
> .>> chris
> .>>
> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
> .>>
> .>>> Hi Brian,
> .>>>
> .>>> I was going to suggest the same thing--though that script is fairly
> .>>> old, it's not as old as the blast2gff script in the GBrowse
> .>>> distribution (which probably should be retired).  I believe it
> .>>> supports GFF3, though I don't have any sample data with which to test
> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
> .>>> it accept it?
> .>>>
> .>>> Scott
> .>>>
> .>>>
> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> .>>>> Here's one:
> .>>>>
> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
> .>>>>
> .>>>> Another one:
> .>>>>
> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
> .>>>> #!perl
> .>>>>
> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
> .>>>> #
> .>>>> =head1 NAME
> .>>>>
> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
> .>>>>
> .>>>>
> .>>>>
> .>>>> Brian O.
> .>>>>
> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
> .>>>>
> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
> .>>>>>
> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
> .create gff with appropriate subfeatures.
> .>>>>>
> .>>>>> Thanks,
> .>>>>>
> .>>>>> Jim
> .>>>>> =====================================
> .>>>>> Jim Hu
> .>>>>> Professor
> .>>>>> Dept. of Biochemistry and Biophysics
> .>>>>> 2128 TAMU
> .>>>>> Texas A&M Univ.
> .>>>>> College Station, TX 77843-2128
> .>>>>> 979-862-4054
> .>>>>>
> .>>>>>
> .>>>>>
> .>>>>> _______________________________________________
> .>>>>> 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
> .>>>
> .>>>
> .>>>
> .>>> --
> .>>> ------------------------------------------------------------------------
> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> .>>> Ontario Institute for Cancer Research
> .>>> _______________________________________________
> .>>> Bioperl-l mailing list
> .>>> Bioperl-l at lists.open-bio.org
> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> .>>
> .>
> .
> .=====================================
> .Jim Hu
> .Professor
> .Dept. of Biochemistry and Biophysics
> .2128 TAMU
> .Texas A&M Univ.
> .College Station, TX 77843-2128
> .979-862-4054
> .
> .
> .
> ._______________________________________________
> .Bioperl-l mailing list
> .Bioperl-l at lists.open-bio.org
> .http://lists.open-bio.org/mailman/listinfo/bioperl-l

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054





From MEC at stowers.org  Fri Jan  4 23:33:04 2013
From: MEC at stowers.org (Cook, Malcolm)
Date: Fri, 4 Jan 2013 17:33:04 -0600
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<7F69D24B-8D4C-41F5-B8A1-CB850EBB1C67@tamu.edu>
	<2C40E43D1F7A56408C4463FD245DDDF907958EE791@EXCHMB-02.stowers-institute.org>
	<2D58FAEB-ED4B-4965-A8CB-890D0012D098@tamu.edu>
Message-ID: <2C40E43D1F7A56408C4463FD245DDDF907958EE7CB@EXCHMB-02.stowers-institute.org>

Jim,

To get a working example for further discussion....

Assuming you have bioperl and blast+ installed....

This command gets a known transcript from ncbi and blasts it back at ncbi into fly genome:

> bp_download_query_genbank.pl --query 'NM_001259364' | blastn -remote -db refseq_genomic  -entrez_query 'melanogaster[Taxid]'  -outfmt 6  > test.blast.tab

Take a look at the results (see below, or run it yourself).

First line output looks like this:

	NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928

Old GFF did not have parent-child.  Depending on where you are going with this, you MIGHT want to use this strategy: http://gmod.org/wiki/GFF#Alignments

Where the ID in column 9 serves to group the features.  There is an 'implicit' parent.

I think this would be respected by both GBrowse and UCSC genome browser (but I'm not positive).

If so, converting blast output would yield one line output per each line input.

You would need to assign a strand, swap sstart and send where sstart>send, and some slight re-formatting

First line of GFF might look like:

	NT_033778.3 est EST_match 9330023	9327897  . + . ID=Match1;Name= NM_001259364;Target= NM_001259364 1869	3995

Is this along the lines of what you need?

~Malcolm

Complete example blast+ output looks like this:

NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	2127	0	0	1869	3995	9330023	9327897	0.0	3928
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	1019	0	0	3995	5013	9327834	9326816	0.0	1882
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	374	0	0	345	718	9332643	9332270	0.0	 691
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	300	0	0	1	300	9337978	9337679	1e-154	 555
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	270	0	0	717	986	9332201	9331932	5e-138	 499
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	243	0	0	1434	1676	9331200	9330958	5e-123	 449
NM_001259364	gi|116010442|ref|NT_033778.3|	99.55	223	0	1	1154	1376	9331611	9331390	1e-109	 405
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	196	0	0	1675	1870	9330634	9330439	7e-97	 363
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	169	0	0	986	1154	9331847	9331679	7e-82	 313
NM_001259364	gi|116010442|ref|NT_033778.3|	97.26	73	2	0	1372	1444	9331322	9331250	3e-25	 124
NM_001259364	gi|116010442|ref|NT_033778.3|	100.00	44	0	0	301	344	9333095	9333052	2e-12	82.4
NM_001259364	gi|195586644|ref|NT_167067.1|	96.52	2127	74	0	1869	3995	7777827	7775701	0.0	3518
NM_001259364	gi|195586644|ref|NT_167067.1|	97.03	404	7	3	4004	4402	7775629	7775226	0.0	 675
NM_001259364	gi|195586644|ref|NT_167067.1|	93.58	374	24	0	345	718	7780392	7780019	8e-156	 558
NM_001259364	gi|195586644|ref|NT_167067.1|	94.37	302	15	1	1	300	7786262	7785961	6e-127	 462
NM_001259364	gi|195586644|ref|NT_167067.1|	96.25	267	10	0	720	986	7779949	7779683	1e-119	 438
NM_001259364	gi|195586644|ref|NT_167067.1|	95.00	240	12	0	1434	1673	7778959	7778720	2e-101	 377
NM_001259364	gi|195586644|ref|NT_167067.1|	96.86	223	6	1	1154	1376	7779370	7779149	1e-99	 372
NM_001259364	gi|195586644|ref|NT_167067.1|	93.88	196	12	0	1675	1870	7778384	7778189	7e-77	 296
NM_001259364	gi|195586644|ref|NT_167067.1|	95.19	187	5	4	4827	5013	7774635	7774453	9e-76	 292
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	168	12	0	987	1154	7779598	7779431	3e-61	 244
NM_001259364	gi|195586644|ref|NT_167067.1|	92.86	70	5	0	1374	1443	7779079	7779010	2e-18	 102
NM_001259364	gi|195586644|ref|NT_167067.1|	100.00	44	0	0	301	344	7780833	7780790	2e-12	82.4
NM_001259364	gi|195489961|ref|NT_167063.1|	92.43	2127	161	0	1869	3995	7628910	7631036	0.0	3037
NM_001259364	gi|195489961|ref|NT_167063.1|	91.94	1030	38	20	3995	5013	7631102	7632097	0.0	1400
NM_001259364	gi|195489961|ref|NT_167063.1|	88.56	376	39	4	345	718	7626215	7626588	4e-124	 453
NM_001259364	gi|195489961|ref|NT_167063.1|	93.67	300	18	1	1	300	7620777	7621075	2e-122	 448
NM_001259364	gi|195489961|ref|NT_167063.1|	95.41	196	9	0	1675	1870	7628263	7628458	7e-82	 313
NM_001259364	gi|195489961|ref|NT_167063.1|	91.93	223	17	1	1154	1376	7627224	7627445	2e-81	 311
NM_001259364	gi|195489961|ref|NT_167063.1|	86.42	265	31	3	720	983	7626653	7626913	1e-73	 285
NM_001259364	gi|195489961|ref|NT_167063.1|	86.18	246	25	4	1434	1673	7627635	7627877	3e-65	 257
NM_001259364	gi|195489961|ref|NT_167063.1|	88.27	162	19	0	993	1154	7626999	7627160	3e-46	 195
NM_001259364	gi|195489961|ref|NT_167063.1|	93.06	72	5	0	1372	1443	7627513	7627584	1e-19	 106
NM_001259364	gi|195489961|ref|NT_167063.1|	100.00	44	0	0	301	344	7625770	7625813	2e-12	82.4


