From chiragmatkarbioinfo at gmail.com  Mon Nov  1 02:58:55 2010
From: chiragmatkarbioinfo at gmail.com (chirag matkar)
Date: Mon, 1 Nov 2010 13:58:55 +0700
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
Message-ID: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar

From Russell.Smithies at agresearch.co.nz  Tue Nov  2 22:11:36 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Nov 2010 15:11:36 +1300
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313A9B7D7C@exchsth.agresearch.co.nz>

Seems a bit like overkill, what's wrong with wget?

wget -i <list_of_urls.txt>

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
Sent: Monday, 1 November 2010 7:59 p.m.
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to download PDB files using Bioperl script

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar
_______________________________________________
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 miguel.pignatelli at uv.es  Wed Nov  3 05:42:49 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 10:42:49 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4C8606FA.3000509@fmi.ch>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch>
Message-ID: <4CD12E99.7080701@uv.es>

Hi all,

I have written a couple of modules that overlap certain functionality 
with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
certain constraints in the environment I had to run it (GRID) made 
impossible to use a bioperl based solution.


The main features of these modules are:

+ No dependencies of non-standard Perl modules
+ NCBI and RDP based taxonomies supported
+ Very fast and low memory footprint -- orders of magnitude faster than 
Bioperl modules (for the tasks they are designed for --).

Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in 
completeness or integration with other tools (e.g. rest of bioperl suit) 
but they are handy for mapping very large datasets (for example blast 
results) with the NCBI or RDP Taxonomy.

The modules are:

Taxonomy::Base -- Finds ancestors, ranks, converts between
                   names, ranks and IDs, etc...

Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file

Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
                   (nodes.dmp and names.dmp)
                   (Similar to Bio::DB::Taxonomy::flatfile)

Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
                             NCBI GIs to Taxids.
                             Uses a binary lookup table.

These modules are being used by several groups now -- mainly working 
with large metagenomics datasets -- and I am considering uploading them 
to CPAN, but I am not clear on where these modules should be placed there.

How do you think I should name these modules? (e.g. where these modules 
should live in CPAN?) Their natural place could be under 
Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
convenient) without being part of Bioperl? Any other suggestions?

Thank you very much in advance,

M;

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

From gabbyteku at gmail.com  Wed Nov  3 07:53:42 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Wed, 3 Nov 2010 13:53:42 +0200
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
Message-ID: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>

I can't get my esearch to work. It's as follows:

my $eut_obj = Bio::DB::EUtilities->new(   -eutil      => 'esearch',
                                                  -email      => '
myemail at gmail.com',
                                                  -term       =>
'$genename[SYMB] AND homo_sapiens[ORGN]',
                                                  -db         => 'geo',
                                                  -usehistory => 'y'
                                              );

When I run this using a gene symbol, it works fine.
But then when I run it as it is with a gene's symbol changed to
$genename(stores the gene's symbol/name), it fails.
How can this be fixed?

Thanks

From miguel.pignatelli at uv.es  Wed Nov  3 09:51:18 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 14:51:18 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>
Message-ID: <4CD168D6.8030100@uv.es>

Hi all,

I have seen in the Nextgen section of the bioperl wiki 
(http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in 
the wish list. I have some code written for parsing SFF files that I can 
refactor and contribute with it.

Does anyone already took this?

Best regards,

M;


From biopython at maubp.freeserve.co.uk  Wed Nov  3 10:28:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 3 Nov 2010 14:28:56 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <AANLkTikAAz5FP3kiN0U6dtnvpgWAHtLu5DoEBcm_yzVD@mail.gmail.com>

On 2010/11/3 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Hi all,
>
> I have seen in the Nextgen section of the bioperl wiki
> (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the
> wish list. I have some code written for parsing SFF files that I can
> refactor and contribute with it.
>
> Does anyone already took this?
>
> Best regards,
>
> M;

Hi,

This sounds like a good thing for BioPerl.

If you hook this up into Bio::SeqIO then for consistency with
Biopython for the format name note we use "sff" as the full
reads, and "sff-trim" for the reads with the quality trimming
applied. If BioPerl has some built in way to hold a trimmed
sequence (with the head/tail still accessible) then this may
not be a good solution.

Peter

From scott at scottcain.net  Wed Nov  3 10:59:12 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 10:59:12 -0400
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
In-Reply-To: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
References: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
Message-ID: <AANLkTi=VgyrfZPPt+--pVJxfgh9QRsh_OLpsBq79F8z1@mail.gmail.com>

Hi Gabriel,

It looks to me like you've got a few things going wrong.  First, you
are using single quotes for the right hand side of the -term value.
In perl, single quotes are non-interpolating, which means variables
won't be substituted in.  However, if you switch to double quotes,
you'll still have a problem, because this:

  $genename[SYMB]

looks like you are trying to access an element of an array called
genename with a constant called SYMB, which of course you aren't, so
the perl interpreter will die with that.  You can rewrite that section
like this:

  $genename . '[SYMB] AND homo_sapiens[ORGN]'

so that the variable interpolation is moved out of the single quotes.

Scott




On Wed, Nov 3, 2010 at 7:53 AM, gabriel teku <gabbyteku at gmail.com> wrote:
> I can't get my esearch to work. It's as follows:
>
> my $eut_obj = Bio::DB::EUtilities->new( ? -eutil ? ? ?=> 'esearch',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-email ? ? ?=> '
> myemail at gmail.com',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-term ? ? ? =>
> '$genename[SYMB] AND homo_sapiens[ORGN]',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-db ? ? ? ? => 'geo',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-usehistory => 'y'
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> When I run this using a gene symbol, it works fine.
> But then when I run it as it is with a gene's symbol changed to
> $genename(stores the gene's symbol/name), it fails.
> How can this be fixed?
>
> Thanks
> _______________________________________________
> 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 cseligman at earthlink.net  Wed Nov  3 12:07:05 2010
From: cseligman at earthlink.net (Chet Seligman)
Date: Wed, 3 Nov 2010 09:07:05 -0700
Subject: [Bioperl-l] BioPerl installation was incomplete
Message-ID: <001001cb7b71$294f12c0$7bed3840$@earthlink.net>

My perl is ActiveState 5.10.1

I installed with PPM using the following repositories:

BioPerl-Regular Releases

BioPerl-Release Candidates

Kobes

Bribes

Trouchelle

 

I got the following warnings:

Can't find any package that provides DB_File:: for Bundle-BioPerl-Core

WARNING: Can't find any package that provides IPC::Run for GraphViz

WARNING: Can't find any package that provides Apache:: for SOAP-Lite

 

I do have DB_File installed but do not have:

IPC::Run or,

Apache:: for SOAP-Lite

 

I did try to install SOAP-Lite according to the instructions in the Wiki but
no luck.

In PPM-edit repositories I saw that Kobes, Bribes & Trouchelle all showed
"0"

So how do I get SOAP-Lite, Apache and IPC::Run?

 

Chet Seligman


From cjfields at illinois.edu  Wed Nov  3 13:18:38 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 12:18:38 -0500
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>

Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  

I suggest, though, for long-term maintenance you could be added as a collaborator.  

chris

On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
> 
> Does anyone already took this?
> 
> Best regards,
> 
> M;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From hanbobio at 126.com  Tue Nov  2 01:29:50 2010
From: hanbobio at 126.com (hanbobio)
Date: Tue, 2 Nov 2010 13:29:50 +0800 (CST)
Subject: [Bioperl-l] bioperl modules
Message-ID: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>

Hi, all.
 I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:

liaoy at linux:~/nd-hn> perl nd-hn.pl

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.

BEGIN failed--compilation aborted at nd-hn.pl line 26.
 The detail of this script in two ways: the attached file and the following script.
Would you be kindly to test my script and give me some modification or suggestion?
 I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
Thank you very much for your advice.
 
Best regards
Yusheng Liao 2010-11-02
 
# retrive sequence from Genbank
use strict;
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;
open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
my $query = Bio::DB::Query::GenBank->new
    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
   -db      => 'nucleotide');
my $seqio = $gb->get_Stream_by_query($query);
my $i=0;
while( defined (my $seq = $seqio->next_seq )) {
$seqout->write_seq($seq);
$i++;
print ".";
}
print "$i \n";
# run multi sequence alignment
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::SimpleAlign;
use Bio::AlignIO::clustalw;
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $ktuple = 3;
$factory->ktuple($ktuple); 
my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
my $aln = $factory->align($inputfilename);
my $alignout->write_aln(my $aln);

my $line;
my @array=('A','C','G','T','-');
my @arrayX=('a','c','g','t','-');
my @arrayA;
my @arrayB;
my ($i,$j,$k);
my (@a, at b);
my %hash;
open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
while($line=<FILE>){
      chomp;
      if($line=~ /CLUSTAL/){
            next;
      }elsif($line=~ /^[A-Za-z0-9]/){
            @a=split /\s+/,$line;
            if(defined($hash{$a[0]})){
                  push @{$hash{$a[0]}}, $line;
            }else{
                  ${$hash{$a[0]}}[0]=$line;
                  push @b,$a[0];
            }
       }
}
for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
      for(my $l=0;$l<=$#b;$l++){
            print OUT ${$hash{$b[$l]}}[$k];
            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
            @arrayA=split //,$seq;
            for($i=0;$i<=$#arrayA;$i++){
                  if($arrayA[$i] =~ /A/i){
                        $arrayB[0][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /C/i){
                        $arrayB[1][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /G/i){
                        $arrayB[2][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /T/i){
                        $arrayB[3][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\./i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\-/i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
            }
       }
       for($j=0;$j<=$#arrayA;$j++){
              my $large=0;my $pos=0;
              for($i=0;$i<=4;$i++){
                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
                    if($arrayB[$i][$j]>$large){
                          $large=$arrayB[$i][$j];
                          $pos=$i;
                    }
              }
                    if($large>0.5){
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]=$array[$pos];
                    }else{
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]='N';
                    }
       }
       for($i=0;$i<=5;$i++){
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                    if($arrayB[$i][$j]>0){
                           printf OUT "%.2f\t",$arrayB[$i][$j];
                    }else{
                           print OUT "0\t";
                    }
              }
              print OUT "\n";
        }
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUT "$arrayB[6][$j]\t";
              }
              print OUT "\n";
              for($j=0;$j<=15;$j++){
                    print OUTA " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUTA "$arrayB[6][$j]";
              }
              print OUTA "\n";
        @arrayB=undef;
}
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From daniel.standage at gmail.com  Wed Nov  3 14:42:07 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 13:42:07 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
Message-ID: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>

Hi

I've got a simple script that is filtering some GFF3 data. The
Bio::Tools::GFF class has methods for reading and writing features and
reading regions (segments), but I cannot find a method for writing regions.
It's not hard to just print out the sequence-region line from the
LocatableSeq object, but then these lines are printed out before the
gff-version line (which is a no-no). Any suggestions about how to handle
this?

Thanks.

-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University

From scott at scottcain.net  Wed Nov  3 16:09:45 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:09:45 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
Message-ID: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>

Hi Daniel,

Why do you need the sequence-region line?  It is mostly just
informational.  If you want to define the reference sequence for the
features in the GFF file, I would suggest printing out a full GFF line
for the reference sequence instead anyway.  That way, it can have all
the information that a GFF line can encode, like a source and type, as
well as information in the ninth column.

That said, Bio::Tools::GFF probably does lack that method.  The code
in it is probably a little outdated.

Scott


On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> Hi
>
> I've got a simple script that is filtering some GFF3 data. The
> Bio::Tools::GFF class has methods for reading and writing features and
> reading regions (segments), but I cannot find a method for writing regions.
> It's not hard to just print out the sequence-region line from the
> LocatableSeq object, but then these lines are printed out before the
> gff-version line (which is a no-no). Any suggestions about how to handle
> this?
>
> Thanks.
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> 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 scott at scottcain.net  Wed Nov  3 16:19:07 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:19:07 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
Message-ID: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>

Ah, I see.  Well, you should complain to the authors that
sequence-region isn't a required directive (though if you made that
complaint to me, I'd say "well, it is for this tool" :-)

Of course, you could also use Bio::Graphics or GBrowse to do the
drawing, then I could do more to help. :-)

Scott


On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I'm using a tool called AnnotationSketch (part of the GenomeTools package)
> to create graphics from my GFF3 files. It complains when sequence-region
> lines are not included, even when the reference is printed as a feature.
> That's what got me interested in the problem in the first place.
>
> Thanks for the info, I'll figure something out.
>
> Daniel
>
> On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> Why do you need the sequence-region line? ?It is mostly just
>> informational. ?If you want to define the reference sequence for the
>> features in the GFF file, I would suggest printing out a full GFF line
>> for the reference sequence instead anyway. ?That way, it can have all
>> the information that a GFF line can encode, like a source and type, as
>> well as information in the ninth column.
>>
>> That said, Bio::Tools::GFF probably does lack that method. ?The code
>> in it is probably a little outdated.
>>
>> Scott
>>
>>
>> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > Hi
>> >
>> > I've got a simple script that is filtering some GFF3 data. The
>> > Bio::Tools::GFF class has methods for reading and writing features and
>> > reading regions (segments), but I cannot find a method for writing
>> > regions.
>> > It's not hard to just print out the sequence-region line from the
>> > LocatableSeq object, but then these lines are printed out before the
>> > gff-version line (which is a no-no). Any suggestions about how to handle
>> > this?
>> >
>> > Thanks.
>> >
>> > --
>> > Daniel S. Standage
>> > Graduate Research Assistant
>> > Bioinformatics and Computational Biology Program
>> > Iowa State University
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



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


From daniel.standage at gmail.com  Wed Nov  3 16:14:02 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:14:02 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
Message-ID: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>

I'm using a tool called AnnotationSketch (part of the GenomeTools package)
to create graphics from my GFF3 files. It complains when sequence-region
lines are not included, even when the reference is printed as a feature.
That's what got me interested in the problem in the first place.

Thanks for the info, I'll figure something out.

Daniel

On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Daniel,
>
> Why do you need the sequence-region line?  It is mostly just
> informational.  If you want to define the reference sequence for the
> features in the GFF file, I would suggest printing out a full GFF line
> for the reference sequence instead anyway.  That way, it can have all
> the information that a GFF line can encode, like a source and type, as
> well as information in the ninth column.
>
> That said, Bio::Tools::GFF probably does lack that method.  The code
> in it is probably a little outdated.
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > Hi
> >
> > I've got a simple script that is filtering some GFF3 data. The
> > Bio::Tools::GFF class has methods for reading and writing features and
> > reading regions (segments), but I cannot find a method for writing
> regions.
> > It's not hard to just print out the sequence-region line from the
> > LocatableSeq object, but then these lines are printed out before the
> > gff-version line (which is a no-no). Any suggestions about how to handle
> > this?
> >
> > Thanks.
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > 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
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University

From daniel.standage at gmail.com  Wed Nov  3 16:29:29 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:29:29 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
	<AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
Message-ID: <AANLkTikv-N-45cgapmZ_yHqHLFtNroBm9KU+ehXn=qad@mail.gmail.com>

Yeah, I guess it's not a show stopper, since it still generates the graphics
fine. The output that clutters the terminal is still annoying, but I can
live with that. Thanks!