~Malcolm


 .-----Original Message-----
 .From: Jim Hu [mailto:jimhu at tamu.edu]
 .Sent: Friday, January 04, 2013 3:58 PM
 .To: Cook, Malcolm
 .Cc: 'Brian Osborne'; 'Fields, Christopher J'; 'Scott Cain'; 'bioperl-l at bioperl.org'
 .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .
 .Malcolm,
 .
 .Thanks, I should have reread the GFF3 spec before posting!
 .
 .In the section on the Gap attrribute and below on alignments it discusses two ways to represent an alignment. I was originally thinking
 .of something like the later example shown for cDNA vs genome. But the gap attribute representation would be fine too. So, I can see
 .how the final output could be done in different ways, but I'm still stuck on how to get there.
 .
 .I don't have a specific application in mind; I'm mostly just trying to understand how to get from having standalone blast+ output to get
 .to things that look like the examples in the gff spec and the gbrowse documentation - really basic display of alignments that are
 .gapped. For my teaching, we do EST vs genomic blast and want gapped cDNA alignments to show where the introns go. My other
 .work is with bacteria where introns are rare, but there are times when I'd like to show an alignment that is interrupted by a
 .transposable element, for example.
 .
 .Excerpting from blastp -help
 .
 . *** Formatting options
 . -outfmt <String>
 .   alignment view options:
 .     0 = pairwise,
 .     1 = query-anchored showing identities,
 .     2 = query-anchored no identities,
 .     3 = flat query-anchored, show identities,
 .     4 = flat query-anchored, no identities,
 .     5 = XML Blast output,
 .     6 = tabular,
 .     7 = tabular with comment lines,
 .     8 = Text ASN.1,
 .     9 = Binary ASN.1,
 .    10 = Comma-separated values,
 .    11 = BLAST archive format (ASN.1)
 .
 .Several of these are "lossy" in terms of where the actual gaps occur (e.g. 6). Others seem to me to be more human readable than
 .suited for parsing. So I was hoping to get pointed to an existing script that would generate either the single feature with gap attribute
 .OR the multi-line match features OR a combination from one of these output formats.
 .
 .I'm probably missing something very, very obvious.
 .
 .Best,
 .
 .Jim
 .
 .
 .On Jan 4, 2013, at 2:20 PM, Cook, Malcolm wrote:
 .
 .> Jim,
 .>
 .> Getting to your original question:
 .>
 .>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and .create
 .gff with appropriate subfeatures.
 .>
 .> Exactly what/how do you want/expect to encode the blast output as GFF{1,2,2.5,3}??
 .>
 .> If GFF3 pe http://www.sequenceontology.org/gff3.shtml then are you hoping to get GFF3 marked up as described in section 'THE
 .GAP ATTRIBUTE' or as in 'ALIGNMENTS'
 .>
 .> I would guess not because neither of them have 'subfeatures'.
 .>
 .> If you could explain more fully with examples (hand cobbled or borrowed from someone else) of what you expect then I might have
 .a better idea of what options might suit your needs.
 .>
 .>
 .> ~Malcolm
 .>
 .>
 .> .-----Original Message-----
 .> .From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jim Hu
 .> .Sent: Friday, January 04, 2013 1:50 PM
 .> .To: Brian Osborne
 .> .Cc: Fields, Christopher J; Scott Cain; bioperl-l at bioperl.org
 .> .Subject: Re: [Bioperl-l] Converting blast+ output to gff (with gaps)
 .> .
 .> .Thanks for the replies, but...
 .> .
 .> .I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback.
 .Putting
 .> .some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.
 .> .
 .> .The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be
 .> .broken, at least on this page:
 .> .
 .> .	http://www.bioperl.org/wiki/Module:Bio::SearchIO
 .> .
 .> .Jim
 .> .
 .> .
 .> .On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:
 .> .
 .> .> Scott and Chris,
 .> .>
 .> .> I'll test it and see...
 .> .>
 .> .> Brian O.
 .> .>
 .> .>
 .> .> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
 .> .>
 .> .>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
 .> .>>
 .> .>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method...
 .> .>>
 .> .>> chris
 .> .>>
 .> .>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
 .> .>>
 .> .>>> Hi Brian,
 .> .>>>
 .> .>>> I was going to suggest the same thing--though that script is fairly
 .> .>>> old, it's not as old as the blast2gff script in the GBrowse
 .> .>>> distribution (which probably should be retired).  I believe it
 .> .>>> supports GFF3, though I don't have any sample data with which to test
 .> .>>> it to be sure.  I also don't know if it supports BLAST+ input--I
 .> .>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
 .> .>>> it accept it?
 .> .>>>
 .> .>>> Scott
 .> .>>>
 .> .>>>
 .> .>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
 .> .>>>> Here's one:
 .> .>>>>
 .> .>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
 .> .>>>>
 .> .>>>> Another one:
 .> .>>>>
 .> .>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
 .> .>>>> #!perl
 .> .>>>>
 .> .>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
 .> .>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
 .> .>>>> #
 .> .>>>> =head1 NAME
 .> .>>>>
 .> .>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
 .> .>>>>
 .> .>>>>
 .> .>>>>
 .> .>>>> Brian O.
 .> .>>>>
 .> .>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
 .> .>>>>
 .> .>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
 .> .>>>>>
 .> .>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and
 .> .create gff with appropriate subfeatures.
 .> .>>>>>
 .> .>>>>> Thanks,
 .> .>>>>>
 .> .>>>>> Jim
 .> .>>>>> =====================================
 .> .>>>>> Jim Hu
 .> .>>>>> Professor
 .> .>>>>> Dept. of Biochemistry and Biophysics
 .> .>>>>> 2128 TAMU
 .> .>>>>> Texas A&M Univ.
 .> .>>>>> College Station, TX 77843-2128
 .> .>>>>> 979-862-4054
 .> .>>>>>
 .> .>>>>>
 .> .>>>>>
 .> .>>>>> _______________________________________________
 .> .>>>>> 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
 .> .>>>
 .> .>>>
 .> .>>>
 .> .>>> --
 .> .>>> ------------------------------------------------------------------------
 .> .>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
 .> .>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
 .> .>>> Ontario Institute for Cancer Research
 .> .>>> _______________________________________________
 .> .>>> Bioperl-l mailing list
 .> .>>> Bioperl-l at lists.open-bio.org
 .> .>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .> .>>
 .> .>
 .> .
 .> .=====================================
 .> .Jim Hu
 .> .Professor
 .> .Dept. of Biochemistry and Biophysics
 .> .2128 TAMU
 .> .Texas A&M Univ.
 .> .College Station, TX 77843-2128
 .> .979-862-4054
 .> .
 .> .
 .> .
 .> ._______________________________________________
 .> .Bioperl-l mailing list
 .> .Bioperl-l at lists.open-bio.org
 .> .http://lists.open-bio.org/mailman/listinfo/bioperl-l
 .
 .=====================================
 .Jim Hu
 .Professor
 .Dept. of Biochemistry and Biophysics
 .2128 TAMU
 .Texas A&M Univ.
 .College Station, TX 77843-2128
 .979-862-4054
 .




From bosborne11 at verizon.net  Sat Jan  5 22:25:37 2013
From: bosborne11 at verizon.net (Brian Osborne)
Date: Sat, 05 Jan 2013 17:25:37 -0500
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
Message-ID: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>

All,

The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.

Brian O.


On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> Scott and Chris,
> 
> I'll test it and see?
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>> 
>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>> 
>> chris
>> 
>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>> 
>>> Hi Brian,
>>> 
>>> I was going to suggest the same thing--though that script is fairly
>>> old, it's not as old as the blast2gff script in the GBrowse
>>> distribution (which probably should be retired).  I believe it
>>> supports GFF3, though I don't have any sample data with which to test
>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>> it accept it?
>>> 
>>> Scott
>>> 
>>> 
>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>> Here's one:
>>>> 
>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>> 
>>>> Another one:
>>>> 
>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>> #!perl
>>>> 
>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>> #
>>>> =head1 NAME
>>>> 
>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>> 
>>>> 
>>>> 
>>>> Brian O.
>>>> 
>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>> 
>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>> 
>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Jim
>>>>> =====================================
>>>>> Jim Hu
>>>>> Professor
>>>>> Dept. of Biochemistry and Biophysics
>>>>> 2128 TAMU
>>>>> Texas A&M Univ.
>>>>> College Station, TX 77843-2128
>>>>> 979-862-4054
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>> 
>>> 
>>> 
>>> -- 
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>> _______________________________________________
>>> 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 jason.stajich at gmail.com  Mon Jan  7 09:35:23 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Mon, 7 Jan 2013 01:35:23 -0800
Subject: [Bioperl-l] Converting blast+ output to gff (with gaps)
In-Reply-To: <12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
References: <072DC877-6A75-4A2E-9E6B-027E1D874C4C@tamu.edu>
	<EB1BBA9B-9B22-47FF-B6A4-7A7AC890FD5B@verizon.net>
	<CA+JTaoy24Njmuy+SLkfQgSQO27VZHp4bvU8u326uT5Gwz7wWUA@mail.gmail.com>
	<118F034CF4C3EF48A96F86CE585B94BF4CF5FFF5@CHIMBX5.ad.uillinois.edu>
	<80636318-ED50-4F05-85C2-35F12E4FF9D8@verizon.net>
	<12E97C07-D3E0-4E21-8A24-A4223468FF70@verizon.net>
Message-ID: <D0FEE7D0-A855-478C-8BA1-08F56FEAD7A7@gmail.com>

with bp_search2gff  I included a cmdline options so you decide what is the reference (seqid column) and what is the target (9th column) since in some cases (BLASTX vs TBLASTN) you may want to be displaying one or the other as the reference. this is the -t option.

You can also have the -m option when you run which will build the grouping match term for a parent and then the sub-children will be HSPs that have that parent per Malcom's description of the parent child info.

Have you tried this with your output - it should work fine with regular vanilla text blast+ output or the -outfmt 6 option (tell bp_search2gff the format is blasttable)  or you can use -outfmt 5 and tell it you are using blastxml format.

 
Jason

On Jan 5, 2013, at 2:25 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> All,
> 
> The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
> 
>> Scott and Chris,
>> 
>> I'll test it and see?
>> 
>> Brian O.
>> 
>> 
>> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
>> 
>>> It should (I recall using it at one point).  If it doesn't we should fix it so it does.
>>> 
>>> How does MAKER deal with this?  IIRC it uses (a modified) SearchIO-based method... 
>>> 
>>> chris
>>> 
>>> On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> wrote:
>>> 
>>>> Hi Brian,
>>>> 
>>>> I was going to suggest the same thing--though that script is fairly
>>>> old, it's not as old as the blast2gff script in the GBrowse
>>>> distribution (which probably should be retired).  I believe it
>>>> supports GFF3, though I don't have any sample data with which to test
>>>> it to be sure.  I also don't know if it supports BLAST+ input--I
>>>> haven't kept up with SearchIO (on which search2gff.pl depends); will
>>>> it accept it?
>>>> 
>>>> Scott
>>>> 
>>>> 
>>>> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>>>>> Here's one:
>>>>> 
>>>>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>>>>> 
>>>>> Another one:
>>>>> 
>>>>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>>>>> #!perl
>>>>> 
>>>>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>>>>> # Description: Turn SearchIO parseable report(s) into a GFF report
>>>>> #
>>>>> =head1 NAME
>>>>> 
>>>>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>>>>> 
>>>>> 
>>>>> 
>>>>> Brian O.
>>>>> 
>>>>> On Jan 2, 2013, at 2:44 PM, Jim Hu <jimhu at tamu.edu> wrote:
>>>>> 
>>>>>> I assume this has already been done many times, but I can't seem to find it on bioperl.org or via google.
>>>>>> 
>>>>>> I'm looking for a script that will take one of the blast+ outformats that includes the positions of gaps and mismatches, and create gff with appropriate subfeatures.
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Jim
>>>>>> =====================================
>>>>>> Jim Hu
>>>>>> Professor
>>>>>> Dept. of Biochemistry and Biophysics
>>>>>> 2128 TAMU
>>>>>> Texas A&M Univ.
>>>>>> College Station, TX 77843-2128
>>>>>> 979-862-4054
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>> _______________________________________________
>>>> 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
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From pengyu.ut at gmail.com  Thu Jan  3 22:41:37 2013
From: pengyu.ut at gmail.com (Peng Yu)
Date: Thu, 3 Jan 2013 14:41:37 -0800 (PST)
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file from
	Pfam
Message-ID: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>