Daniel

On Wed, Nov 3, 2010 at 3:19 PM, Scott Cain <scott at scottcain.net> wrote:

> Ah, I see.  Well, you should complain to the authors that
> sequence-region isn't a required directive (though if you made that
> complaint to me, I'd say "well, it is for this tool" :-)
>
> Of course, you could also use Bio::Graphics or GBrowse to do the
> drawing, then I could do more to help. :-)
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > I'm using a tool called AnnotationSketch (part of the GenomeTools
> package)
> > to create graphics from my GFF3 files. It complains when sequence-region
> > lines are not included, even when the reference is printed as a feature.
> > That's what got me interested in the problem in the first place.
> >
> > Thanks for the info, I'll figure something out.
> >
> > Daniel
> >
> > On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Daniel,
> >>
> >> Why do you need the sequence-region line?  It is mostly just
> >> informational.  If you want to define the reference sequence for the
> >> features in the GFF file, I would suggest printing out a full GFF line
> >> for the reference sequence instead anyway.  That way, it can have all
> >> the information that a GFF line can encode, like a source and type, as
> >> well as information in the ninth column.
> >>
> >> That said, Bio::Tools::GFF probably does lack that method.  The code
> >> in it is probably a little outdated.
> >>
> >> Scott
> >>
> >>
> >> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> >> <daniel.standage at gmail.com> wrote:
> >> > Hi
> >> >
> >> > I've got a simple script that is filtering some GFF3 data. The
> >> > Bio::Tools::GFF class has methods for reading and writing features and
> >> > reading regions (segments), but I cannot find a method for writing
> >> > regions.
> >> > It's not hard to just print out the sequence-region line from the
> >> > LocatableSeq object, but then these lines are printed out before the
> >> > gff-version line (which is a no-no). Any suggestions about how to
> handle
> >> > this?
> >> >
> >> > Thanks.
> >> >
> >> > --
> >> > Daniel S. Standage
> >> > Graduate Research Assistant
> >> > Bioinformatics and Computational Biology Program
> >> > Iowa State University
> >> > _______________________________________________
> >> > 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
> >
> >
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University

From cjfields at illinois.edu  Wed Nov  3 17:27:28 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 16:27:28 -0500
Subject: [Bioperl-l] bioperl modules
In-Reply-To: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
References: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
Message-ID: <2A3F6A7D-CF80-4C6D-8BE2-EEDA873BCC3D@illinois.edu>

You need to install bioperl-run to get Bio::Tools::Run::Alignment::Clustalw.

chris

On Nov 2, 2010, at 12:29 AM, hanbobio wrote:

> Hi, all.
> I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:
> 
> liaoy at linux:~/nd-hn> perl nd-hn.pl
> 
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.
> 
> BEGIN failed--compilation aborted at nd-hn.pl line 26.
> The detail of this script in two ways: the attached file and the following script.
> Would you be kindly to test my script and give me some modification or suggestion?
> I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
> Thank you very much for your advice.
> 
> Best regards
> Yusheng Liao 2010-11-02
> 
> # retrive sequence from Genbank
> use strict;
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> my $gb = new Bio::DB::GenBank;
> open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
> my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
> my $query = Bio::DB::Query::GenBank->new
>    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
>   -db      => 'nucleotide');
> my $seqio = $gb->get_Stream_by_query($query);
> my $i=0;
> while( defined (my $seq = $seqio->next_seq )) {
> $seqout->write_seq($seq);
> $i++;
> print ".";
> }
> print "$i \n";
> # run multi sequence alignment
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::SimpleAlign;
> use Bio::AlignIO::clustalw;
> my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
> my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> my $ktuple = 3;
> $factory->ktuple($ktuple); 
> my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
> my $aln = $factory->align($inputfilename);
> my $alignout->write_aln(my $aln);
> 
> my $line;
> my @array=('A','C','G','T','-');
> my @arrayX=('a','c','g','t','-');
> my @arrayA;
> my @arrayB;
> my ($i,$j,$k);
> my (@a, at b);
> my %hash;
> open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
> open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
> open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
> while($line=<FILE>){
>      chomp;
>      if($line=~ /CLUSTAL/){
>            next;
>      }elsif($line=~ /^[A-Za-z0-9]/){
>            @a=split /\s+/,$line;
>            if(defined($hash{$a[0]})){
>                  push @{$hash{$a[0]}}, $line;
>            }else{
>                  ${$hash{$a[0]}}[0]=$line;
>                  push @b,$a[0];
>            }
>       }
> }
> for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
>      for(my $l=0;$l<=$#b;$l++){
>            print OUT ${$hash{$b[$l]}}[$k];
>            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
>            @arrayA=split //,$seq;
>            for($i=0;$i<=$#arrayA;$i++){
>                  if($arrayA[$i] =~ /A/i){
>                        $arrayB[0][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /C/i){
>                        $arrayB[1][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /G/i){
>                        $arrayB[2][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /T/i){
>                        $arrayB[3][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\./i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\-/i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>            }
>       }
>       for($j=0;$j<=$#arrayA;$j++){
>              my $large=0;my $pos=0;
>              for($i=0;$i<=4;$i++){
>                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
>                    if($arrayB[$i][$j]>$large){
>                          $large=$arrayB[$i][$j];
>                          $pos=$i;
>                    }
>              }
>                    if($large>0.5){
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]=$array[$pos];
>                    }else{
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]='N';
>                    }
>       }
>       for($i=0;$i<=5;$i++){
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                    if($arrayB[$i][$j]>0){
>                           printf OUT "%.2f\t",$arrayB[$i][$j];
>                    }else{
>                           print OUT "0\t";
>                    }
>              }
>              print OUT "\n";
>        }
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUT "$arrayB[6][$j]\t";
>              }
>              print OUT "\n";
>              for($j=0;$j<=15;$j++){
>                    print OUTA " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUTA "$arrayB[6][$j]";
>              }
>              print OUTA "\n";
>        @arrayB=undef;
> }
> <Moduletest.pl.pl>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Wed Nov  3 22:34:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 21:34:30 -0500
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
Message-ID: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>

Miguel,

(Caveat: You should also ask this on the perl module-authors list, just in case: http://lists.perl.org/list/module-authors.html)

Not sure how the other devs feel, but I personally don't think the Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, for example).  It's a fairly generic top-level name.  The only worry I have is if these are too similar to current BioPerl modules; Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN related to BioPerl modules.   

Saying that, tagging them as *::Lite might be fine, as long as the documentation indicated these are not related to BioPerl.  Anyone else want to chime in?  Maybe releasing them as a top-level Taxonomy?  

chris

On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have written a couple of modules that overlap certain functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because certain constraints in the environment I had to run it (GRID) made impossible to use a bioperl based solution.
> 
> 
> The main features of these modules are:
> 
> + No dependencies of non-standard Perl modules
> + NCBI and RDP based taxonomies supported
> + Very fast and low memory footprint -- orders of magnitude faster than Bioperl modules (for the tasks they are designed for --).
> 
> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in completeness or integration with other tools (e.g. rest of bioperl suit) but they are handy for mapping very large datasets (for example blast results) with the NCBI or RDP Taxonomy.
> 
> The modules are:
> 
> Taxonomy::Base -- Finds ancestors, ranks, converts between
>                  names, ranks and IDs, etc...
> 
> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
> 
> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>                  (nodes.dmp and names.dmp)
>                  (Similar to Bio::DB::Taxonomy::flatfile)
> 
> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>                            NCBI GIs to Taxids.
>                            Uses a binary lookup table.
> 
> These modules are being used by several groups now -- mainly working with large metagenomics datasets -- and I am considering uploading them to CPAN, but I am not clear on where these modules should be placed there.
> 
> How do you think I should name these modules? (e.g. where these modules should live in CPAN?) Their natural place could be under Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and convenient) without being part of Bioperl? Any other suggestions?
> 
> Thank you very much in advance,
> 
> M;
> 
> ----------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From David.Messina at sbc.su.se  Thu Nov  4 04:54:33 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 4 Nov 2010 09:54:33 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <4F9F218F-22EC-46B8-8BAB-82BD0956FB76@sbc.su.se>

I agree with Chris. You're welcome to put your code in the Bio:: namespace ? it's not reserved for BioPerl ? but since there are already modules with Taxonomy in their names, it would be likely to cause confusion.

So, if your modules are renamed to be sufficiently distinguishable from existing Taxonomy modules, putting them under Bio:: should be no problem.

Otherwise, I would go whatever the modules list folks recommend.

Dave


From miguel.pignatelli at uv.es  Thu Nov  4 07:13:20 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:13:20 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>
	<4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
Message-ID: <4CD29550.6030005@uv.es>

Thanks Chris,

I will get in touch again when I am able to hook a working module (I 
will check Biopython's Bio.Seq.SffIO)

M;


Chris Fields wrote:
> Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  
> 
> I suggest, though, for long-term maintenance you could be added as a collaborator.  
> 
> chris
> 
> On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:
> 
>> Hi all,
>>
>> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
>>
>> Does anyone already took this?
>>
>> Best regards,
>>
>> M;
>>
>> _______________________________________________
>> 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 biopython at maubp.freeserve.co.uk  Thu Nov  4 07:40:13 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 4 Nov 2010 11:40:13 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD29550.6030005@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
	<4CD29550.6030005@uv.es>
Message-ID: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>

2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Thanks Chris,
>
> I will get in touch again when I am able to hook a working module (I will
> check Biopython's Bio.Seq.SffIO)
>
> M;

Hi Miguel,

In case it helps, the Biopython SFF code is here - this includes embedded
documentation with test examples:

http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

We also have some test SFF files here (see the README file for details):

http://github.com/biopython/biopython/tree/master/Tests/Roche/

Peter

From pignatelli_mig at gva.es  Thu Nov  4 07:49:07 2010
From: pignatelli_mig at gva.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:49:07 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>	<4CD168D6.8030100@uv.es>	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>	<4CD29550.6030005@uv.es>
	<AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
Message-ID: <4CD29DB3.9010805@gva.es>

Thanks Peter, I have already took a look at the module. It will 
certainly help a lot. I also have some real SFF files from different 
collaborations that I can use for testing.

Let's roll up the sleeves...

M;


Peter wrote:
> 2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
>> Thanks Chris,
>>
>> I will get in touch again when I am able to hook a working module (I will
>> check Biopython's Bio.Seq.SffIO)
>>
>> M;
> 
> Hi Miguel,
> 
> In case it helps, the Biopython SFF code is here - this includes embedded
> documentation with test examples:
> 
> http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
> 
> We also have some test SFF files here (see the README file for details):
> 
> http://github.com/biopython/biopython/tree/master/Tests/Roche/
> 
> Peter

From hlapp at drycafe.net  Thu Nov  4 12:12:04 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 4 Nov 2010 12:12:04 -0400
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>

I agree - Bio:: isn't exclusive to BioPerl, but in choosing module  
name and namespace, as well as in documentation, try to minimize  
potential confusion for users.

	-hilmar
On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:

> Miguel,
>
> (Caveat: You should also ask this on the perl module-authors list,  
> just in case: http://lists.perl.org/list/module-authors.html)
>
> Not sure how the other devs feel, but I personally don't think the  
> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo,  
> for example).  It's a fairly generic top-level name.  The only worry  
> I have is if these are too similar to current BioPerl modules;  
> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN  
> related to BioPerl modules.
>
> Saying that, tagging them as *::Lite might be fine, as long as the  
> documentation indicated these are not related to BioPerl.  Anyone  
> else want to chime in?  Maybe releasing them as a top-level Taxonomy?
>
> chris
>
> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>
>> Hi all,
>>
>> I have written a couple of modules that overlap certain  
>> functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write  
>> them because certain constraints in the environment I had to run it  
>> (GRID) made impossible to use a bioperl based solution.
>>
>>
>> The main features of these modules are:
>>
>> + No dependencies of non-standard Perl modules
>> + NCBI and RDP based taxonomies supported
>> + Very fast and low memory footprint -- orders of magnitude faster  
>> than Bioperl modules (for the tasks they are designed for --).
>>
>> Of course, they do not compete with Bio::DB::Taxonomy and  
>> Bio::Taxon in completeness or integration with other tools (e.g.  
>> rest of bioperl suit) but they are handy for mapping very large  
>> datasets (for example blast results) with the NCBI or RDP Taxonomy.
>>
>> The modules are:
>>
>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>                 names, ranks and IDs, etc...
>>
>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>
>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>                 (nodes.dmp and names.dmp)
>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>
>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>                           NCBI GIs to Taxids.
>>                           Uses a binary lookup table.
>>
>> These modules are being used by several groups now -- mainly  
>> working with large metagenomics datasets -- and I am considering  
>> uploading them to CPAN, but I am not clear on where these modules  
>> should be placed there.
>>
>> How do you think I should name these modules? (e.g. where these  
>> modules should live in CPAN?) Their natural place could be under  
>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite /  
>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and  
>> convenient) without being part of Bioperl? Any other suggestions?
>>
>> Thank you very much in advance,
>>
>> M;
>>
>> ----------------------------------------------------
>> _______________________________________________
>> 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

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================





From kellert at ohsu.edu  Thu Nov  4 20:45:25 2010
From: kellert at ohsu.edu (Tom Keller)
Date: Thu, 4 Nov 2010 17:45:25 -0700
Subject: [Bioperl-l] parsing PubMed retrievals
Message-ID: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>

Greetings,
I'm getting the following error from the bioplerl 1.6.1 example

$ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.


Any suggestions for getting this to work?

thanks,


Tom
MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
503-494-2442
kellert at ohsu.edu<mailto:kellert at ohsu.edu>
Office: 6588 RJH (CROET/BasicScience)







From cjfields at illinois.edu  Fri Nov  5 00:28:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 4 Nov 2010 23:28:01 -0500
Subject: [Bioperl-l] parsing PubMed retrievals
In-Reply-To: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <EA90A6B2-7D87-4CC0-B4FB-D8A00FD5C77D@illinois.edu>

It seems that in some cases a webenv/querykey are not returned.  I have committed a fix to github for this which seems to fix the problem from our end.

https://github.com/bioperl/bioperl-live/commit/7c64e8410d291dbd7097b2cd8fc948d95063d153

chris

On Nov 4, 2010, at 7:45 PM, Tom Keller wrote:

> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> 
> Tom
> MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert at ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From miguel.pignatelli at uv.es  Fri Nov  5 05:31:46 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Fri, 05 Nov 2010 10:31:46 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
Message-ID: <4CD3CF02.9010608@uv.es>

Hi all,

In the perl module-authors list I have been suggested two nice alternatives:

Bio::Lite::Taxonomy::*
BioX::Taxonomy::*

If the devs don't have any objection/preference I will follow the first one.

Regards,

M;


Hilmar Lapp wrote:
> I agree - Bio:: isn't exclusive to BioPerl, but in choosing module name 
> and namespace, as well as in documentation, try to minimize potential 
> confusion for users.
> 
>     -hilmar
> On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:
> 
>> Miguel,
>>
>> (Caveat: You should also ask this on the perl module-authors list, 
>> just in case: http://lists.perl.org/list/module-authors.html)
>>
>> Not sure how the other devs feel, but I personally don't think the 
>> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, 
>> for example).  It's a fairly generic top-level name.  The only worry I 
>> have is if these are too similar to current BioPerl modules; 
>> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN 
>> related to BioPerl modules.
>>
>> Saying that, tagging them as *::Lite might be fine, as long as the 
>> documentation indicated these are not related to BioPerl.  Anyone else 
>> want to chime in?  Maybe releasing them as a top-level Taxonomy?
>>
>> chris
>>
>> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>>
>>> Hi all,
>>>
>>> I have written a couple of modules that overlap certain functionality 
>>> with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
>>> certain constraints in the environment I had to run it (GRID) made 
>>> impossible to use a bioperl based solution.
>>>
>>>
>>> The main features of these modules are:
>>>
>>> + No dependencies of non-standard Perl modules
>>> + NCBI and RDP based taxonomies supported
>>> + Very fast and low memory footprint -- orders of magnitude faster 
>>> than Bioperl modules (for the tasks they are designed for --).
>>>
>>> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon 
>>> in completeness or integration with other tools (e.g. rest of bioperl 
>>> suit) but they are handy for mapping very large datasets (for example 
>>> blast results) with the NCBI or RDP Taxonomy.
>>>
>>> The modules are:
>>>
>>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>>                 names, ranks and IDs, etc...
>>>
>>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>>
>>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>>                 (nodes.dmp and names.dmp)
>>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>>
>>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>>                           NCBI GIs to Taxids.
>>>                           Uses a binary lookup table.
>>>
>>> These modules are being used by several groups now -- mainly working 
>>> with large metagenomics datasets -- and I am considering uploading 
>>> them to CPAN, but I am not clear on where these modules should be 
>>> placed there.
>>>
>>> How do you think I should name these modules? (e.g. where these 
>>> modules should live in CPAN?) Their natural place could be under 
>>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
>>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
>>> convenient) without being part of Bioperl? Any other suggestions?
>>>
>>> Thank you very much in advance,
>>>
>>> M;
>>>
>>> ----------------------------------------------------
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

From David.Messina at sbc.su.se  Fri Nov  5 06:36:38 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 11:36:38 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD3CF02.9010608@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
	<4CD3CF02.9010608@uv.es>
Message-ID: <5E0858F2-3957-46E1-BCD7-0F75FF44DE7D@sbc.su.se>

> Bio::Lite::Taxonomy::*
> BioX::Taxonomy::*

Either works for me.

Thanks for asking, Miguel, and I'm looking forward to checking them out!

Dave

From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 07:33:44 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 12:33:44 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
Message-ID: <4CD3EB98.3050508@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi folks,

https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser
contains my attempt to get a hmmer parser that is able to detect which
hmmer version output it's given and which parser to call in turn.