Hi,

I tried the following code on the Pfam stockholm file (downloaded at
ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
But it gives me the following error. Is it a bug in bioperl or it is
an error in the Pfam-A.full.gz file?

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;

#use FindBin;
#use lib "$FindBin::Bin/.";

use Bio::AlignIO;
use Data::Dumper;

my $in = Bio::AlignIO->new(
  -format => 'stockholm',
  -file   => '/dev/stdin'
);

while(my $aln=$in->next_aln) {
  print $aln->accession, "\n";
}

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
#!/usr/bin/env bash

zcat ~/db/Pfam-A.full.gz | ./main.pl

~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh

...

------------- EXCEPTION -------------
MSG: '1985D' is not an integer.

STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
Range.pm:227
STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
lib/Bio/Annotation/Target.pm:81
STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:293
STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:73
STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
STACK toplevel ./main.pl:17
-------------------------------------


From thomas.girke at gmail.com  Wed Jan  9 20:59:08 2013
From: thomas.girke at gmail.com (Thomas Girke)
Date: Wed, 9 Jan 2013 12:59:08 -0800 (PST)
Subject: [Bioperl-l] Bioinformatics Position Opening
Message-ID: <9a99afb9-4a67-4d20-89ce-4d416fa7a46b@googlegroups.com>

Dear List,

Below is an announcement for a Ph.D. level bioinformatics position at
UCR. It is a long-term position with a competitive salary in a vibrant
research environment with cutting edge high-performance compute and
genomics facilities. Application instructions are given in the
announcement. Potential candidates are welcome to email me their
questions about this position directly, e.g.  prior or after submitting
a formal application. 

Best,

Thomas

--
Thomas Girke
Associate Professor of Bioinformatics
Institute for Integrative Genome Biology (IIGB)
1207F Genomics Building
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Ph: 951-905-5232
Fax: 951-827-5155


POSITION ANNOUNCEMENT

POSITION
The Institute for Integrative Genome Biology (IIGB) at the University of
California, Riverside is seeking a Ph.D. level bioinformatician to
manage its bioinformatics research activities and computing facility.  

TITLE/RANK
Bioinformatics Facility Director. Salary will be competitive and
commensurate with accomplishments.

LOCATION
University of California, Riverside. 

BACKGROUND
Successful candidates will join an innovative and multidisciplinary
Institute for Integrative Genome Biology (IIGB) that connects
theoretical and experimental researchers from different departments in
Life, Physical and Mathematical Sciences, Medicine, Engineering and
various campus based Centers. The IIGB is organized around a 10,000
sq.ft. suite of Instrumentation Facilities that serve as a centralized,
shared-use resource for faculty, staff and students, offering advanced
tools in bioinformatics, microscopy, proteomics and genomics. Its
bioinformatic component is equipped with an extensive high-performance
compute (HPC) infrastructure. 

QUALIFICATIONS
Applicants must have a Ph.D. from a recognized university in
bioinformatics; or combined degrees in computer science and a biological
science; or a degree in either computer science combined with relevant
experience in biological science; or a degree in a biological science
combined with relevant experience in computer science. The successful
candidate will have at least 2 years of professional hands-on experience
with next generation sequence data analysis, scientific data programming
and high-performance computing. A strong publication record of
bioinformatics research in collaboration with experimental biologists is
expected. Another requirement is several years of professional
experience with common programming languages/environments. This includes
at least one statistical programming environment (preferentially R), one
or more general-purpose scripting languages (e.g. Python, Perl or Ruby),
experience with web development frameworks and relational database
design. Several years of computational research experience using HPC
systems will be beneficial.  The incumbent should also have experience
with the analysis of modern biological data sets, such as microarrays,
next generation sequence data (e.g. genotyping, RNA profiling, de novo
assemblies), phylogenetics and/or molecular dynamics simulations.

RESPONSIBILITIES
The Bioinformatics Facility Director manages IIGB's computational
infrastructure jointly with its bioinformatics staff, including an
HPC/Linux systems administrator, one or more programmers and students
workers. The incumbent will be required to provide data analysis support
to collaborative research activities and make available findings through
presentations and contribute as team member to scientific publications
as well as participate in the preparation of joint grant applications
and reports. The teaching expectations include the development of a
state-of-the-art workshop program on large-scale data analysis and
programming. Participation in collaborative equipment grants will be
another core responsibility to secure future growth of the facility?s
computing resources. 

TO APPLY
Review of applications will continue until the position is filled.
Interested individuals should: (1) submit a curriculum vitae, (2)
provide a statement of research interests, and (3) arrange to have three
letters of reference sent on their behalf. All information should be
emailed to: thomas.girke at ucr.edu

WEBSITE
http://facility.bioinformatics.ucr.edu/position-opening




From frej.tulin at gmail.com  Fri Jan 11 02:53:16 2013
From: frej.tulin at gmail.com (Frej Tulin)
Date: Thu, 10 Jan 2013 21:53:16 -0500
Subject: [Bioperl-l] stand alone blast plus problem
Message-ID: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>

Hi

I have been trying for a long time to control my blast searches with the
Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was
a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing
seems to help.
When I build a database using the makeblastdb directly from the command
line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







-- 
Frej Tulin
Fred Cross lab
Rockefeller University


From cjfields at illinois.edu  Fri Jan 11 05:04:12 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Fri, 11 Jan 2013 05:04:12 +0000
Subject: [Bioperl-l] Error when using Bio::AlignIO on stockholm file
 from	Pfam
In-Reply-To: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
References: <f57b6055-cc40-4500-ac39-d8cb9eae1221@c16g2000yqi.googlegroups.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF6A00B@CHIMBX5.ad.uillinois.edu>

I haven't used the '/dev/stdin' file like this, I typically do:

> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -fh   => \*STDIN
> );


but if it works?