I chose to sneak in a Bio::SearchIO::hmmer class into the object
hierarchy that the hmmer2 parser (renamed to Bio::SearchIO::hmmer2) and
the hmmer3 parser subclass from.

I'm not sure if this is the best way to go, though, and I'd like to get
some feedback on the implementation.
The last six patches on
https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser are
the full changeset, the core of the change is in
https://github.com/kblin/bioperl-live/commit/2d4816f1d67880c69948b2ce529fdeb52e0d843f

Thanks in advance for your time,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From David.Messina at sbc.su.se  Fri Nov  5 08:35:32 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 13:35:32 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
Message-ID: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>

I may have missed some recent off-list discussion, but I thought we explicitly talked about *not* merging these since it will complicate future maintenance and Hmmer2 will be obsolete in the near future.


Dave



From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 08:56:23 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 13:56:23 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
Message-ID: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 13:35, Dave Messina wrote:
> I may have missed some recent off-list discussion, but I thought we
> explicitly talked about *not* merging these since it will complicate
> future maintenance and Hmmer2 will be obsolete in the near future.

Yes, that's what I thought until about last week. Then I was bitten by
the fact that Hmmer3 can't do global alignments, so you can't reliably
use Hmmer3 to extract protein domains using the domain's motif. As this
seems to be a common use case, I think we'll end up supporting hmmer2
for quite a while now.

There's currently no plans by the Hmmer authors to add globlal and
glocal (whole profile alignments against parts of the sequence)
alignments to hmmer3. They suggested to keep using hmmer2 for now.

For this reason I decided to try and merge the two parsers to a point
where users don't have to care which version of hmmer their file is.

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 10:17:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 09:17:03 -0500
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
Message-ID: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>

On Nov 5, 2010, at 7:56 AM, Kai Blin wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On 2010-11-05 13:35, Dave Messina wrote:
>> I may have missed some recent off-list discussion, but I thought we
>> explicitly talked about *not* merging these since it will complicate
>> future maintenance and Hmmer2 will be obsolete in the near future.
> 
> Yes, that's what I thought until about last week. Then I was bitten by
> the fact that Hmmer3 can't do global alignments, so you can't reliably
> use Hmmer3 to extract protein domains using the domain's motif. As this
> seems to be a common use case, I think we'll end up supporting hmmer2
> for quite a while now.
> 
> There's currently no plans by the Hmmer authors to add globlal and
> glocal (whole profile alignments against parts of the sequence)
> alignments to hmmer3. They suggested to keep using hmmer2 for now.
> 
> For this reason I decided to try and merge the two parsers to a point
> where users don't have to care which version of hmmer their file is.
> 
> Cheers,
> Kai

Makes sense to me.  We're tackling some Bio::Tree revisions next week, my guess is we can also get this added in.  I'm really keen on getting 1.6.2 out sometime soon, before things get really crazy for me this spring.

Key things to test: can specify the exact hmmer2/3 parser directly?  

   my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

Can one explicitly specify the hmmer parser variant?

   my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file => 'foo')

This will more than likely pop up.  I did something with Bio::SeqIO::fastq to allow specifying sanger/illumina/solexa variants, this would be similar in respect.

chris

From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 10:53:24 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 15:53:24 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
	<283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
Message-ID: <4CD41A64.4070104@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 15:17, Chris Fields wrote:

> Makes sense to me.  We're tackling some Bio::Tree revisions next
> week, my guess is we can also get this added in.  I'm really keen on
> getting 1.6.2 out sometime soon, before things get really crazy for
> me this spring.

I changed my mind about the hmmer parser just in time then, I guess. :)

> Key things to test: can specify the exact hmmer2/3 parser directly?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

That's how I started the development. But I just see I changed all tests
over, so I can't prove it. I've added some tests to show this is
equivalent. (907b7d0a2b93d4961f64)

> Can one explicitly specify the hmmer parser variant?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file
> => 'foo')

I didn't think about this, but that certainly seems reasonable. If
somebody specifies a format explicitly, we can short-circuit the other
detection code. I've added code and a couple of tests to support this.
See c9cd75df492dbef90fff.

Thanks for the input,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 11:06:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:06:01 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
Message-ID: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>

All,

I have a local Blat wrapper refactoring that I had to quickly write up for some local work.  Unfortunately, the original Blat wrapper in BioPerl-Run (Bio::Tools::Run::Alignment::Blat) had parameters that weren't compatible with more recent versions of Blat, and which didn't even use most passed parameters, so it was unfortunately pretty much useless in my hands (one couldn't designate whether the query/db was dna, prot, dnax, etc).

Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?  I plan on having it pass the original tests and adding a bit more.

As a small semi-'bonus', along with this I am also writing up additional code for Bio::SearchIO::psl that allows switching parsing logic to cluster distinct regional hits; basically, same query = Result, each Hit = distinct region, each set of blocks = HSP.  This is in response from some users here to making the bp_search2gff.pl script work with PSL a little better.  Should be added in over the next few weeks.

chris

From cjfields at illinois.edu  Fri Nov  5 11:43:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:43:13 -0500
Subject: [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utility GEO Database
	name change
References: <A9D8BF3D8A74DF4A925FB541C0F39D2A14C4E64EE2@NIHMLBX15.nih.gov>
Message-ID: <0831372A-B40C-4B62-B423-5BEB7B5D3543@illinois.edu>

FYI, for those GEO users out there.

-c

Begin forwarded message:

> From: <utilities-announce at ncbi.nlm.nih.gov>
> Date: November 5, 2010 10:39:27 AM CDT
> To: NLM/NCBI List utilities-announce <utilities-announce at ncbi.nlm.nih.gov>
> Subject: [Utilities-announce] NCBI E-Utility GEO Database name change
> Reply-To: utilities-announce at ncbi.nlm.nih.gov
> 
> Dear E-Utility Users,
>  
> Recently the name of the GEO Profiles database used within the E-utilities changed from 'geo' to 'geoprofiles'. While the old name (&db=geo) will still function, users are encouraged to change their requests to use the new name (db=geoprofiles). ELink users should be aware that all linknames including 'geo' will no longer function. Instead, these names should include 'geoprofiles' rather than 'geo'. For example, the linkname of links from Gene to GEO Profiles is now &linkname=gene_geoprofiles.
>  
> Thank you.
>  
> 
>  
> _______________________________________________
> Utilities-announce mailing list
> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce



From David.Messina at sbc.su.se  Fri Nov  5 12:11:41 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 17:11:41 +0100
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
Message-ID: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>

On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:

> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?


Sounds great! Go for it.


Dave



From njauxiongjie at gmail.com  Fri Nov  5 05:12:33 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Fri, 05 Nov 2010 02:12:33 -0700 (PDT)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd3ca81.123f970a.39e2.ffff8e89@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  


From alpita at uvigo.es  Fri Nov  5 11:52:58 2010
From: alpita at uvigo.es (alpita at uvigo.es)
Date: Fri, 05 Nov 2010 16:52:58 +0100
Subject: [Bioperl-l] Primer3
Message-ID: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>

Hi

I am a PhD-student working with EST sequences. I have got an input  
file for Primer3 and the program does not run. I try directly in the  
windows console and with Bioperl. I suppose the problem is with the  
syntax, because I have never used these tools, so I would appreciate  
some help.

How can I invoked my input file in primer 3? If it is easy to run it  
with BioPerl, tell me

Thank you very much

From cjfields at illinois.edu  Fri Nov  5 13:27:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 12:27:13 -0500
Subject: [Bioperl-l] Primer3
In-Reply-To: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
References: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
Message-ID: <8BBED864-BB9A-4FF7-9B09-2549D927F858@illinois.edu>

This all depends on what version of Primer3 you are using; the Primer3 tools in bioperl-live and bioperl-run do not work with primer3 v2 due to significant changes in the primer3 API.  However, I wrote up a full refactor of these tools, along with tests, here:

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

This includes both the wrapper and the parser (see the test files for examples on how to run them).  They have been renamed because of a change in the module API.  Let me know if they work for you.

chris

On Nov 5, 2010, at 10:52 AM, alpita at uvigo.es wrote:

> Hi
> 
> I am a PhD-student working with EST sequences. I have got an input file for Primer3 and the program does not run. I try directly in the windows console and with Bioperl. I suppose the problem is with the syntax, because I have never used these tools, so I would appreciate some help.
> 
> How can I invoked my input file in primer 3? If it is easy to run it with BioPerl, tell me
> 
> Thank you very much
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Fri Nov  5 16:57:56 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 15:57:56 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
	<D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
Message-ID: <374003E7-0F9F-466F-99D9-89F85F22CFF9@illinois.edu>


On Nov 5, 2010, at 11:11 AM, Dave Messina wrote:

> On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?
> 
> 
> Sounds great! Go for it.
> 
> 
> Dave

Okay, now in bioperl-run, master branch.  This passes all prior tests; I added a few more.

chris

From gabbyteku at gmail.com  Fri Nov  5 17:17:55 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Fri, 5 Nov 2010 23:17:55 +0200
Subject: [Bioperl-l] Bad request from efetch Bio::DB::EUtilities
Message-ID: <AANLkTimT2-K7cA3N1esBQSHb9Q8btUy3572y6L0rv5J=@mail.gmail.com>

Hi
I don't know what the problem is, but the efetch code snippet throws a Bad
request error,

while( my $id = <$in> ){           # $in, file contains list of uids
                chomp $id;

                my $eut_obj = Bio::DB::EUtilities->new(   -eutil      =>
'efetch',
                                                          -email      => '
myemail at gmail.com',
                                                          -db         =>
'geoprofile',
                                                          -id         =>
$id,
                                                      );

                open( my $tmpOut, '>' ,'doc' ) or die "Can't open doc: $!";

                eval{
                        $eut_obj->get_Response(-cb => sub {my ($data) = @_;
print $tmpOut $data );
                };
                .....
}

What is wrong with the request?

Thanks in advance

From cselig01 at students.poly.edu  Sat Nov  6 00:07:16 2010
From: cselig01 at students.poly.edu (Chet Seligman)
Date: Sat, 6 Nov 2010 04:07:16 +0000
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
 Graphics in perl 5.8 in windows 7
Message-ID: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>


I'd like to use ppm or cpan.
Does anyone know which repositories to use for the modules in the subject line?

Chet Seligman
 		 	   		  

From Kevin.M.Brown at asu.edu  Mon Nov  8 10:35:56 2010
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Mon, 8 Nov 2010 08:35:56 -0700
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
	Graphics in perl 5.8 in windows 7
In-Reply-To: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
References: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
Message-ID: <1A4207F8295607498283FE9E93B775B4072A9051@EX02.asurite.ad.asu.edu>

Follow the directions at:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
To get the main parts of BioPerl installed.

Bio::Graphics is now a separate module
http://search.cpan.org/~lds/Bio-Graphics-2.15/


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Chet Seligman
> Sent: Friday, November 05, 2010 9:07 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Problem installing Bio::SeqIO, 
> ::SearchIO, ; ; Graphics in perl 5.8 in windows 7
> 
> 
> I'd like to use ppm or cpan.
> Does anyone know which repositories to use for the modules in 
> the subject line?
> 
> Chet Seligman
>  		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From dan.bolser at gmail.com  Tue Nov  9 05:41:53 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 9 Nov 2010 10:41:53 +0000
Subject: [Bioperl-l] BP reports "All tests successful.", but some failed ...
Message-ID: <AANLkTing=D4xRTV6Lxzz6z0m=ap7-a7H5jO7eKhev7FK@mail.gmail.com>

I see the following error in the output of ./Build test:

...
t/LocalDB/SeqFeature_BDB.t ................... ok
t/LocalDB/SeqFeature_mysql.t ................. 1/84 DBI
connect('database=test','',...) failed: Can't connect to local MySQL
server through socket '/var/lib/mysql/mysql.sock' (2) at
Bio/DB/SeqFeature/Store/DBI/mysql.pm line 217
sh: -user: command not found
t/LocalDB/SeqFeature_mysql.t ................. ok
...


Related to a bug I filed a while back:
http://bugzilla.open-bio.org/show_bug.cgi?id=2899

IIRC there are a few bugs in Bio::SeqFeature::Store that are hidden
due to this initial failure.


Anyway, the point is that later I see:

All tests successful.
Files=348, Tests=24136, 249 wallclock secs ( 8.99 usr  2.04 sys +
197.16 cusr 26.85 csys = 235.04 CPU)
Result: PASS


How come we get "All tests successful." when there has clearly been an
error in "t/LocalDB/SeqFeature_mysql.t"?



BioPerl version is git bcd3b66f0422493e5f1d7c05220a4e58cced6313


Cheers,
Dan.

# The place to be
irc://irc.freenode.net/#BioPerl

# Sometimes good
irc://irc.perl.org/#gmod

From cjfields at illinois.edu  Tue Nov  9 07:58:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 06:58:40 -0600
Subject: [Bioperl-l] bioperl-primer3
In-Reply-To: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
References: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
Message-ID: <532C3550-5AA1-4A47-9C8D-82899E78B7E5@illinois.edu>

On Nov 9, 2010, at 6:05 AM, alpita at uvigo.es wrote:

> Hi Chris
> 
> As I wrote last day, I have never used bioperl and Primer3. All of this is completely new for me. It seems very interesting but I am in a student exchange, so I have got no-time to deep into it now (I will do this in the future, because I think it is very interesting to my work).
> 
> I want to design some primers, so I have used the tools of Thomas Thiel (MISA and p3_in) to obtain the input file of primer3 software. The next step would be to invoked the primer3 in the windows console (directly with the primer3 software or with bioperl tools) but I always have got problems with error messages. I suppose that I am writting some errors.
> 
> If you can, I would greatly appreciate you to tell me what tool to use and how to write it in the windows console.
> 
> Thank you very much for you effort. I hope to be improving slowly in this task
> Regards

Please make responses to the main bioperl list.  

I rewrote the main set of tools for Primer3, which I believe i pointed out to you previously (unless I'm mistaken):

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

I can't tell you what to use for Windows: I don't develop on that platform.  Any patches are welcome in case you find problems there and fix them.

chris




From njauxiongjie at gmail.com  Tue Nov  9 04:05:04 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Tue, 09 Nov 2010 01:05:04 -0800 (PST)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  


From singh.amarv at epa.gov  Tue Nov  9 13:38:18 2010
From: singh.amarv at epa.gov (Amar Singh)
Date: Tue, 9 Nov 2010 18:38:18 +0000 (UTC)
Subject: [Bioperl-l] parsing PubMed retrievals
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <loom.20101109T193516-922@post.gmane.org>

Tom Keller <kellert <at> ohsu.edu> writes:

> 
> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at
/Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> Tom
> MMI DNA Services Core
Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert <at> ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 


Tom,

I am also facing the same problem. This was working a month back and now when I
wanted to test new thing it is giving me the same error. I think this is due to
some changes in the way we access the data. Will keep updated if I find a
solution and same way you too. 

Thanks,

Amar


From Russell.Smithies at agresearch.co.nz  Tue Nov  9 15:08:23 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 10 Nov 2010 09:08:23 +1300
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313BCA1138@exchsth.agresearch.co.nz>

Not sure if this will work but have you tried using STDOUT as the filename then piping all the output to a single file?
The other (much simpler) option is just concatenate all the outputs into a single file when it's finished.

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of njauxiongjie
Sent: Tuesday, 9 November 2010 10:05 p.m.
To: bioperl-l
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  

_______________________________________________
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http://lists.open-bio.org/mailman/listinfo/bioperl-l
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to which it is addressed and may contain confidential and/or privileged
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taking of any action in reliance upon, this information by persons or
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Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From florent.angly at gmail.com  Tue Nov  9 19:54:58 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 10 Nov 2010 10:54:58 +1000
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <4CD9ED62.50102@gmail.com>

Wouldn't using a single filename be the way to go?
> my $filename = "blast_ressults.out";
>            $factory->save_output($filename);
Florent


On 09/11/10 19:05, njauxiongjie wrote:
> Hi,
>
> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>
> there are two line of the code like below:
> my $filename = $result->query_name()."\.out";
>            $factory->save_output($filename);
> this saved the blast result in separated files by the query name.
>
> my question is: how can i save the blast results of all querys in one file?
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From cjfields at illinois.edu  Tue Nov  9 22:46:00 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 21:46:00 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4CD9ED62.50102@gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
Message-ID: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>

Only if the output appends to that file (I don't recall personally, so it's worth a try).

chris

On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:

> Wouldn't using a single filename be the way to go?
>> my $filename = "blast_ressults.out";
>>           $factory->save_output($filename);
> Florent
> 
> 
> On 09/11/10 19:05, njauxiongjie wrote:
>> Hi,
>> 
>> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>> 
>> there are two line of the code like below:
>> my $filename = $result->query_name()."\.out";
>>           $factory->save_output($filename);
>> this saved the blast result in separated files by the query name.
>> 
>> my question is: how can i save the blast results of all querys in one file?
>> 
>> 
>> 
>> _______________________________________________
>> 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 roy.chaudhuri at gmail.com  Wed Nov 10 11:11:27 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 10 Nov 2010 16:11:27 +0000
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
In-Reply-To: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
References: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
Message-ID: <4CDAC42F.9020708@gmail.com>

Hi Jim,

I don't think you ever got a reply to this. I think you want 
$tree->splice() rather than $tree->remove_Node().