That does look like a bug in the parser.  Would you know the Pfam alignmet accessions that triggered it, or maybe ones just prior to the fail?

chris

On Jan 3, 2013, at 4:41 PM, Peng Yu <pengyu.ut at gmail.com> wrote:

> Hi,
> 
> I tried the following code on the Pfam stockholm file (downloaded at
> ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
> But it gives me the following error. Is it a bug in bioperl or it is
> an error in the Pfam-A.full.gz file?
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> 
> #use FindBin;
> #use lib "$FindBin::Bin/.";
> 
> use Bio::AlignIO;
> use Data::Dumper;
> 
> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -file   => '/dev/stdin'
> );
> 
> while(my $aln=$in->next_aln) {
>  print $aln->accession, "\n";
> }
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
> #!/usr/bin/env bash
> 
> zcat ~/db/Pfam-A.full.gz | ./main.pl
> 
> ~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh
> 
> ...
> 
> ------------- EXCEPTION -------------
> MSG: '1985D' is not an integer.
> 
> STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
> Range.pm:227
> STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
> lib/Bio/Annotation/Target.pm:81
> STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
> Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:293
> STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
> py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
> GenericAlignHandler.pm:73
> STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
> ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
> STACK toplevel ./main.pl:17
> -------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From Russell.Smithies at agresearch.co.nz  Sun Jan 13 22:25:16 2013
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Mon, 14 Jan 2013 11:25:16 +1300
Subject: [Bioperl-l] stand alone blast plus problem
In-Reply-To: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
References: <CAK3Z5aPYSp5C2=m4sq2kQNg-zFpy6Krqb5HYVPDKZvLZ0XFLpQ@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF372E99EE4C1@exchsth.agresearch.co.nz>

Hi Frej,
Here's a few things to try:
Is it possible you need to escape the special chars in your IDs? i.e. the pipes and colons?
Have you tried it with simpler IDs?
Is your BioPerl sequence object collection created correctly?
Can you create the database by just passing it the fasta file?

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
  -db_name => 'mydb',
  -db_data => 'myseqs.fas',
  -create => 1
);

--Russell 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Frej Tulin
Sent: Friday, 11 January 2013 3:53 p.m.
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] stand alone blast plus problem

Hi

I have been trying for a long time to control my blast searches with the Bio::Tools::Run::StandAloneBlastPlus module.

The module is installed and gets loaded ok.

However, when calling:
my $blast_db = Bio::Tools::Run::StandAloneBlastPlus -> new
(    -db_data => \@seq_arr,
    -create => 1);

$blast_db -> make_db();
----------------------------------------------------------------------
I get this error
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb call crashed: There was a problem running /home/frej/ncbi-blast-2.2.27+/bin/makeblastdb : Error:
NCBI C++ Exception:

"/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp",
line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type
ATCG00500.1


STACK: Error::throw
STACK: Bio::Root::Root::throw
/home/frej/perl5/lib/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::Run::WrapperBase::_run
/home/frej/perl5/lib/perl5/Bio/Tools/Run/WrapperBase/CommandExts.pm:1012
STACK: Bio::Tools::Run::StandAloneBlastPlus::make_db
/home/frej/perl5/lib/perl5/Bio/Tools/Run/StandAloneBlastPlus.pm:776
STACK: comp2fasta.pl:57
-------------------------------------------------------------------------------------------------------------------------------

The general header format of the fasta files I've tried are
>ATCG00500.1|PACid:19637947
or
>g8540.t1|PACid:26887931

I always get the same message.
I have tried modifying the header by putting 'lcl|' in from but nothing seems to help.
When I build a database using the makeblastdb directly from the command line it works ok, it just doesn't work from within bioperl.

How can this be? What am I doing wrong?

helpful for any assistance

best
/frej







--
Frej Tulin
Fred Cross lab
Rockefeller University
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l

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From awitney at sgul.ac.uk  Thu Jan 17 11:45:40 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 11:45:40 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
Message-ID: <50F7E464.3090906@sgul.ac.uk>

Hi,

I would like to produces graphics as shown in this section (cross 
linking between genome tracks) [scroll down a little to see the pictures]:

http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211

but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, 
but this works within a web browser, I would like to generate these 
diagrams from a stand alone script. If not does anyone know any perl 
libraries that can be used to show genome comparisons?

Thanks

Adam


From cjfields at illinois.edu  Thu Jan 17 13:37:04 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 13:37:04 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F7E464.3090906@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>

Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.

chris

On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> Hi,
> 
> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
> 
> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
> 
> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
> 
> Thanks
> 
> Adam
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From awitney at sgul.ac.uk  Thu Jan 17 17:33:42 2013
From: awitney at sgul.ac.uk (Adam Witney)
Date: Thu, 17 Jan 2013 17:33:42 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
Message-ID: <50F835F6.5090603@sgul.ac.uk>


Thanks Chris. I hadn't seen SynBrowse before, looks good.

But I would like to do this without all the database/webserver overhead, 
I have a perl script that can interact with a gbrowse_syn database to 
generate images ie no webserver, I just need to separate out the 
database stuff now.

Thanks again

Adam

On 17/01/2013 13:37, Fields, Christopher J wrote:
> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>
> chris
>
> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>
>> Hi,
>>
>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>
>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>
>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>
>> Thanks
>>
>> Adam
>> _______________________________________________
>> 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  Thu Jan 17 17:41:47 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Thu, 17 Jan 2013 17:41:47 +0000
Subject: [Bioperl-l] drawing genome comparison cross linking tracks?
In-Reply-To: <50F835F6.5090603@sgul.ac.uk>
References: <50F7E464.3090906@sgul.ac.uk>
	<118F034CF4C3EF48A96F86CE585B94BF69BFAE17@CITESMBX5.ad.uillinois.edu>
	<50F835F6.5090603@sgul.ac.uk>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF69BFD4BA@CITESMBX5.ad.uillinois.edu>

Let us know if this can be of use to the community, I'm sure others would find it useful as well.