Cheers,
Roy.

On 21/10/2010 18:52, Jim Hu wrote:
> I'm trying to take an unreadable tree from PFAM and prune it down to
> just show the paralogs from E. coli.
>
> When you run remove_Node on an internal node, is it supposed to
> reconnect the ancestors to the descendants?  This seems to be way to
> aggressive in what it's removing.
>
> while( my $tree = $treeio->next_tree ) { for my $node (
> $tree->get_nodes ) { if ($node->id =~ m/_ECOLI/){ #	leave this node
> alone #	print $node->id."\n"; }else{ if ($node->is_Leaf){
> $tree->remove_Node($node); }else{ my $num_children =
> scalar($node->each_Descendent); if ($num_children == 1){ print
> "removing ".$node->id."\n"; $tree->remove_Node($node); } } } }
> $treeio_out->write_tree($tree); }
>
> The idea is that when I've pruned the non-ECOLI leaves, some internal
> nodes will not be branches anymore.  But at the end, all the ECOLI
> nodes are gone, presumably because an ancestor got removed and the
> whole branch was lost.  Is there a way to remove just a node and
> graft the tree back together?  My plan, once I get that working is to
> repeat the traversal until the output stops changing.
>
> Jim
>
>
> ===================================== Jim Hu Associate 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 chandan.kr.singh at gmail.com  Thu Nov 11 06:10:25 2010
From: chandan.kr.singh at gmail.com (CHANDAN SINGH)
Date: Thu, 11 Nov 2010 16:40:25 +0530
Subject: [Bioperl-l] each_gene_symbol() is missing from
	Bio::Phenotype::OMIM::OMIMentry
Message-ID: <AANLkTinSX5oUFNYJFZwos2ODfsXFLj=xntxg43umfxs9@mail.gmail.com>

Hi Christian

The implementation of each_gene_symbol() is missing from
Bio::Phenotype::OMIM::OMIMentry even though the method has been referred in
the module and also in OMIMparser. I'm sure it was just a overlook; in which
case will you be implementing the method in the near future.

Thanks
Chandan

From cjfields at illinois.edu  Sun Nov 14 16:49:52 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 14 Nov 2010 15:49:52 -0600
Subject: [Bioperl-l] GitHub down
Message-ID: <E008728D-057A-415F-9415-EFD68F5F2B6F@illinois.edu>

Just a note that GitHub (and the main bioperl repo) appear to be down at the moment with a major disruption of service.  If anyone absolutely needs code, we have a synced repo set up here:

http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-db.git
http://repo.or.cz/w/bioperl-run.git
http://repo.or.cz/w/bioperl-network.git

chris

From maj at fortinbras.us  Mon Nov 15 20:08:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 15 Nov 2010 20:08:25 -0500
Subject: [Bioperl-l] use Bio::Search::Tiling::MapTiling
In-Reply-To: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
References: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
Message-ID: <E703F129EE074EFD9ACA421FED2A87F2@NewLife>

Hi Wei, 
You'll need to install the trunk code to access this method; the "release" is woefully out of date (not that I'm helping much on that these days). Use git to obtain the latests bioperl-live and bioperl-run from https://github.com/bioperl/, or the synchronized repos
http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-run.git
cheers, 
MAJ
----- Original Message ----- 
  From: Shao, Wei (NIH/NCI) [C] 
  To: Mark A Jensen 
  Sent: Monday, November 15, 2010 10:47 AM
  Subject: use Bio::Search::Tiling::MapTiling


Dear Dr. Jensen, I am looking for a bioperl module that can be used to concatenate HSP from a blast into a sequence. I found that your Bio::Search::Tiling::MapTilingcan do exactly that. I used your example script to test it. I got an error message:?Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::MapTiling" at get_hsp.pl line 29, <GEN1> line 2630?.It seems that method ?get_tiled_alns? is not in the bioperl we installed. Is that possible? The script I used is this one:  use Bio::SearchIO;use Bio::Search::Tiling::MapTiling # Note that to get one hit, the user first blasts# the set of contigs against single sequence, the reference sequence.# The result of this BLAST run is in 'contig_tile.bls' $blio = Bio::SearchIO->new( -file => 'contig_tile.bls');$result = $blio->next_result;$hit = $result->next_hit;$tiling = Bio::Search::Tiling::MapTiling->new($hit);@alns = $tiling->get_tiled_alns('query'); # here's the concatenation:$concat_seq_obj = $alns[0]->get_seq_by_id('query'); 

  Best regards,

   

   

  Wei Shao, Ph.D. [Contractor] 
  Bioinformatics Analyst IV

  Advanced Biomedical Computing Center/HIV Drug Resistance Program
  SAIC-Frederick, Inc. 

  National Cancer Institute at Frederick
  P.O. Box B, Frederick, MD 21702
  Phone: 301/846-6021

  Fax:  301/846-6013
  Email:  shaow at mail.nih.gov


  NOTICE:  This communication may contain privileged or other confidential information.  If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information.  Please indicate to the sender that you have received this email in error and delete the copy you received.

   


From dimitark at bii.a-star.edu.sg  Mon Nov 15 21:44:15 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 16 Nov 2010 10:44:15 +0800
Subject: [Bioperl-l] about tblastn and strand
Message-ID: <4CE1EFFF.70304@bii.a-star.edu.sg>

Hi guys,
i have a simple question. How exactly is defined on which strand is 
located a certain HSP in tblastn? I know it is used the strand function 
but i would like to know how is implemented. I ask cos here i made a 
perl script using bioperl but other people want to implement it in Java.

In the output of tblastn there is no strand string only frame+ or 
frame-. Do you just take the + or - to determine on which strand is the HSP?

Thank you for your time and help.

Dimitar

From mmuratet at hudsonalpha.org  Tue Nov 16 16:56:08 2010
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Tue, 16 Nov 2010 15:56:08 -0600
Subject: [Bioperl-l] Obtaining Refseq status with eutils
Message-ID: <EEABA734-39A8-44B4-9540-A20FE1BC575E@hudsonalpha.org>

Greetings

I have been trying to get to the Refseq status info that shows up NCBI  
gene webpage. My latest attempt is:

my @accs = qw(SAAV_0049);

my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -email => 'mmuratet at hudsonalpha.org 
',
                                        -db    => 'gene',
                                        -term  => join(',', at accs));

my @uids = $factory->get_ids;

$factory->reset_parameters(-eutil => 'elink',
                            -dbfrom => 'gene',
                            -db => 'nuccore',
                            -linkname => 'gene_nuccore_refseqgene',
                            -id    => \@uids);

$factory->get_Response(-file => 'temp.txt');

All I get back is the ID number I gave it. Also, $factory->next_DocSum  
returns nothing.

A big part of the problem is that I don't know what field I'm looking  
for. I am also unsure that I am using the elink interface properly.

Does anyone know how to get to the Refseq data for a gene? I am  
looking for evidence of expression of gene models--is there a better  
annotation to use?

Thanks

Mike


Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806






From pcantalupo at gmail.com  Wed Nov 17 12:38:05 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 12:38:05 -0500
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
Message-ID: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>

Hi,

Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm


---
 Bio/SeqIO.pm |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
index fe49822..cf6d3a2 100644
--- a/Bio/SeqIO.pm
+++ b/Bio/SeqIO.pm
@@ -651,6 +651,7 @@ sub _guess_format {
    return 'phd'     if /\.(phd|phred)$/i;
    return 'pir'     if /\.pir$/i;
    return 'pln'     if /\.pln$/i;
+   return 'qual'    if /\.qual$/i;
    return 'raw'     if /\.(txt)$/i;
    return 'scf'     if /\.scf$/i;
    return 'swiss'   if /\.(swiss|sp)$/i;
-- 
1.6.4.2



Paul

Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260

From maj at fortinbras.us  Wed Nov 17 17:59:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 17 Nov 2010 22:59:25 +0000
Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] GO annotation
Message-ID: <W347038377283011290034765@webmail27>


redirect to list
-----Original Message-----
From: Christos Noutsos [mailto:cnoutsos at cshl.edu]
Sent: Wednesday, November 17, 2010 05:35 PM
To: bioperl-guts-l at lists.open-bio.org
Subject: [Bioperl-guts-l] GO annotation

Hi all,
I have several clusters of coregulated genes from Arabidopsis and I would like to check  their GO annotation? Is there a module in bioperl which I can use? 
Thank you for your help
Christos


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




From lskatz at gatech.edu  Wed Nov 17 22:20:03 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Wed, 17 Nov 2010 22:20:03 -0500
Subject: [Bioperl-l] Status of assembly modules
Message-ID: <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc@mail.gmail.com>

I have read on the BioPerl site that a 454 ace is not standardized due to
its coordinate system.  How can I convert it to the standard ace file?

When I run this code either by using contig or assembly objects, I get an
error.
Can't call method "get_consensus_sequence" on an undefined value at
Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.

    sub _newblerAceToAce($args){
      my($self,$args)=@_;
      my
$ace454=Bio::Assembly::IO->new(-file=>$$args{ace454Path},-format=>"ace",-variant=>'454');
      my
$ace=Bio::Assembly::IO->new(-file=>">$$args{acePath}",-format=>"ace");
      #while(my $contig=$ace454->next_contig){
      while(my $scaffold=$ace454->next_assembly){
        print Dumper $scaffold;
      }
      return $$args{acePath};
    }


On Fri, Jun 18, 2010 at 5:59 AM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 13
> Date: Fri, 18 Jun 2010 15:39:39 +1000
> From: Florent Angly <florent.angly at gmail.com>
> Subject: [Bioperl-l] Status of assembly modules
> To: Joshua Udall <jaudall at gmail.com>,   bioperl-l List
>        <bioperl-l at lists.open-bio.org>
> Message-ID: <4C1B069B.5020105 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Joshua,
>
> Yes, there have been interesting improvements in the assembly BioPerl
> module since v1.6.1. You can find these changes in the development
> version of BioPerl at http://github.com/bioperl/. I'll take this
> opportunity to introduce people who don't follow the commit messages to
> the new features that have been introduced:
>
> First, there is support for more file formats from high-throughput
> platforms, including those generated by de novo assembly and comparative
> assembly tools, such as:
>     * Roche 454 GS Assembler, aka Newbler (the ACE-454 variant)
>     * Maq
>     * Sam
>     * Bowtie
> There is support for running a lot more of these tools in Bioperl-run
> Bio::Tools::Run :
>     * Roche 454 GS Assembler, aka Newbler
>     * Minimo
>     * Maq
>     * Samtools
>     * Bowtie
> In terms of writing assembly file, I added the option to write ACE
> files, which is quite useful because maybe assembly programs recognize
> this format. So now you can read assemblies, modify them as you see fit
> and exporting them to other programs by writing the modified assembly in
> an ACE file.
> The internals of the IO parsers have acquired some granularity as it is
> now possible to read/write assembly files entirely, or one contig at a
> time. This is terrific to reduce memory usage.
>
> That's about it...
>
> Regards,
>
> Florent
>
> PS/ Josh, you filed bug reports related to several of these issues
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2726,
> http://bugzilla.open-bio.org/show_bug.cgi?id=2483). I am closing the
> ones that were not closed yet and thank you for submitting patches.
>
>
> On 18/06/10 14:00, Joshua Udall wrote:
> > Florent -
> >
> > I didn't want to ask a direct question on-list to perhaps avoid
> > confusion.  Were you able to improve/submit a ContigIO to bioperl that
> > works with one entry at a time (instead of slurping the entire ace
> > file)?
> >
> >
>



-- 
Lee Katz
http://leeskatz.com

From rmb32 at cornell.edu  Thu Nov 18 02:03:46 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 17 Nov 2010 23:03:46 -0800
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
In-Reply-To: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
References: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
Message-ID: <4CE4CFD2.3000901@cornell.edu>

Applied!  Thanks Paul!

Rob

Paul Cantalupo wrote:
> Hi,
> 
> Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm
> 
> 
> ---
>  Bio/SeqIO.pm |    1 +
>  1 files changed, 1 insertions(+), 0 deletions(-)
> 
> diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
> index fe49822..cf6d3a2 100644
> --- a/Bio/SeqIO.pm
> +++ b/Bio/SeqIO.pm
> @@ -651,6 +651,7 @@ sub _guess_format {
>     return 'phd'     if /\.(phd|phred)$/i;
>     return 'pir'     if /\.pir$/i;
>     return 'pln'     if /\.pln$/i;
> +   return 'qual'    if /\.qual$/i;
>     return 'raw'     if /\.(txt)$/i;
>     return 'scf'     if /\.scf$/i;
>     return 'swiss'   if /\.(swiss|sp)$/i;


From pcantalupo at gmail.com  Thu Nov 18 10:15:04 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 18 Nov 2010 10:15:04 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTikW_cKGovyGyKLZMxAeP1E6Vs8P=KOzAXQsKBxK@mail.gmail.com>

Hi,

I'm resending this to the list (without an attachment) since it got
flagged as having a suspicious header.


I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string":

---
 Bio/Seq/PrimaryQual.pm |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/Bio/Seq/PrimaryQual.pm b/Bio/Seq/PrimaryQual.pm
index 4935639..30383fc 100644
--- a/Bio/Seq/PrimaryQual.pm
+++ b/Bio/Seq/PrimaryQual.pm
@@ -461,7 +461,7 @@ sub qualat {
 sub to_string {
     my ($self,$out,$result) = shift;
     $out = "qual: ".join(',',@{$self->qual()});
-    foreach (qw(display_id accession_number primary_id desc id)) {
+    foreach (qw(display_id accession_number primary_id desc id length)) {
 	$result = $self->$_();
 	if (!$result) { $result = "<unset>"; }
 	$out .= "$_: $result\n";
-- 
1.6.4.2






Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260

From pcantalupo at gmail.com  Wed Nov 17 10:55:52 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 10:55:52 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>

Hi,

I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string"

Paul


Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260
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From twaddlac at gmail.com  Fri Nov 19 15:03:14 2010
From: twaddlac at gmail.com (Alan Twaddle)
Date: Fri, 19 Nov 2010 15:03:14 -0500
Subject: [Bioperl-l] bioperl-ext package installation error
Message-ID: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>

Hello all,

     I am trying to write a simple script to parse an ABI file into usable
data which requires the staden io_lib of which I installed. However, am
receiving an error message when trying to run my script that says the
following:
------------- EXCEPTION: Bio::Root::SystemException -------------
MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
package has been installed successfully!
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
abi.pm:100
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
STACK: AB1_parser.pl:10

I didn't receive any error messages when installing the staden package so
I'm assuming that there's some path specified in some file that is pointing
to the wrong place. I don't know if this is the case but if you have any
suggestions about how to fix this I would greatly appreciate it! Thank you
very much!

-- 

Alan Twaddle, B.S.
MUC class of 2010

From cjfields at illinois.edu  Fri Nov 19 23:33:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:33:14 -0600
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
In-Reply-To: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
References: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
Message-ID: <644615D3-8F59-4E59-B7A1-6BCE6159E9C9@illinois.edu>

Paul, 

Committed this to github master branch.  Thanks for pointing that out.

chris

On Nov 17, 2010, at 9:55 AM, Paul Cantalupo wrote:

> Hi,
> 
> I simply added "length" to the foreach loop in sub "to_string" of
> Bio/Seq/PrimaryQual.pm to match documentation of "to_string"
> 
> Paul
> 
> 
> Paul Cantalupo
> Research Specialist/Systems Programmer
> University of Pittsburgh
> Pittsburgh, PA 15260
> <0001-Added-length-to-foreach-loop-to-match-documentation-.patch>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Fri Nov 19 23:50:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:50:17 -0600
Subject: [Bioperl-l] bioperl-ext package installation error
In-Reply-To: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
References: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
Message-ID: <D0C6F261-EFF7-46D3-823D-171BAA240A91@illinois.edu>

Alan, 

You need to install the bioperl-ext module Bio::SeqIO::staden::read, which uses XS bindings to io_lib, but there's a bit of a caveat: we're not really maintaining that code anymore.  Saying that, it does work using io_lib version 1.12.2 (my local version). 