chris

On Jan 17, 2013, at 11:33 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

> 
> Thanks Chris. I hadn't seen SynBrowse before, looks good.
> 
> But I would like to do this without all the database/webserver overhead, I have a perl script that can interact with a gbrowse_syn database to generate images ie no webserver, I just need to separate out the database stuff now.
> 
> Thanks again
> 
> Adam
> 
> On 17/01/2013 13:37, Fields, Christopher J wrote:
>> Gbrowse_syn, SynBrowse, and others can do this, but there isn't a pre-packaged way of drawing this that I know of analogous to Biopython's.  It would be nice to have, though.
>> 
>> chris
>> 
>> On Jan 17, 2013, at 5:45 AM, Adam Witney <awitney at sgul.ac.uk> wrote:
>> 
>>> Hi,
>>> 
>>> I would like to produces graphics as shown in this section (cross linking between genome tracks) [scroll down a little to see the pictures]:
>>> 
>>> http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#htoc211
>>> 
>>> but using perl. Can Bio::Graphics do this? I can only find Gbrowse_syn, but this works within a web browser, I would like to generate these diagrams from a stand alone script. If not does anyone know any perl libraries that can be used to show genome comparisons?
>>> 
>>> Thanks
>>> 
>>> Adam
>>> _______________________________________________
>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From buschj at hhu.de  Sat Jan 19 16:12:54 2013
From: buschj at hhu.de (jobu)
Date: Sat, 19 Jan 2013 17:12:54 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking .."
Message-ID: <50FAC606.2060800@hhu.de>

Dear List,

I've got quite a lot of  hits from blasting against nt-database that state:

"Features flanking this part of subject sequence: "

where the subject-accession only will give information about complete
genomic sequences,
the detailed information inside the "Features flanking" section of the
HSP about annotations of upstream and downstream elements would be what
I need.

Is there any elegant way to make Bio::SearchIO do this job for me?

greetings
Jochen


From saladi1 at illinois.edu  Tue Jan 22 21:45:23 2013
From: saladi1 at illinois.edu (Shyam Saladi)
Date: Tue, 22 Jan 2013 13:45:23 -0800
Subject: [Bioperl-l] Bio::DB::Taxonomy example
Message-ID: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>

Hi,

There is an example on how to use Bio::DB::Taxonomy at
http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy

I tried the script but could not get it to work properly. After looking
through the documentation it seems that

my @extant_children = grep { $_->rank eq 'species' }
$node->get_all_Descendents;

should instead be

my @extant_children = grep { $_->rank eq 'species' }
$db->get_all_Descendents($node)

I found this solves the problem for me. If my fix is in fact correct, an
admin may want to change the example script online.

Thanks,
Shyam
**


From cjfields at illinois.edu  Tue Jan 22 23:40:05 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Tue, 22 Jan 2013 23:40:05 +0000
Subject: [Bioperl-l] Bio::DB::Taxonomy example
In-Reply-To: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
References: <CAARX5cXSP3eHagNFTYKTceO_P_b=vVby3DX2zwhFBpSmgeFrkQ@mail.gmail.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CDFE139@CITESMBX5.ad.uillinois.edu>

Done.  Thanks for pointing that out!

chris

On Jan 23, 2013, at 5:45 AM, Shyam Saladi <saladi1 at illinois.edu>
 wrote:

> Hi,
> 
> There is an example on how to use Bio::DB::Taxonomy at
> http://www.bioperl.org/wiki/Module:Bio::DB::Taxonomy
> 
> I tried the script but could not get it to work properly. After looking
> through the documentation it seems that
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $node->get_all_Descendents;
> 
> should instead be
> 
> my @extant_children = grep { $_->rank eq 'species' }
> $db->get_all_Descendents($node)
> 
> I found this solves the problem for me. If my fix is in fact correct, an
> admin may want to change the example script online.
> 
> Thanks,
> Shyam
> **
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From buschj at hhu.de  Fri Jan 25 10:20:22 2013
From: buschj at hhu.de (jobu)
Date: Fri, 25 Jan 2013 11:20:22 +0100
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
Message-ID: <51025C66.6060008@hhu.de>

Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
> What upstream and downstream elements are you interested in?


I've got a huge pile of short RNA reads.
Part of the question now is whether those RNA fragments originate from
siRNA events,
or may represent miRNAs / parts of pre-miRNAs.

So I did an online  blast search against database nt.
The resulting report quite often just gives subject information like this:

-----
> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
Length=23459830
-----

Now I would like to get the hit's neighbouring regions  for further
analysis.
Preferably I would like to do that  in an automized way, but the only
possible action with this kind of subject gi | description would be to
fetch the entire chromosomal  sequence I guess ?

However,
right below the line above, the report states more precisely:

------
 Features flanking this part of subject sequence:
   8872 bp at 5' side: cytochrome P450 90B1
   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
------

Still I would like to have the possibility to automatically fetch the
subject's sequence(s),
as of now I think  parsing the report with SearchIO won't let me aquire
that information, because SearchIO does not recognize report sections
like those.

I hope I did not miss any of SearchIOs capabilities, but I could not
find any method covering my wish?!

Right now maybe the only way to get the information I want is to
construct my own parser and write it out into a separate file, which in
turn again  I could read into a hash before processing the Blast-Report
with SearchIO to combine both data for further automized work.

I am aware though that even successfully getting the flanking features
would leave me with the more or less wide  intergenic gap my hsp is
located in.

However I'm in need of a way to get the flanking features including
their annotation and the region spanning between them.
But I hope I do not have to get complete sequences to accomplish that,
as this would be kind of an overkill.

with kind regards
Jochen





From afonsomduarte at gmail.com  Mon Jan 14 10:09:48 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 14 Jan 2013 02:09:48 -0800 (PST)
Subject: [Bioperl-l] Parsing Blast results for different genus
Message-ID: <217cf8ac-5323-48f5-8a81-aba032cba68b@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


PS sorry if this message appears twice ... as i was having some trouble 
posting the first time.


From afonsomduarte at gmail.com  Sun Jan 13 19:17:19 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Sun, 13 Jan 2013 11:17:19 -0800 (PST)
Subject: [Bioperl-l] Split blast result by genus. How to parse it ?
Message-ID: <83857a34-14a0-43e2-a2b3-5ca538d41bcd@googlegroups.com>



Dear All,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


From afonsomduarte at gmail.com  Mon Jan 21 09:03:44 2013
From: afonsomduarte at gmail.com (Afonso Duarte)
Date: Mon, 21 Jan 2013 01:03:44 -0800 (PST)
Subject: [Bioperl-l] spliting genbank file into smaller ones via organism
Message-ID: <f8a60619-c086-4a29-8541-13b136b716f3@googlegroups.com>



Dear List,

I have obtained several .gb BLAST results that I want to split in different 
.gb or .fasta files accordingly to genus.

I searched for different ways to do it in the web, but didn't find a way to 
do it when one has something like 50 genus in the blast.

(to do it for a short number or genus I could use splitgb.pl from 
http://www.bioperl.org/wiki/HOWTO:SeqIO but it will not be feasible for a 
large number of genus).

Is there a script of way to do it in a efficient way ?

Best


From jason.stajich at gmail.com  Tue Jan 29 19:00:16 2013
From: jason.stajich at gmail.com (Jason Stajich)
Date: Tue, 29 Jan 2013 11:00:16 -0800
Subject: [Bioperl-l] Parsing Blast-Report extracting "Features flanking
	.."
In-Reply-To: <51025C66.6060008@hhu.de>
References: <50FAC606.2060800@hhu.de>
	<CAJm=ba9uOiFF3d2B4_D7-W6g5KiVHeNP6fEStj7eOUZosNcL+g@mail.gmail.com>
	<51025C66.6060008@hhu.de>
Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D@gmail.com>

We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.

However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.

basically:
- download the genome and GFF for arabidopsis
- align your sRNA to the genome with a short read aligner - bowtie, bwa, others
- convert your sam to bam file with SAMtools or picard
- compare the location of features with the reads to get expression summaries or individuals reads with BEDTools


On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:

> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>> What upstream and downstream elements are you interested in?
> 
> 
> I've got a huge pile of short RNA reads.
> Part of the question now is whether those RNA fragments originate from
> siRNA events,
> or may represent miRNAs / parts of pre-miRNAs.
> 
> So I did an online  blast search against database nt.
> The resulting report quite often just gives subject information like this:
> 
> -----
>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
> Length=23459830
> -----
> 
> Now I would like to get the hit's neighbouring regions  for further
> analysis.
> Preferably I would like to do that  in an automized way, but the only
> possible action with this kind of subject gi | description would be to
> fetch the entire chromosomal  sequence I guess ?
> 
> However,
> right below the line above, the report states more precisely:
> 
> ------
> Features flanking this part of subject sequence:
>   8872 bp at 5' side: cytochrome P450 90B1
>   402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
> ------
> 
> Still I would like to have the possibility to automatically fetch the
> subject's sequence(s),
> as of now I think  parsing the report with SearchIO won't let me aquire
> that information, because SearchIO does not recognize report sections
> like those.
> 
> I hope I did not miss any of SearchIOs capabilities, but I could not
> find any method covering my wish?!
> 
> Right now maybe the only way to get the information I want is to
> construct my own parser and write it out into a separate file, which in
> turn again  I could read into a hash before processing the Blast-Report
> with SearchIO to combine both data for further automized work.
> 
> I am aware though that even successfully getting the flanking features
> would leave me with the more or less wide  intergenic gap my hsp is
> located in.
> 
> However I'm in need of a way to get the flanking features including
> their annotation and the region spanning between them.
> But I hope I do not have to get complete sequences to accomplish that,
> as this would be kind of an overkill.
> 
> with kind regards
> Jochen
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org




From dr_kilburn59 at yahoo.com  Wed Jan 30 21:40:26 2013
From: dr_kilburn59 at yahoo.com (Dan kilburn)
Date: Wed, 30 Jan 2013 16:40:26 -0500
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
Message-ID: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>

Hi Jason,

Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.

--Dan
Sent from my iPhone

On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:

> Send Bioperl-l mailing list submissions to
>    bioperl-l at lists.open-bio.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>    http://lists.open-bio.org/mailman/listinfo/bioperl-l
> or, via email, send a message with subject or body 'help' to
>    bioperl-l-request at lists.open-bio.org
> 
> You can reach the person managing the list at
>    bioperl-l-owner at lists.open-bio.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
> 
> 
> Today's Topics:
> 
>   1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>      (Jason Stajich)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 29 Jan 2013 11:00:16 -0800
> From: Jason Stajich <jason.stajich at gmail.com>
> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>    flanking    .."
> To: buschj at hhu.de
> Cc: bioperl-l at lists.open-bio.org
> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
> Content-Type: text/plain;    charset=us-ascii
> 
> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
> 
> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
> 
> basically:
> - download the genome and GFF for arabidopsis
> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
> - convert your sam to bam file with SAMtools or picard
> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
> 
> 
> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
> 
>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>> What upstream and downstream elements are you interested in?
>> 
>> 
>> I've got a huge pile of short RNA reads.
>> Part of the question now is whether those RNA fragments originate from
>> siRNA events,
>> or may represent miRNAs / parts of pre-miRNAs.
>> 
>> So I did an online  blast search against database nt.
>> The resulting report quite often just gives subject information like this:
>> 
>> -----
>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>> Length=23459830
>> -----
>> 
>> Now I would like to get the hit's neighbouring regions  for further
>> analysis.
>> Preferably I would like to do that  in an automized way, but the only
>> possible action with this kind of subject gi | description would be to
>> fetch the entire chromosomal  sequence I guess ?
>> 
>> However,
>> right below the line above, the report states more precisely:
>> 
>> ------
>> Features flanking this part of subject sequence:
>>  8872 bp at 5' side: cytochrome P450 90B1
>>  402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>> ------
>> 
>> Still I would like to have the possibility to automatically fetch the
>> subject's sequence(s),
>> as of now I think  parsing the report with SearchIO won't let me aquire
>> that information, because SearchIO does not recognize report sections
>> like those.
>> 
>> I hope I did not miss any of SearchIOs capabilities, but I could not
>> find any method covering my wish?!
>> 
>> Right now maybe the only way to get the information I want is to
>> construct my own parser and write it out into a separate file, which in
>> turn again  I could read into a hash before processing the Blast-Report
>> with SearchIO to combine both data for further automized work.
>> 
>> I am aware though that even successfully getting the flanking features
>> would leave me with the more or less wide  intergenic gap my hsp is
>> located in.
>> 
>> However I'm in need of a way to get the flanking features including
>> their annotation and the region spanning between them.
>> But I hope I do not have to get complete sequences to accomplish that,
>> as this would be kind of an overkill.
>> 
>> with kind regards
>> Jochen
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> End of Bioperl-l Digest, Vol 117, Issue 13
> ******************************************



From cjfields at illinois.edu  Wed Jan 30 23:13:49 2013
From: cjfields at illinois.edu (Fields, Christopher J)
Date: Wed, 30 Jan 2013 23:13:49 +0000
Subject: [Bioperl-l] Bioperl-l Digest, Vol 117, Issue 13
In-Reply-To: <575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
References: <mailman.7.1359565204.26693.bioperl-l@lists.open-bio.org>
	<575B184F-C051-4FEF-9BEB-7AB98E3C52A6@yahoo.com>
Message-ID: <118F034CF4C3EF48A96F86CE585B94BF6CE1175C@CHIMBX5.ad.uillinois.edu>

We certainly accept support for updates to the code.  In fact, if you are familiar with git/github the process is fairly straightforward:

1) Fork the code to your github account
2) Make and commit changes
3) Submit a pull request
4) Post something to the list just in case.