Here's the code, please make sure to note the README (specifically, the version of io_lib you will need and the problems you may run into):

https://github.com/bioperl/bioperl-ext/tree/master/Bio/SeqIO/staden/

chris

On Nov 19, 2010, at 2:03 PM, Alan Twaddle wrote:

> Hello all,
> 
>     I am trying to write a simple script to parse an ABI file into usable
> data which requires the staden io_lib of which I installed. However, am
> receiving an error message when trying to run my script that says the
> following:
> ------------- EXCEPTION: Bio::Root::SystemException -------------
> MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
> package has been installed successfully!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
> abi.pm:100
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
> STACK: AB1_parser.pl:10
> 
> I didn't receive any error messages when installing the staden package so
> I'm assuming that there's some path specified in some file that is pointing
> to the wrong place. I don't know if this is the case but if you have any
> suggestions about how to fix this I would greatly appreciate it! Thank you
> very much!
> 
> -- 
> 
> Alan Twaddle, B.S.
> MUC class of 2010
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jordi.durban at gmail.com  Mon Nov 22 15:01:34 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Mon, 22 Nov 2010 21:01:34 +0100
Subject: [Bioperl-l] parse multi xml
Message-ID: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>

Hi all,
I'm a newbie in the list although I've been using bioperl for 2 years.
Now I have a problem with a XML file and I don't know how to parse it.
That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
resulted from  Blast2go software the usage and I suppose the file is the
outcome of multiple blast results concatenation.
Well, I would like to split all 795 different xml chunks in 795 different
files in order to parse them looking for the best hit.
The problem appears using the blastxml parse
(*Bio::SearchIO::blastxml) *because
(and that's a personal opinion) there's another top tag not expected and I
get a error message once the first blast result was parsed.
How can I do that split function?
I hope I was clear
Thanks




-- 
Jordi

From biopython at maubp.freeserve.co.uk  Mon Nov 22 15:23:29 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Nov 2010 20:23:29 +0000
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
Message-ID: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>

On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
> Hi all,
> I'm a newbie in the list although I've been using bioperl for 2 years.
> Now I have a problem with a XML file and I don't know how to parse it.
> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
> resulted from ?Blast2go software the usage and I suppose the file is the
> outcome of multiple blast results concatenation.

Such a file is NOT a valid XML file (but see below), you can't just
concatenate XML files. I'm pretty sure people have posted scripts
to fix such files on the blast2go mailing list.

> Well, I would like to split all 795 different xml chunks in 795 different
> files in order to parse them looking for the best hit.
> The problem appears using the blastxml parse
> (*Bio::SearchIO::blastxml) *because
> (and that's a personal opinion) there's another top tag not expected
> and I get a error message once the first blast result was parsed.
> How can I do that split function?
> I hope I was clear
> Thanks

Historically the NCBI standalone BLAST used to create these
concatenated XML files when used on multiple queries. It has
since been fixed, but perhaps BioPerl has code still in it to
handle these legacy invalid XML files?

My suggestion (until a BioPerl guru speaks up) would be to
split the file into chunks (in memory) by looking for the string
<?xml version="1.0">, and parsing each chunk individually.
Each chunk should be a valid XML file on its own.

Peter


From lskatz at gatech.edu  Mon Nov 22 15:18:10 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Mon, 22 Nov 2010 15:18:10 -0500
Subject: [Bioperl-l] Re(2): Status of assembly modules
Message-ID: <AANLkTi=JShCLsHDxHK4eeWD3Da=vWmRkGN2rkuLwCjxn@mail.gmail.com>

I figured it out (I haven't tested much though).

To whoever works on Assembly::IO::ace.pm:
I changed a regular expression on line 231 because the contig object was not
initializing properly.  For some reason the 454 ace file had adopted the
reference assembly's ID and therefore there was a GI number followed by a
pipe.  The pipe was not captured with \w+.  I think that the regex will be
safe with \s(\S+)\s.

 if (/^CO\s(\S+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!
#if (/^CO\s(\w+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!

On Thu, Nov 18, 2010 at 12:04 PM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 3
> Date: Wed, 17 Nov 2010 22:20:03 -0500
> From: Lee Katz <lskatz at gatech.edu>
> Subject: Re: [Bioperl-l] Status of assembly modules
> To: bioperl-l at lists.open-bio.org
> Message-ID:
>        <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I have read on the BioPerl site that a 454 ace is not standardized due to
> its coordinate system.  How can I convert it to the standard ace file?
>
> When I run this code either by using contig or assembly objects, I get an
> error.
> Can't call method "get_consensus_sequence" on an undefined value at
> Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.
>
>    sub _newblerAceToAce($args){
>      my($self,$args)=@_;
>      my
>
> $ace454=Bio::Assembly::IO->new(-file=>$args{ace454Path},-format=>"ace",-variant=>'454');
>      my
> $ace=Bio::Assembly::IO->new(-file=>">$args{acePath}",-format=>"ace");
>      #while(my $contig=$ace454->next_contig){
>      while(my $scaffold=$ace454->next_assembly){
>        print Dumper $scaffold;
>      }
>      return $args{acePath};
>    }
>



-- 
Lee Katz
http://leeskatz.com

From thomas.sharpton at gmail.com  Mon Nov 22 17:28:52 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 22 Nov 2010 14:28:52 -0800
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
Message-ID: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>

Hi Evan,

Glad to hear this software is a promising solution to your needs. I  
just tried running the test script under Bio/t/SearchIO/hmmer3.t and  
everything passed. Can you verify that you are using an up-to-date  
version of bioperl-live? You can grab a snapshot from github if you  
haven't already:

https://github.com/bioperl/bioperl-live

Also, I'm cc'ing this to the bioperl list so that others may benefit  
from our discourse (and chime in - Kai Blin, who created the test  
tools, and others have made substantial contributions and improvements  
to the original code and they might have good suggestions).

T



On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:

> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3  
> reports. Everything seems to be working nicely with the test data  
> and my own reports except for getting the $hsp->query_string and  
> $hsp->hit_string. I noticed that these HSP routines were not working  
> with the test script/data (for me anyway) so I thought I would ask  
> before spending days trying to solve this one.
>
> Thanks,
>
> Evan
>
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602


From jordi.durban at gmail.com  Mon Nov 22 18:34:03 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Tue, 23 Nov 2010 00:34:03 +0100
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <AANLkTi=RBBL1vC4XRQM=_gf+5CPLiw2+6xdtwzZjFy6a@mail.gmail.com>

Thanks Peter.
That's exactly what I was looking for but so far I've not been able to do
that properly.
Any ideas??


2010/11/22 Peter <biopython at maubp.freeserve.co.uk>

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com>
> wrote:
> > Hi all,
> > I'm a newbie in the list although I've been using bioperl for 2 years.
> > Now I have a problem with a XML file and I don't know how to parse it.
> > That file has 795 xml top tags (thta's is <?xml version="1.0">) because
> they
> > resulted from  Blast2go software the usage and I suppose the file is the
> > outcome of multiple blast results concatenation.
>
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
>
> > Well, I would like to split all 795 different xml chunks in 795 different
> > files in order to parse them looking for the best hit.
> > The problem appears using the blastxml parse
> > (*Bio::SearchIO::blastxml) *because
> > (and that's a personal opinion) there's another top tag not expected
> > and I get a error message once the first blast result was parsed.
> > How can I do that split function?
> > I hope I was clear
> > Thanks
>
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?
>
> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
>
> Peter
>



-- 
Jordi

From cjfields at illinois.edu  Mon Nov 22 19:27:43 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 22 Nov 2010 18:27:43 -0600
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <348A592A-D634-4C1C-9F05-DB20FE87F61C@illinois.edu>

On Nov 22, 2010, at 2:23 PM, Peter wrote:

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
>> Hi all,
>> I'm a newbie in the list although I've been using bioperl for 2 years.
>> Now I have a problem with a XML file and I don't know how to parse it.
>> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
>> resulted from  Blast2go software the usage and I suppose the file is the
>> outcome of multiple blast results concatenation.
> 
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
> 
>> Well, I would like to split all 795 different xml chunks in 795 different
>> files in order to parse them looking for the best hit.
>> The problem appears using the blastxml parse
>> (*Bio::SearchIO::blastxml) *because
>> (and that's a personal opinion) there's another top tag not expected
>> and I get a error message once the first blast result was parsed.
>> How can I do that split function?
>> I hope I was clear
>> Thanks
> 
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?

It does (last I looked).

> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
> 
> Peter

Or, better yet, push the blast2go folks to create valid XML output or use an updated version of BLAST.  This bug was fixed about 3 years ago.

chris




From statonse at uga.edu  Mon Nov 22 18:41:26 2010
From: statonse at uga.edu (Evan Staton)
Date: Mon, 22 Nov 2010 18:41:26 -0500
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
Message-ID: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>

Hi Thomas,

Everything works with the latest release of bioperl-live. My bioperl was
1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
did not realize it had been incorporated into the latest distribution). All
the tests passed and all the routines worked before except for the
$hsp->query_string and $hsp->hit_string, but that is resolved now.

Thanks for the quick response, it saved me a lot of time.

Evan

On Mon, Nov 22, 2010 at 5:28 PM, Thomas Sharpton
<thomas.sharpton at gmail.com>wrote:

> Hi Evan,
>
> Glad to hear this software is a promising solution to your needs. I just
> tried running the test script under Bio/t/SearchIO/hmmer3.t and everything
> passed. Can you verify that you are using an up-to-date version of
> bioperl-live? You can grab a snapshot from github if you haven't already:
>
> https://github.com/bioperl/bioperl-live
>
> Also, I'm cc'ing this to the bioperl list so that others may benefit from
> our discourse (and chime in - Kai Blin, who created the test tools, and
> others have made substantial contributions and improvements to the original
> code and they might have good suggestions).
>
> T
>
>
>
> On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:
>
> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3 reports.
> Everything seems to be working nicely with the test data and my own reports
> except for getting the $hsp->query_string and $hsp->hit_string. I noticed
> that these HSP routines were not working with the test script/data (for me
> anyway) so I thought I would ask before spending days trying to solve this
> one.
>
> Thanks,
>
> Evan
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602
>
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
S. Evan Staton
PhD Student - Burke Lab
University of Georgia
Department of Genetics
3507 Miller Plant Sciences
Athens, GA 30602

From kris.richardson at tufts.edu  Tue Nov 23 12:10:56 2010
From: kris.richardson at tufts.edu (kris richardson)
Date: Tue, 23 Nov 2010 12:10:56 -0500
Subject: [Bioperl-l] GeneMapper
Message-ID: <BA6B80D7-732A-4333-83AD-54AB14BF334D@tufts.edu>

Dear Members,

 I have a list mRNA target positions,  for various mRNAs and  I also have the RefSeq accession NM_#s for their genes  and mRNA (ex; gene: NM_198155 --- mRNA positions: NM_004649: 800-890).   

I would like to use this info to pull the chromosomal coordinates of NM_198155 corresponding to the resulting transcript positions NM:_004649:800-890.  I am familiarizing myself with bioperl and GeneMapper seems like it can provide this info.  However, the documentation on the module code is sparse, and there are no examples.  I was wondering if anyone has experience with this and could point me in the right direction, or perhaps provide some example code?  

Regards,

Kris






From kai.blin at biotech.uni-tuebingen.de  Wed Nov 24 01:24:22 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Wed, 24 Nov 2010 07:24:22 +0100
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
	<AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
Message-ID: <4CECAF96.7010706@biotech.uni-tuebingen.de>

On 2010-11-23 00:41, Evan Staton wrote:

Hi Evan,

> Everything works with the latest release of bioperl-live. My bioperl was
> 1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
> did not realize it had been incorporated into the latest distribution). All
> the tests passed and all the routines worked before except for the
> $hsp->query_string and $hsp->hit_string, but that is resolved now.

I recently fixed this in bioperl-live when I bumped into that feature
missing. I didn't bother to update the bioperl-hmmer3 repository.
Perhaps it should be deleted to avoid the confusion.

Also, in bioperl-live, the Bio::SearchIO::hmmer parser now supports
hmmer2 and hmmer3 parsing, but by all means go for the specific parser
class if you know the version of hmmer result you're loading. :)

On a side note, even though you're probably aware of this... HMMer3 only
does local alignments, so it's not really good for domain extraction. It
is very fast, but if your software uses a profile based search to
extract specific amino acid motifs HMMer3 might let you down.
Just as a caveat that has bitten me recently.

Cheers,
Kai

-- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-University of T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Deutschland
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben

From dimitark at bii.a-star.edu.sg  Wed Nov 24 21:38:52 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:38:52 +0800
Subject: [Bioperl-l] update: genpept module
Message-ID: <4CEDCC3C.9070707@bii.a-star.edu.sg>

Hi guys,
just managed to get GenPept to give me the fasta in the full form. I 
modified GenPept in this way:

sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); 
#DIMITAR
   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
   $self->request_format($self->default_format($format));
   return $self;
}

Cheers
Dimitar

From cjfields at illinois.edu  Wed Nov 24 22:24:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 24 Nov 2010 21:24:40 -0600
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDCC3C.9070707@bii.a-star.edu.sg>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
Message-ID: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>

Dimitar,

Missed your original post, but was it reported as a bug?  

chris

On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:

> Hi guys,
> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
> 
> sub new {
>  my($class, @args) = @_;
>  my $self = $class->SUPER::new(@args);
>  my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>  $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>  $self->request_format($self->default_format($format));
>  return $self;
> }
> 
> Cheers
> Dimitar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason at bioperl.org  Wed Nov 24 22:57:11 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Nov 2010 19:57:11 -0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
Message-ID: <4CEDDE97.5020406@bioperl.org>

This doesn't seem like the right fix -- you don't want to updated a 
default variable -- why didn't you just use it like this: ?

my $db = new Bio::DB::GenPept->new(-format => 'fasta');



Chris Fields wrote, On 11/24/10 7:24 PM:
> Dimitar,
>
> Missed your original post, but was it reported as a bug?
>
> chris
>
> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>
>> Hi guys,
>> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
>>
>> sub new {
>>   my($class, @args) = @_;
>>   my $self = $class->SUPER::new(@args);
>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>   $self->request_format($self->default_format($format));
>>   return $self;
>> }
>>
>> Cheers
>> Dimitar
>> _______________________________________________
>> 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 at bioperl.org


From dimitark at bii.a-star.edu.sg  Thu Nov 25 00:34:39 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 13:34:39 +0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDDE97.5020406@bioperl.org>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
	<4CEDDE97.5020406@bioperl.org>
Message-ID: <4CEDF56F.3020409@bii.a-star.edu.sg>

I used it like this in the script:

if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


}

i added $retformat to getoptlong as well. but that didnt work well as 
did for GenBank. May be GenBank and GenPept should be made to work in 
the same way. Now they are a bit different. I tried to see why they 
react different but i couldnt understand why.

now my GenPept new method looks like this:
sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
FORMAT)], at args);#dimitar
   $DEFAULTFORMAT=$format if (defined $format);#dimitar
   $self->request_format($self->default_format($format));
   return $self;
}

this way i can get sequences in any format which Eutils is allowing.

On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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
>



On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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 dimitark at bii.a-star.edu.sg  Thu Nov 25 02:05:36 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 15:05:36 +0800
Subject: [Bioperl-l] about NCBI seq reports
Message-ID: <4CEE0AC0.6050104@bii.a-star.edu.sg>

Hi again,
now i can get the sequences in full fasta as NCBI provides them. But can 
I also get and the GenPept reports in some way?
I tried using 'download_query_genbank.pl' but i always get some fasta 
seq but not the GenPept report even though the generated by the script 
request is valid. When i put it in browser i get the report file but the 
script itself returns fasta. I think is limitation of the modules which 
the scripts uses, right? Or am i mistaken.