We also accept code patches; the best way to submit these is as a bug report to the redmine repository (doesn't hurt to post here as well):

https://redmine.open-bio.org/

chris

On Jan 30, 2013, at 3:40 PM, Dan kilburn <dr_kilburn59 at yahoo.com> wrote:

> Hi Jason,
> 
> Are there any plans to keep SearchIO up to date with ncbi blast? I know they change formats ridiculously often, but I had to write my own parser to get sequence identity, which I would rather not have done. I realize that this job would be a big load on anyone who takes it, but it's so fundamental. Maybe I can help.
> 
> --Dan
> Sent from my iPhone
> 
> On Jan 30, 2013, at 12:00 PM, bioperl-l-request at lists.open-bio.org wrote:
> 
>> Send Bioperl-l mailing list submissions to
>>   bioperl-l at lists.open-bio.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>>   http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> or, via email, send a message with subject or body 'help' to
>>   bioperl-l-request at lists.open-bio.org
>> 
>> You can reach the person managing the list at
>>   bioperl-l-owner at lists.open-bio.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Bioperl-l digest..."
>> 
>> 
>> Today's Topics:
>> 
>>  1. Re:  Parsing Blast-Report extracting "Features flanking    .."
>>     (Jason Stajich)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Tue, 29 Jan 2013 11:00:16 -0800
>> From: Jason Stajich <jason.stajich at gmail.com>
>> Subject: Re: [Bioperl-l] Parsing Blast-Report extracting "Features
>>   flanking    .."
>> To: buschj at hhu.de
>> Cc: bioperl-l at lists.open-bio.org
>> Message-ID: <6E83E3F3-C304-4DC4-9A11-FE1CA90F207D at gmail.com>
>> Content-Type: text/plain;    charset=us-ascii
>> 
>> We don't parse the NCBI feature info from the BLAST reports per your query. To look up a specific feature you can use Bio::DB::GenBank to query for sequence from a specific feature by accession number - see the HOWTOs for that.
>> 
>> However, most people use tools that generate SAM/BAM files with short reads - then you can use a tool like bedtools to find overlaps of reads with the locations of features.
>> 
>> basically:
>> - download the genome and GFF for arabidopsis
>> - align your sRNA to the genome with a short read aligner - bowtie, bwa, others
>> - convert your sam to bam file with SAMtools or picard
>> - compare the location of features with the reads to get expression summaries or individuals reads with BEDTools
>> 
>> 
>> On Jan 25, 2013, at 2:20 AM, jobu <buschj at hhu.de> wrote:
>> 
>>> Am 22.01.2013 19:03, schrieb Mgavi Brathwaite:
>>>> What upstream and downstream elements are you interested in?
>>> 
>>> 
>>> I've got a huge pile of short RNA reads.
>>> Part of the question now is whether those RNA fragments originate from
>>> siRNA events,
>>> or may represent miRNAs / parts of pre-miRNAs.
>>> 
>>> So I did an online  blast search against database nt.
>>> The resulting report quite often just gives subject information like this:
>>> 
>>> -----
>>>> gb|CP002686.1| Arabidopsis thaliana chromosome 3, complete sequence
>>> Length=23459830
>>> -----
>>> 
>>> Now I would like to get the hit's neighbouring regions  for further
>>> analysis.
>>> Preferably I would like to do that  in an automized way, but the only
>>> possible action with this kind of subject gi | description would be to
>>> fetch the entire chromosomal  sequence I guess ?
>>> 
>>> However,
>>> right below the line above, the report states more precisely:
>>> 
>>> ------
>>> Features flanking this part of subject sequence:
>>> 8872 bp at 5' side: cytochrome P450 90B1
>>> 402 bp at 3' side: U1 small nuclear ribonucleoprotein-70K
>>> ------
>>> 
>>> Still I would like to have the possibility to automatically fetch the
>>> subject's sequence(s),
>>> as of now I think  parsing the report with SearchIO won't let me aquire
>>> that information, because SearchIO does not recognize report sections
>>> like those.
>>> 
>>> I hope I did not miss any of SearchIOs capabilities, but I could not
>>> find any method covering my wish?!
>>> 
>>> Right now maybe the only way to get the information I want is to
>>> construct my own parser and write it out into a separate file, which in
>>> turn again  I could read into a hash before processing the Blast-Report
>>> with SearchIO to combine both data for further automized work.
>>> 
>>> I am aware though that even successfully getting the flanking features
>>> would leave me with the more or less wide  intergenic gap my hsp is
>>> located in.
>>> 
>>> However I'm in need of a way to get the flanking features including
>>> their annotation and the region spanning between them.
>>> But I hope I do not have to get complete sequences to accomplish that,
>>> as this would be kind of an overkill.
>>> 
>>> with kind regards
>>> Jochen
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>> 
>> 
>> 
>> 
>> ------------------------------
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> End of Bioperl-l Digest, Vol 117, Issue 13
>> ******************************************
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From thiago.venancio at gmail.com  Thu Jan 31 17:10:39 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:10:39 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
Message-ID: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>

Hi all,

I am trying to install bioperl-ext and the compilation gives me the error:

/usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
can not be used when making a shared object; recompile with -fPIC
libs/libsw.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1
make[1]: Leaving directory 
`/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align'
make: *** [subdirs] Error 2

However, the Makefile says that -fPIC is already being used, which is 
puzzling me.

Any clues ?

Thanks.
Thiago





From thiago.venancio at gmail.com  Thu Jan 31 17:25:12 2013
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Thu, 31 Jan 2013 09:25:12 -0800 (PST)
Subject: [Bioperl-l] bioperl-ext
In-Reply-To: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
References: <5523d5a2-b103-4cf3-8c84-bd33ef675a6d@googlegroups.com>
Message-ID: <e22d2881-ddd3-42af-9a69-f03503b8fb5a@googlegroups.com>

Solved using the solution posted by jmf here :
https://groups.google.com/forum/?fromgroups=#!searchin/bioperl-l/bioperl-ext/bioperl-l/FgJo_g8UQE8/FB1DEjJkTooJ

Which I found after posting.

T


On Thursday, January 31, 2013 3:10:39 PM UTC-2, Thiago Venancio wrote:
>
> Hi all, 
>
> I am trying to install bioperl-ext and the compilation gives me the error: 
>
> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against `.rodata' 
> can not be used when making a shared object; recompile with -fPIC 
> libs/libsw.a: could not read symbols: Bad value 
> collect2: ld returned 1 exit status 
> make[1]: *** [blib/arch/auto/Bio/Ext/Align/Align.so] Error 1 
> make[1]: Leaving directory 
> `/home/thiago/temp/bioperl-ext-master/Bio/Ext/Align' 
> make: *** [subdirs] Error 2 
>
> However, the Makefile says that -fPIC is already being used, which is 
> puzzling me. 
>
> Any clues ? 
>
> Thanks. 
> Thiago 
>
>
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Bioperl-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>