Cheers
Dimitar

From Marc.Perry at oicr.on.ca  Fri Nov 26 23:53:48 2010
From: Marc.Perry at oicr.on.ca (Marc Perry)
Date: Fri, 26 Nov 2010 23:53:48 -0500
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm; 'sizes' method is broken
Message-ID: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>

Hi,

I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:

=+=+=+=
#!/usr/bin/perl

use strict;
use warnings;
use Bio::SeqIO;
use Bio::Restriction::Analysis;
use Bio::Restriction::Enzyme;
use Bio::Restriction::EnzymeCollection;

my $input = shift or die "No fasta file on command line.";

my $seqio_obj = Bio::SeqIO->new(-file   => $input,
                                                -format => "fasta" );

my $seq = $seqio_obj->next_seq;

my $all_enz = Bio::Restriction::EnzymeCollection->new();

my $h3 = $all_enz->get_enzyme('HindIII');

my $ra = Bio::Restriction::Analysis->new(-seq => $seq);

print join "\n", $ra->sizes($h3), "\n\n";
print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
print join "\n", $ra->sizes($h3, 1, 1), "\n\n";

exit;
=+=+=+=

And here is the output:

48502


48502


48.502

As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:


sub sizes {

    my ($self, $enz, $kb, $sort) = @_;

    $self->throw('no enzyme selected to get fragments for')

        unless $enz;

    $self->cut unless $self->{'_cut'};

    my @frag; my $lastsite=0;

    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG

      $kb ? push (@frag, (int($site-($lastsite))/100)/10)

          : push (@frag, $site-($lastsite));

      $lastsite=$site;

    }

    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)

        : push (@frag, $self->{'_seq'}->length-($lastsite));

    if ($self->{'_seq'}->is_circular) {

       my $first=shift @frag;

       my $last=pop @frag;

       push @frag, ($first+$last);

    }

    $sort ? @frag = sort {$b <=> $a} @frag : 1;



    return @frag;

}


I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:

my $name = $enz->{_seq}->{display_id};
foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {

And now my script yields this output:

23130
2027
2322
9416
564
6682
4361


23130
9416
6682
4361
2322
2027
564


23.13
9.416
6.682
4.361
2.322
2.027
0.564

which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:


You should be able to do these:



  # to see all the fragment sizes,

  print join "\n", @{$re->sizes($enz)}, "\n";

  # to see all the fragment sizes sorted

  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";

  # to see all the fragment sizes in kb sorted

  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";

--Marc

Marc Perry
Scientific Associate

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:       416-673-8593
Toll-free:  1-866-678-6427
Cell:      416-904-8037
www.oicr.on.ca<http://www.oicr.on.ca/>

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all



From cjfields at illinois.edu  Sat Nov 27 00:15:46 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 26 Nov 2010 23:15:46 -0600
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm;
	'sizes' method is broken
In-Reply-To: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
References: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
Message-ID: <66A351B0-D483-490A-90CC-BF7C596D6505@illinois.edu>

Marc,

I've entered this into bugzilla for tracking (the best place for this, BTW).  I can't promise when we'll get to it, but since there is a proposed fix it may be handled fairly soon.  Thanks for pointing this out!

chris

On Nov 26, 2010, at 10:53 PM, Marc Perry wrote:

> Hi,
> 
> I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:
> 
> =+=+=+=
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::SeqIO;
> use Bio::Restriction::Analysis;
> use Bio::Restriction::Enzyme;
> use Bio::Restriction::EnzymeCollection;
> 
> my $input = shift or die "No fasta file on command line.";
> 
> my $seqio_obj = Bio::SeqIO->new(-file   => $input,
>                                                -format => "fasta" );
> 
> my $seq = $seqio_obj->next_seq;
> 
> my $all_enz = Bio::Restriction::EnzymeCollection->new();
> 
> my $h3 = $all_enz->get_enzyme('HindIII');
> 
> my $ra = Bio::Restriction::Analysis->new(-seq => $seq);
> 
> print join "\n", $ra->sizes($h3), "\n\n";
> print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
> print join "\n", $ra->sizes($h3, 1, 1), "\n\n";
> 
> exit;
> =+=+=+=
> 
> And here is the output:
> 
> 48502
> 
> 
> 48502
> 
> 
> 48.502
> 
> As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:
> 
> 
> sub sizes {
> 
>    my ($self, $enz, $kb, $sort) = @_;
> 
>    $self->throw('no enzyme selected to get fragments for')
> 
>        unless $enz;
> 
>    $self->cut unless $self->{'_cut'};
> 
>    my @frag; my $lastsite=0;
> 
>    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG
> 
>      $kb ? push (@frag, (int($site-($lastsite))/100)/10)
> 
>          : push (@frag, $site-($lastsite));
> 
>      $lastsite=$site;
> 
>    }
> 
>    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)
> 
>        : push (@frag, $self->{'_seq'}->length-($lastsite));
> 
>    if ($self->{'_seq'}->is_circular) {
> 
>       my $first=shift @frag;
> 
>       my $last=pop @frag;
> 
>       push @frag, ($first+$last);
> 
>    }
> 
>    $sort ? @frag = sort {$b <=> $a} @frag : 1;
> 
> 
> 
>    return @frag;
> 
> }
> 
> 
> I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:
> 
> my $name = $enz->{_seq}->{display_id};
> foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {
> 
> And now my script yields this output:
> 
> 23130
> 2027
> 2322
> 9416
> 564
> 6682
> 4361
> 
> 
> 23130
> 9416
> 6682
> 4361
> 2322
> 2027
> 564
> 
> 
> 23.13
> 9.416
> 6.682
> 4.361
> 2.322
> 2.027
> 0.564
> 
> which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:
> 
> 
> You should be able to do these:
> 
> 
> 
>  # to see all the fragment sizes,
> 
>  print join "\n", @{$re->sizes($enz)}, "\n";
> 
>  # to see all the fragment sizes sorted
> 
>  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";
> 
>  # to see all the fragment sizes in kb sorted
> 
>  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";
> 
> --Marc
> 
> Marc Perry
> Scientific Associate
> 
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
> 
> Tel:       416-673-8593
> Toll-free:  1-866-678-6427
> Cell:      416-904-8037
> www.oicr.on.ca<http://www.oicr.on.ca/>
> 
> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From dimitark at bii.a-star.edu.sg  Mon Nov 29 04:35:26 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 17:35:26 +0800
Subject: [Bioperl-l] genbank
Message-ID: <4CF373DE.4070902@bii.a-star.edu.sg>

Hi again,
it seems that when i download (with 'download_query_genbank.pl') the 
whole proteome from NCBI in fasta format it is first being downloaded 
and from it is being created some kind of SeqFastaSpeedFactory and after 
that from it is being copied to the output file. But i want to download 
and write to output file one by one so i can see the download 
progress(which is working for genbank data).

Its frustrating :)

Any ideas where to look for solution
Cheers
Dimitar



From cjfields at illinois.edu  Mon Nov 29 09:39:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 08:39:16 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF373DE.4070902@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
Message-ID: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>

On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:

> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
> 
> Its frustrating :)
> 
> Any ideas where to look for solution
> Cheers
> Dimitar

You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:

my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
	$out->write_seq($seq);
}

insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.

If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.

chris

From dimitark at bii.a-star.edu.sg  Wed Nov 24 21:20:28 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:20:28 +0800
Subject: [Bioperl-l] question about GenPept.pm
Message-ID: <4CEDC7EC.1000903@bii.a-star.edu.sg>

Hi guys,
i want to get some genomes and proteomes from NCBI in fasta format. I 
found i have to use 'download_query_genbank.pl' for that. It works but 
not as i would like. It uses the modules GenPept and GenBank. They 
retrieve the data in fasta but in different format than i want.

Example:
a) i want the fasta to be like the following:
 >gi|5834889|ref|NP_006959.1|COX3_10021 cytochrome c oxidase subunit III 
[Caenorhabditis elegans]
here sequense...

b) but it comes like this:
 >COX3_10021 cytochrome c oxidase subunit III [Caenorhabditis elegans]
here sequense...

But i need the gi and NP as well. So i dug up a bit and after playing 
with 'download_query_genbank.pl' i managed to make GenBank to give the 
fasta seqs in the format i want.
I made the following changes:
1. added $retformat option for Getopt
2.modified this section:
if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


} else {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenBank->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenBank->new(-verbose => $debug);
     }
}

But i go problem with GenPept. I still cant get the seqs in full fasta 
format as i explained above. Its interesting cos both modules GenPept 
and GenBank are almost identical except that GenBank uses the new method 
of NCBIHelper while GenPept has its own which still uses the 
NCBIHelper's as well.

With my modification i pass the format i want but then somehow it 
reverts to the default set in GenPept which is 'gp' while i need it to 
be 'fasta'.

If i change the defaultformat in GenPept to fasta it works but thats 
just doing the job without adding the needed flexibility.

Any help would be appreciated. I will try to find solution as well.
Cheers

PS: i attache the modified 'download_query_genbank.pl'
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From dimitark at bii.a-star.edu.sg  Mon Nov 29 02:17:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 15:17:50 +0800
Subject: [Bioperl-l] about genpept and genbank
Message-ID: <4CF3539E.8030002@bii.a-star.edu.sg>

hi guys,
i dug up a bit more and found a solution. i think the problem is that in 
'download_query_genbank.pl' there is the 'format' option which only is 
responsible for the format of the output file to which seqs are 
downloaded. While i need 'ret_type' format option according to NCBI 
Eutils. So now i found that i can use GenBank.pm for all DBs in NCBI. I 
restored the GenPept as it was in original but i do not use it, its more 
tricky than GenBank.pm. Now modified 'download_query_genbank.pl' to use 
only GenBank and added one more option 'retformat' which can be set 
according to NCBI 'rettype'. Also added a simple progress bar to follow 
the download. Unfortunately it is working only if im downloading genbank 
data(Bio::SeqIO::genbank) when i download fasta(Bio::SeqIO::fasta) i 
cant use it. Seems that the fasta stream is a big chunk or somewhere the 
flush is set to zero. I dont know yet, still trying to figgure that out.

The modified script is attached.

Cheers
Dimitar


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From lsbrath at gmail.com  Mon Nov 29 16:22:09 2010
From: lsbrath at gmail.com (Mgavi Brathwaite)
Date: Mon, 29 Nov 2010 16:22:09 -0500
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
Message-ID: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>

Hello,

When I run
Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
package but can't figure out what the deal is. Any suggestions.

LomSpace

On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Only if the output appends to that file (I don't recall personally, so it's
> worth a try).
>
> chris
>
> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>
> > Wouldn't using a single filename be the way to go?
> >> my $filename = "blast_ressults.out";
> >>           $factory->save_output($filename);
> > Florent
> >
> >
> > On 09/11/10 19:05, njauxiongjie wrote:
> >> Hi,
> >>
> >> I have used the scripts list in section of "SYNOPSIS" in th webpage
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
> .
> >>
> >> there are two line of the code like below:
> >> my $filename = $result->query_name()."\.out";
> >>           $factory->save_output($filename);
> >> this saved the blast result in separated files by the query name.
> >>
> >> my question is: how can i save the blast results of all querys in one
> file?
> >>
> >>
> >>
> >> _______________________________________________
> >> 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 cjfields at illinois.edu  Mon Nov 29 16:40:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 15:40:08 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
	<AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
Message-ID: <EE86D059-1DAF-478B-9610-0821D6D239E7@illinois.edu>

You haven't installed BioPerl (you need more than Bio::Tools::Run::RemoteBlast).  Please see bioperl.org for installation instructions.

chris

On Nov 29, 2010, at 3:22 PM, Mgavi Brathwaite wrote:

> Hello,
> 
> When I run
> Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
> Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
> package but can't figure out what the deal is. Any suggestions.
> 
> LomSpace
> 
> On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Only if the output appends to that file (I don't recall personally, so it's
>> worth a try).
>> 
>> chris
>> 
>> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>> 
>>> Wouldn't using a single filename be the way to go?
>>>> my $filename = "blast_ressults.out";
>>>>          $factory->save_output($filename);
>>> Florent
>>> 
>>> 
>>> On 09/11/10 19:05, njauxiongjie wrote:
>>>> Hi,
>>>> 
>>>> I have used the scripts list in section of "SYNOPSIS" in th webpage
>> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
>> .
>>>> 
>>>> there are two line of the code like below:
>>>> my $filename = $result->query_name()."\.out";
>>>>          $factory->save_output($filename);
>>>> this saved the blast result in separated files by the query name.
>>>> 
>>>> my question is: how can i save the blast results of all querys in one
>> file?
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason at bioperl.org  Mon Nov 29 21:19:56 2010
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 29 Nov 2010 18:19:56 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45F4C.7050102@bioperl.org>

Dimitar -

In terms of your question - a GenBank db query previously (ie 4-5 years 
ago when this was written) WOULD NOT return a sequence if a GenPept ID 
was specified so we had to have a separate module for GenBank and 
GenPept db querying since there was a different set of parameters - I 
think that changed so that most of the queries can run through GenBank

I see that must have been improved at NCBI.  For the record if you want 
the full GenPept record with features and annotations you just request a 
different db, in this case 'gb' for genbank instead of the fasta source
As in: http://gist.github.com/721012

But maybe you already figured it out?

-jason
Chris Fields wrote, On 11/29/10 6:39 AM:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org


From dimitark at bii.a-star.edu.sg  Mon Nov 29 21:54:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 10:54:50 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF45F4C.7050102@bioperl.org>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org>
Message-ID: <4CF4677A.5010604@bii.a-star.edu.sg>

On 11/30/2010 10:19 AM, Jason Stajich wrote:
> Dimitar -
>
> In terms of your question - a GenBank db query previously (ie 4-5 
> years ago when this was written) WOULD NOT return a sequence if a 
> GenPept ID was specified so we had to have a separate module for 
> GenBank and GenPept db querying since there was a different set of 
> parameters - I think that changed so that most of the queries can run 
> through GenBank
>
> I see that must have been improved at NCBI.  For the record if you 
> want the full GenPept record with features and annotations you just 
> request a different db, in this case 'gb' for genbank instead of the 
> fasta source
> As in: http://gist.github.com/721012
>
> But maybe you already figured it out?
>
> -jason
> Chris Fields wrote, On 11/29/10 6:39 AM:
>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>
>>> Hi again,
>>> it seems that when i download (with 'download_query_genbank.pl') the 
>>> whole proteome from NCBI in fasta format it is first being 
>>> downloaded and from it is being created some kind of 
>>> SeqFastaSpeedFactory and after that from it is being copied to the 
>>> output file. But i want to download and write to output file one by 
>>> one so i can see the download progress(which is working for genbank 
>>> data).
>>>
>>> Its frustrating :)
>>>
>>> Any ideas where to look for solution
>>> Cheers
>>> Dimitar
>>
>> You can't do this with the default script, but you can use a modified 
>> version and, where you are retrieving a sequence stream, in the last 
>> four lines:
>>
>> my $stream = $dbh->get_Stream_by_query($query);
>> while( my $seq = $stream->next_seq ) {
>>     $out->write_seq($seq);
>> }
>>
>> insert an iterator in the loop that indicates progress.  Realize the 
>> sequence data is processed through Bio::SeqIO, so it won't be exactly 
>> the same as what is retrieved from GenBank, but it should be very close.
>>
>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a 
>> bit more complicated.
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Thank you Jason,
i figured that out yes :)
I know am wandering how to get the GI list so i can download by ID or 
ACC and not by query when i download fasta. I have the simple code:
-------------
my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
                                        -query=>$query_str);

my $count=$query->count;
my @ids=$query->ids; <------- error msg here
------------
but i get an error msg:

MSG: Id list has been truncated even after maxids requested.

How can i get the ID/ACC? Any idea?

Thank you
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg


From dimitark at bii.a-star.edu.sg  Mon Nov 29 20:39:07 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:39:07 +0800
Subject: [Bioperl-l] Bioperl-l Digest, Vol 91, Issue 20
In-Reply-To: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
References: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
Message-ID: <4CF455BB.4060608@bii.a-star.edu.sg>

On 11/30/2010 01:00 AM, 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.  genbank (Dimitar Kenanov)
>     2. Re:  genbank (Chris Fields)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Nov 2010 17:35:26 +0800
> From: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Subject: [Bioperl-l] genbank
> To: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<4CF373DE.4070902 at bii.a-star.edu.sg>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the
> whole proteome from NCBI in fasta format it is first being downloaded
> and from it is being created some kind of SeqFastaSpeedFactory and after
> that from it is being copied to the output file. But i want to download
> and write to output file one by one so i can see the download
> progress(which is working for genbank data).
>
> Its frustrating :)
>
> Any ideas where to look for solution
> Cheers
> Dimitar
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 29 Nov 2010 08:39:16 -0600
> From: Chris Fields<cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] genbank
> To: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Cc: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<F3C80557-52DE-4D60-9E72-0660031D8F46 at illinois.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>
>
> ------------------------------
>
> _______________________________________________
> 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 91, Issue 20
> *****************************************
>
>    

Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

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From dimitark at bii.a-star.edu.sg  Mon Nov 29 20:50:42 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:50:42 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45872.1060405@bii.a-star.edu.sg>

On 11/29/2010 10:39 PM, Chris Fields wrote:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>    
Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

-------------- next part --------------
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Name: download_query_genbank.pl
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20101130/f288933b/attachment.pl>

From cjfields at illinois.edu  Mon Nov 29 22:42:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 21:42:14 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4677A.5010604@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
Message-ID: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>

On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:

> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>> Dimitar -
>> 
>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>> 
>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>> As in: http://gist.github.com/721012
>> 
>> But maybe you already figured it out?
>> 
>> -jason
>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>> 
>>>> Hi again,
>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>> 
>>>> Its frustrating :)
>>>> 
>>>> Any ideas where to look for solution
>>>> Cheers
>>>> Dimitar
>>> 
>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>> 
>>> my $stream = $dbh->get_Stream_by_query($query);
>>> while( my $seq = $stream->next_seq ) {
>>>    $out->write_seq($seq);
>>> }
>>> 
>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>> 
>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>> 
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> Thank you Jason,
> i figured that out yes :)
> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
> -------------
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>                                       -query=>$query_str);
> 
> my $count=$query->count;
> my @ids=$query->ids; <------- error msg here
> ------------
> but i get an error msg:
> 
> MSG: Id list has been truncated even after maxids requested.
> 
> How can i get the ID/ACC? Any idea?
> 
> Thank you
> Dimitar

Dimitar, 

You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:

----------------------------------------------
use Bio::DB::Query::GenBank;

my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-maxids => 40000,
                                       -db=>'protein',
                                      -query=>$query_str);

my $count=$query->count;
say "Count: $count";

my @ids=$query->ids;
say scalar(@ids); # equal to $count
----------------------------------------------

Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.

chris





From dimitark at bii.a-star.edu.sg  Tue Nov 30 04:04:30 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 17:04:30 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
Message-ID: <4CF4BE1E.6090100@bii.a-star.edu.sg>

On 11/30/2010 11:42 AM, Chris Fields wrote:
> On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:
>
>    
>> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>>      
>>> Dimitar -
>>>
>>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>>>
>>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>>> As in: http://gist.github.com/721012
>>>
>>> But maybe you already figured it out?
>>>
>>> -jason
>>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>>        
>>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>>>
>>>>          
>>>>> Hi again,
>>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>>>
>>>>> Its frustrating :)
>>>>>
>>>>> Any ideas where to look for solution
>>>>> Cheers
>>>>> Dimitar
>>>>>            
>>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>>>
>>>> my $stream = $dbh->get_Stream_by_query($query);
>>>> while( my $seq = $stream->next_seq ) {
>>>>     $out->write_seq($seq);
>>>> }
>>>>
>>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>>>
>>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>>>
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>          
>>>        
>> Thank you Jason,
>> i figured that out yes :)
>> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
>> -------------
>> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
>> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>>                                        -query=>$query_str);
>>
>> my $count=$query->count;
>> my @ids=$query->ids;<------- error msg here
>> ------------
>> but i get an error msg:
>>
>> MSG: Id list has been truncated even after maxids requested.
>>
>> How can i get the ID/ACC? Any idea?
>>
>> Thank you
>> Dimitar
>>      
> Dimitar,
>
> You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:
>
> ----------------------------------------------
> use Bio::DB::Query::GenBank;
>
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-maxids =>  40000,
>                                         -db=>'protein',
>                                        -query=>$query_str);
>
> my $count=$query->count;
> say "Count: $count";
>
> my @ids=$query->ids;
> say scalar(@ids); # equal to $count
> ----------------------------------------------
>
> Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.
>
> chris
>
>
>
>    
Hi again,
i managed to solve my problem. It may be dirty but it works the way i 
want :)
I reworked the 'download_query_genbank.pl' (attached). Now i can get the 
seqs in full fasta for proteomes and genomes and the genpept report 
files for the proteomes.
For DB handle i only use GenPept now cos it gives me stream which i can 
track with term::progressbar.

For the output i use 2 cases:
-----------------
while( my $seq = $stream->next_seq ) {
     #DIMITAR
     my($gi,$locus,$refnum,$desc,$seqstr);
     if($retformat eq 'fasta'){ <-------------------------| for the 
fasta as i want it
         check_progress($prgs,$seqnum,$count);
         $locus=$seq->display_id;
         $refnum=$seq->accession_number;
         $gi=$seq->primary_id;
         $desc=$seq->desc;
         $desc=~s/\.$//;
         $seqstr=$seq->seq;
         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
     }else{
         check_progress($prgs,$seqnum,$count);
         $out->write_seq($seq); <--------------------------| for the 
genbank reports
     }
     $seqnum++;
     #DIMITAR

#    $out->write_seq($seq);#original

}
------------------

Thank you for your help and time.

Cheers
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

-------------- next part --------------
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From jason at bioperl.org  Tue Nov 30 12:06:08 2010
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Nov 2010 09:06:08 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4BE1E.6090100@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
	<4CF4BE1E.6090100@bii.a-star.edu.sg>
Message-ID: <4CF52F00.5000803@bioperl.org>

great - the whole point of the scripts are as examples really, not that 
you need to send patches back to show everything that you modified, but 
that you modify to use modules and code to do whatever special thing you 
want. The hope is that the modules are flexible enough that you can 
write the script to accomplish your goal.

BTW - the one thing you can't recover from the GBK version of the file 
is the source of the accession number -- you have hardcoded in 'ref' but 
it can be 'gb', 'emb', 'sp' etc this field isn't part of the genbank 
record unfortunately -- one can come up with a pattern based on 
knowledge of accession number formats but I don't know that anyone has 
really been that worried about that sort of thing to try and write 
something for it.

>>
> Hi again,
> i managed to solve my problem. It may be dirty but it works the way i 
> want :)
> I reworked the 'download_query_genbank.pl' (attached). Now i can get 
> the seqs in full fasta for proteomes and genomes and the genpept 
> report files for the proteomes.
> For DB handle i only use GenPept now cos it gives me stream which i 
> can track with term::progressbar.
>
> For the output i use 2 cases:
> -----------------
> while( my $seq = $stream->next_seq ) {
>     #DIMITAR
>     my($gi,$locus,$refnum,$desc,$seqstr);
>     if($retformat eq 'fasta'){ <-------------------------| for the 
> fasta as i want it
>         check_progress($prgs,$seqnum,$count);
>         $locus=$seq->display_id;
>         $refnum=$seq->accession_number;
>         $gi=$seq->primary_id;
>         $desc=$seq->desc;
>         $desc=~s/\.$//;
>         $seqstr=$seq->seq;
>         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
>     }else{
>         check_progress($prgs,$seqnum,$count);
>         $out->write_seq($seq); <--------------------------| for the 
> genbank reports
>     }
>     $seqnum++;
>     #DIMITAR
>
> #    $out->write_seq($seq);#original
>
> }
> ------------------
>
> Thank you for your help and time.
>
> Cheers
> Dimitar
>

-- 
Jason Stajich
jason at bioperl.org


From chiragmatkarbioinfo at gmail.com  Mon Nov  1 02:58:55 2010
From: chiragmatkarbioinfo at gmail.com (chirag matkar)
Date: Mon, 1 Nov 2010 13:58:55 +0700
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
Message-ID: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar


From Russell.Smithies at agresearch.co.nz  Tue Nov  2 22:11:36 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Nov 2010 15:11:36 +1300
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313A9B7D7C@exchsth.agresearch.co.nz>

Seems a bit like overkill, what's wrong with wget?

wget -i <list_of_urls.txt>

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
Sent: Monday, 1 November 2010 7:59 p.m.
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to download PDB files using Bioperl script

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar
_______________________________________________
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 miguel.pignatelli at uv.es  Wed Nov  3 05:42:49 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 10:42:49 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4C8606FA.3000509@fmi.ch>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch>
Message-ID: <4CD12E99.7080701@uv.es>

Hi all,

I have written a couple of modules that overlap certain functionality 
with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
certain constraints in the environment I had to run it (GRID) made 
impossible to use a bioperl based solution.


The main features of these modules are:

+ No dependencies of non-standard Perl modules
+ NCBI and RDP based taxonomies supported
+ Very fast and low memory footprint -- orders of magnitude faster than 
Bioperl modules (for the tasks they are designed for --).

Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in 
completeness or integration with other tools (e.g. rest of bioperl suit) 
but they are handy for mapping very large datasets (for example blast 
results) with the NCBI or RDP Taxonomy.

The modules are:

Taxonomy::Base -- Finds ancestors, ranks, converts between
                   names, ranks and IDs, etc...

Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file

Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
                   (nodes.dmp and names.dmp)
                   (Similar to Bio::DB::Taxonomy::flatfile)

Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
                             NCBI GIs to Taxids.
                             Uses a binary lookup table.

These modules are being used by several groups now -- mainly working 
with large metagenomics datasets -- and I am considering uploading them 
to CPAN, but I am not clear on where these modules should be placed there.

How do you think I should name these modules? (e.g. where these modules 
should live in CPAN?) Their natural place could be under 
Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
convenient) without being part of Bioperl? Any other suggestions?

Thank you very much in advance,

M;

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


From gabbyteku at gmail.com  Wed Nov  3 07:53:42 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Wed, 3 Nov 2010 13:53:42 +0200
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
Message-ID: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>

I can't get my esearch to work. It's as follows:

my $eut_obj = Bio::DB::EUtilities->new(   -eutil      => 'esearch',
                                                  -email      => '
myemail at gmail.com',
                                                  -term       =>
'$genename[SYMB] AND homo_sapiens[ORGN]',
                                                  -db         => 'geo',
                                                  -usehistory => 'y'
                                              );

When I run this using a gene symbol, it works fine.
But then when I run it as it is with a gene's symbol changed to
$genename(stores the gene's symbol/name), it fails.
How can this be fixed?

Thanks


From miguel.pignatelli at uv.es  Wed Nov  3 09:51:18 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 14:51:18 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>
Message-ID: <4CD168D6.8030100@uv.es>

Hi all,

I have seen in the Nextgen section of the bioperl wiki 
(http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in 
the wish list. I have some code written for parsing SFF files that I can 
refactor and contribute with it.

Does anyone already took this?

Best regards,

M;



From biopython at maubp.freeserve.co.uk  Wed Nov  3 10:28:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 3 Nov 2010 14:28:56 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <AANLkTikAAz5FP3kiN0U6dtnvpgWAHtLu5DoEBcm_yzVD@mail.gmail.com>

On 2010/11/3 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Hi all,
>
> I have seen in the Nextgen section of the bioperl wiki
> (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the
> wish list. I have some code written for parsing SFF files that I can
> refactor and contribute with it.
>
> Does anyone already took this?
>
> Best regards,
>
> M;

Hi,

This sounds like a good thing for BioPerl.

If you hook this up into Bio::SeqIO then for consistency with
Biopython for the format name note we use "sff" as the full
reads, and "sff-trim" for the reads with the quality trimming
applied. If BioPerl has some built in way to hold a trimmed
sequence (with the head/tail still accessible) then this may
not be a good solution.

Peter


From scott at scottcain.net  Wed Nov  3 10:59:12 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 10:59:12 -0400
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
In-Reply-To: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
References: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
Message-ID: <AANLkTi=VgyrfZPPt+--pVJxfgh9QRsh_OLpsBq79F8z1@mail.gmail.com>

Hi Gabriel,

It looks to me like you've got a few things going wrong.  First, you
are using single quotes for the right hand side of the -term value.
In perl, single quotes are non-interpolating, which means variables
won't be substituted in.  However, if you switch to double quotes,
you'll still have a problem, because this:

  $genename[SYMB]

looks like you are trying to access an element of an array called
genename with a constant called SYMB, which of course you aren't, so
the perl interpreter will die with that.  You can rewrite that section
like this:

  $genename . '[SYMB] AND homo_sapiens[ORGN]'

so that the variable interpolation is moved out of the single quotes.

Scott




On Wed, Nov 3, 2010 at 7:53 AM, gabriel teku <gabbyteku at gmail.com> wrote:
> I can't get my esearch to work. It's as follows:
>
> my $eut_obj = Bio::DB::EUtilities->new( ? -eutil ? ? ?=> 'esearch',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-email ? ? ?=> '
> myemail at gmail.com',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-term ? ? ? =>
> '$genename[SYMB] AND homo_sapiens[ORGN]',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-db ? ? ? ? => 'geo',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-usehistory => 'y'
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> When I run this using a gene symbol, it works fine.
> But then when I run it as it is with a gene's symbol changed to
> $genename(stores the gene's symbol/name), it fails.
> How can this be fixed?
>
> Thanks
> _______________________________________________
> 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 cseligman at earthlink.net  Wed Nov  3 12:07:05 2010
From: cseligman at earthlink.net (Chet Seligman)
Date: Wed, 3 Nov 2010 09:07:05 -0700
Subject: [Bioperl-l] BioPerl installation was incomplete
Message-ID: <001001cb7b71$294f12c0$7bed3840$@earthlink.net>

My perl is ActiveState 5.10.1

I installed with PPM using the following repositories:

BioPerl-Regular Releases

BioPerl-Release Candidates

Kobes

Bribes

Trouchelle

 

I got the following warnings:

Can't find any package that provides DB_File:: for Bundle-BioPerl-Core

WARNING: Can't find any package that provides IPC::Run for GraphViz

WARNING: Can't find any package that provides Apache:: for SOAP-Lite

 

I do have DB_File installed but do not have:

IPC::Run or,

Apache:: for SOAP-Lite

 

I did try to install SOAP-Lite according to the instructions in the Wiki but
no luck.

In PPM-edit repositories I saw that Kobes, Bribes & Trouchelle all showed
"0"

So how do I get SOAP-Lite, Apache and IPC::Run?

 

Chet Seligman



From cjfields at illinois.edu  Wed Nov  3 13:18:38 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 12:18:38 -0500
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>

Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  

I suggest, though, for long-term maintenance you could be added as a collaborator.  

chris

On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
> 
> Does anyone already took this?
> 
> Best regards,
> 
> M;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hanbobio at 126.com  Tue Nov  2 01:29:50 2010
From: hanbobio at 126.com (hanbobio)
Date: Tue, 2 Nov 2010 13:29:50 +0800 (CST)
Subject: [Bioperl-l] bioperl modules
Message-ID: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>

Hi, all.
 I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:

liaoy at linux:~/nd-hn> perl nd-hn.pl

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.

BEGIN failed--compilation aborted at nd-hn.pl line 26.
 The detail of this script in two ways: the attached file and the following script.
Would you be kindly to test my script and give me some modification or suggestion?
 I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
Thank you very much for your advice.
 
Best regards
Yusheng Liao 2010-11-02
 
# retrive sequence from Genbank
use strict;
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;
open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
my $query = Bio::DB::Query::GenBank->new
    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
   -db      => 'nucleotide');
my $seqio = $gb->get_Stream_by_query($query);
my $i=0;
while( defined (my $seq = $seqio->next_seq )) {
$seqout->write_seq($seq);
$i++;
print ".";
}
print "$i \n";
# run multi sequence alignment
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::SimpleAlign;
use Bio::AlignIO::clustalw;
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $ktuple = 3;
$factory->ktuple($ktuple); 
my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
my $aln = $factory->align($inputfilename);
my $alignout->write_aln(my $aln);

my $line;
my @array=('A','C','G','T','-');
my @arrayX=('a','c','g','t','-');
my @arrayA;
my @arrayB;
my ($i,$j,$k);
my (@a, at b);
my %hash;
open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
while($line=<FILE>){
      chomp;
      if($line=~ /CLUSTAL/){
            next;
      }elsif($line=~ /^[A-Za-z0-9]/){
            @a=split /\s+/,$line;
            if(defined($hash{$a[0]})){
                  push @{$hash{$a[0]}}, $line;
            }else{
                  ${$hash{$a[0]}}[0]=$line;
                  push @b,$a[0];
            }
       }
}
for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
      for(my $l=0;$l<=$#b;$l++){
            print OUT ${$hash{$b[$l]}}[$k];
            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
            @arrayA=split //,$seq;
            for($i=0;$i<=$#arrayA;$i++){
                  if($arrayA[$i] =~ /A/i){
                        $arrayB[0][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /C/i){
                        $arrayB[1][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /G/i){
                        $arrayB[2][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /T/i){
                        $arrayB[3][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\./i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\-/i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
            }
       }
       for($j=0;$j<=$#arrayA;$j++){
              my $large=0;my $pos=0;
              for($i=0;$i<=4;$i++){
                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
                    if($arrayB[$i][$j]>$large){
                          $large=$arrayB[$i][$j];
                          $pos=$i;
                    }
              }
                    if($large>0.5){
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]=$array[$pos];
                    }else{
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]='N';
                    }
       }
       for($i=0;$i<=5;$i++){
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                    if($arrayB[$i][$j]>0){
                           printf OUT "%.2f\t",$arrayB[$i][$j];
                    }else{
                           print OUT "0\t";
                    }
              }
              print OUT "\n";
        }
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUT "$arrayB[6][$j]\t";
              }
              print OUT "\n";
              for($j=0;$j<=15;$j++){
                    print OUTA " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUTA "$arrayB[6][$j]";
              }
              print OUTA "\n";
        @arrayB=undef;
}
-------------- next part --------------
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From daniel.standage at gmail.com  Wed Nov  3 14:42:07 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 13:42:07 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
Message-ID: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>

Hi

I've got a simple script that is filtering some GFF3 data. The
Bio::Tools::GFF class has methods for reading and writing features and
reading regions (segments), but I cannot find a method for writing regions.
It's not hard to just print out the sequence-region line from the
LocatableSeq object, but then these lines are printed out before the
gff-version line (which is a no-no). Any suggestions about how to handle
this?

Thanks.

-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From scott at scottcain.net  Wed Nov  3 16:09:45 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:09:45 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
Message-ID: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>

Hi Daniel,

Why do you need the sequence-region line?  It is mostly just
informational.  If you want to define the reference sequence for the
features in the GFF file, I would suggest printing out a full GFF line
for the reference sequence instead anyway.  That way, it can have all
the information that a GFF line can encode, like a source and type, as
well as information in the ninth column.

That said, Bio::Tools::GFF probably does lack that method.  The code
in it is probably a little outdated.

Scott


On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> Hi
>
> I've got a simple script that is filtering some GFF3 data. The
> Bio::Tools::GFF class has methods for reading and writing features and
> reading regions (segments), but I cannot find a method for writing regions.
> It's not hard to just print out the sequence-region line from the
> LocatableSeq object, but then these lines are printed out before the
> gff-version line (which is a no-no). Any suggestions about how to handle
> this?
>
> Thanks.
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> 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 scott at scottcain.net  Wed Nov  3 16:19:07 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:19:07 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
Message-ID: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>

Ah, I see.  Well, you should complain to the authors that
sequence-region isn't a required directive (though if you made that
complaint to me, I'd say "well, it is for this tool" :-)

Of course, you could also use Bio::Graphics or GBrowse to do the
drawing, then I could do more to help. :-)

Scott


On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I'm using a tool called AnnotationSketch (part of the GenomeTools package)
> to create graphics from my GFF3 files. It complains when sequence-region
> lines are not included, even when the reference is printed as a feature.
> That's what got me interested in the problem in the first place.
>
> Thanks for the info, I'll figure something out.
>
> Daniel
>
> On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> Why do you need the sequence-region line? ?It is mostly just
>> informational. ?If you want to define the reference sequence for the
>> features in the GFF file, I would suggest printing out a full GFF line
>> for the reference sequence instead anyway. ?That way, it can have all
>> the information that a GFF line can encode, like a source and type, as
>> well as information in the ninth column.
>>
>> That said, Bio::Tools::GFF probably does lack that method. ?The code
>> in it is probably a little outdated.
>>
>> Scott
>>
>>
>> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > Hi
>> >
>> > I've got a simple script that is filtering some GFF3 data. The
>> > Bio::Tools::GFF class has methods for reading and writing features and
>> > reading regions (segments), but I cannot find a method for writing
>> > regions.
>> > It's not hard to just print out the sequence-region line from the
>> > LocatableSeq object, but then these lines are printed out before the
>> > gff-version line (which is a no-no). Any suggestions about how to handle
>> > this?
>> >
>> > Thanks.
>> >
>> > --
>> > Daniel S. Standage
>> > Graduate Research Assistant
>> > Bioinformatics and Computational Biology Program
>> > Iowa State University
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



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



From daniel.standage at gmail.com  Wed Nov  3 16:14:02 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:14:02 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
Message-ID: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>

I'm using a tool called AnnotationSketch (part of the GenomeTools package)
to create graphics from my GFF3 files. It complains when sequence-region
lines are not included, even when the reference is printed as a feature.
That's what got me interested in the problem in the first place.

Thanks for the info, I'll figure something out.

Daniel

On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Daniel,
>
> Why do you need the sequence-region line?  It is mostly just
> informational.  If you want to define the reference sequence for the
> features in the GFF file, I would suggest printing out a full GFF line
> for the reference sequence instead anyway.  That way, it can have all
> the information that a GFF line can encode, like a source and type, as
> well as information in the ninth column.
>
> That said, Bio::Tools::GFF probably does lack that method.  The code
> in it is probably a little outdated.
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > Hi
> >
> > I've got a simple script that is filtering some GFF3 data. The
> > Bio::Tools::GFF class has methods for reading and writing features and
> > reading regions (segments), but I cannot find a method for writing
> regions.
> > It's not hard to just print out the sequence-region line from the
> > LocatableSeq object, but then these lines are printed out before the
> > gff-version line (which is a no-no). Any suggestions about how to handle
> > this?
> >
> > Thanks.
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > 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
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From daniel.standage at gmail.com  Wed Nov  3 16:29:29 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:29:29 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
	<AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
Message-ID: <AANLkTikv-N-45cgapmZ_yHqHLFtNroBm9KU+ehXn=qad@mail.gmail.com>

Yeah, I guess it's not a show stopper, since it still generates the graphics
fine. The output that clutters the terminal is still annoying, but I can
live with that. Thanks!

Daniel

On Wed, Nov 3, 2010 at 3:19 PM, Scott Cain <scott at scottcain.net> wrote:

> Ah, I see.  Well, you should complain to the authors that
> sequence-region isn't a required directive (though if you made that
> complaint to me, I'd say "well, it is for this tool" :-)
>
> Of course, you could also use Bio::Graphics or GBrowse to do the
> drawing, then I could do more to help. :-)
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > I'm using a tool called AnnotationSketch (part of the GenomeTools
> package)
> > to create graphics from my GFF3 files. It complains when sequence-region
> > lines are not included, even when the reference is printed as a feature.
> > That's what got me interested in the problem in the first place.
> >
> > Thanks for the info, I'll figure something out.
> >
> > Daniel
> >
> > On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Daniel,
> >>
> >> Why do you need the sequence-region line?  It is mostly just
> >> informational.  If you want to define the reference sequence for the
> >> features in the GFF file, I would suggest printing out a full GFF line
> >> for the reference sequence instead anyway.  That way, it can have all
> >> the information that a GFF line can encode, like a source and type, as
> >> well as information in the ninth column.
> >>
> >> That said, Bio::Tools::GFF probably does lack that method.  The code
> >> in it is probably a little outdated.
> >>
> >> Scott
> >>
> >>
> >> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> >> <daniel.standage at gmail.com> wrote:
> >> > Hi
> >> >
> >> > I've got a simple script that is filtering some GFF3 data. The
> >> > Bio::Tools::GFF class has methods for reading and writing features and
> >> > reading regions (segments), but I cannot find a method for writing
> >> > regions.
> >> > It's not hard to just print out the sequence-region line from the
> >> > LocatableSeq object, but then these lines are printed out before the
> >> > gff-version line (which is a no-no). Any suggestions about how to
> handle
> >> > this?
> >> >
> >> > Thanks.
> >> >
> >> > --
> >> > Daniel S. Standage
> >> > Graduate Research Assistant
> >> > Bioinformatics and Computational Biology Program
> >> > Iowa State University
> >> > _______________________________________________
> >> > 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
> >
> >
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From cjfields at illinois.edu  Wed Nov  3 17:27:28 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 16:27:28 -0500
Subject: [Bioperl-l] bioperl modules
In-Reply-To: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
References: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
Message-ID: <2A3F6A7D-CF80-4C6D-8BE2-EEDA873BCC3D@illinois.edu>

You need to install bioperl-run to get Bio::Tools::Run::Alignment::Clustalw.

chris

On Nov 2, 2010, at 12:29 AM, hanbobio wrote:

> Hi, all.
> I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:
> 
> liaoy at linux:~/nd-hn> perl nd-hn.pl
> 
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.
> 
> BEGIN failed--compilation aborted at nd-hn.pl line 26.
> The detail of this script in two ways: the attached file and the following script.
> Would you be kindly to test my script and give me some modification or suggestion?
> I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
> Thank you very much for your advice.
> 
> Best regards
> Yusheng Liao 2010-11-02
> 
> # retrive sequence from Genbank
> use strict;
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> my $gb = new Bio::DB::GenBank;
> open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
> my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
> my $query = Bio::DB::Query::GenBank->new
>    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
>   -db      => 'nucleotide');
> my $seqio = $gb->get_Stream_by_query($query);
> my $i=0;
> while( defined (my $seq = $seqio->next_seq )) {
> $seqout->write_seq($seq);
> $i++;
> print ".";
> }
> print "$i \n";
> # run multi sequence alignment
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::SimpleAlign;
> use Bio::AlignIO::clustalw;
> my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
> my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> my $ktuple = 3;
> $factory->ktuple($ktuple); 
> my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
> my $aln = $factory->align($inputfilename);
> my $alignout->write_aln(my $aln);
> 
> my $line;
> my @array=('A','C','G','T','-');
> my @arrayX=('a','c','g','t','-');
> my @arrayA;
> my @arrayB;
> my ($i,$j,$k);
> my (@a, at b);
> my %hash;
> open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
> open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
> open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
> while($line=<FILE>){
>      chomp;
>      if($line=~ /CLUSTAL/){
>            next;
>      }elsif($line=~ /^[A-Za-z0-9]/){
>            @a=split /\s+/,$line;
>            if(defined($hash{$a[0]})){
>                  push @{$hash{$a[0]}}, $line;
>            }else{
>                  ${$hash{$a[0]}}[0]=$line;
>                  push @b,$a[0];
>            }
>       }
> }
> for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
>      for(my $l=0;$l<=$#b;$l++){
>            print OUT ${$hash{$b[$l]}}[$k];
>            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
>            @arrayA=split //,$seq;
>            for($i=0;$i<=$#arrayA;$i++){
>                  if($arrayA[$i] =~ /A/i){
>                        $arrayB[0][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /C/i){
>                        $arrayB[1][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /G/i){
>                        $arrayB[2][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /T/i){
>                        $arrayB[3][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\./i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\-/i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>            }
>       }
>       for($j=0;$j<=$#arrayA;$j++){
>              my $large=0;my $pos=0;
>              for($i=0;$i<=4;$i++){
>                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
>                    if($arrayB[$i][$j]>$large){
>                          $large=$arrayB[$i][$j];
>                          $pos=$i;
>                    }
>              }
>                    if($large>0.5){
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]=$array[$pos];
>                    }else{
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]='N';
>                    }
>       }
>       for($i=0;$i<=5;$i++){
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                    if($arrayB[$i][$j]>0){
>                           printf OUT "%.2f\t",$arrayB[$i][$j];
>                    }else{
>                           print OUT "0\t";
>                    }
>              }
>              print OUT "\n";
>        }
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUT "$arrayB[6][$j]\t";
>              }
>              print OUT "\n";
>              for($j=0;$j<=15;$j++){
>                    print OUTA " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUTA "$arrayB[6][$j]";
>              }
>              print OUTA "\n";
>        @arrayB=undef;
> }
> <Moduletest.pl.pl>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Wed Nov  3 22:34:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 21:34:30 -0500
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
Message-ID: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>

Miguel,

(Caveat: You should also ask this on the perl module-authors list, just in case: http://lists.perl.org/list/module-authors.html)

Not sure how the other devs feel, but I personally don't think the Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, for example).  It's a fairly generic top-level name.  The only worry I have is if these are too similar to current BioPerl modules; Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN related to BioPerl modules.   

Saying that, tagging them as *::Lite might be fine, as long as the documentation indicated these are not related to BioPerl.  Anyone else want to chime in?  Maybe releasing them as a top-level Taxonomy?  

chris

On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have written a couple of modules that overlap certain functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because certain constraints in the environment I had to run it (GRID) made impossible to use a bioperl based solution.
> 
> 
> The main features of these modules are:
> 
> + No dependencies of non-standard Perl modules
> + NCBI and RDP based taxonomies supported
> + Very fast and low memory footprint -- orders of magnitude faster than Bioperl modules (for the tasks they are designed for --).
> 
> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in completeness or integration with other tools (e.g. rest of bioperl suit) but they are handy for mapping very large datasets (for example blast results) with the NCBI or RDP Taxonomy.
> 
> The modules are:
> 
> Taxonomy::Base -- Finds ancestors, ranks, converts between
>                  names, ranks and IDs, etc...
> 
> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
> 
> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>                  (nodes.dmp and names.dmp)
>                  (Similar to Bio::DB::Taxonomy::flatfile)
> 
> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>                            NCBI GIs to Taxids.
>                            Uses a binary lookup table.
> 
> These modules are being used by several groups now -- mainly working with large metagenomics datasets -- and I am considering uploading them to CPAN, but I am not clear on where these modules should be placed there.
> 
> How do you think I should name these modules? (e.g. where these modules should live in CPAN?) Their natural place could be under Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and convenient) without being part of Bioperl? Any other suggestions?
> 
> Thank you very much in advance,
> 
> M;
> 
> ----------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Thu Nov  4 04:54:33 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 4 Nov 2010 09:54:33 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <4F9F218F-22EC-46B8-8BAB-82BD0956FB76@sbc.su.se>

I agree with Chris. You're welcome to put your code in the Bio:: namespace ? it's not reserved for BioPerl ? but since there are already modules with Taxonomy in their names, it would be likely to cause confusion.

So, if your modules are renamed to be sufficiently distinguishable from existing Taxonomy modules, putting them under Bio:: should be no problem.

Otherwise, I would go whatever the modules list folks recommend.

Dave



From miguel.pignatelli at uv.es  Thu Nov  4 07:13:20 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:13:20 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>
	<4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
Message-ID: <4CD29550.6030005@uv.es>

Thanks Chris,

I will get in touch again when I am able to hook a working module (I 
will check Biopython's Bio.Seq.SffIO)

M;


Chris Fields wrote:
> Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  
> 
> I suggest, though, for long-term maintenance you could be added as a collaborator.  
> 
> chris
> 
> On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:
> 
>> Hi all,
>>
>> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
>>
>> Does anyone already took this?
>>
>> Best regards,
>>
>> M;
>>
>> _______________________________________________
>> 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 biopython at maubp.freeserve.co.uk  Thu Nov  4 07:40:13 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 4 Nov 2010 11:40:13 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD29550.6030005@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
	<4CD29550.6030005@uv.es>
Message-ID: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>

2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Thanks Chris,
>
> I will get in touch again when I am able to hook a working module (I will
> check Biopython's Bio.Seq.SffIO)
>
> M;

Hi Miguel,

In case it helps, the Biopython SFF code is here - this includes embedded
documentation with test examples:

http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

We also have some test SFF files here (see the README file for details):

http://github.com/biopython/biopython/tree/master/Tests/Roche/

Peter


From pignatelli_mig at gva.es  Thu Nov  4 07:49:07 2010
From: pignatelli_mig at gva.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:49:07 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>	<4CD168D6.8030100@uv.es>	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>	<4CD29550.6030005@uv.es>
	<AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
Message-ID: <4CD29DB3.9010805@gva.es>

Thanks Peter, I have already took a look at the module. It will 
certainly help a lot. I also have some real SFF files from different 
collaborations that I can use for testing.

Let's roll up the sleeves...

M;


Peter wrote:
> 2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
>> Thanks Chris,
>>
>> I will get in touch again when I am able to hook a working module (I will
>> check Biopython's Bio.Seq.SffIO)
>>
>> M;
> 
> Hi Miguel,
> 
> In case it helps, the Biopython SFF code is here - this includes embedded
> documentation with test examples:
> 
> http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
> 
> We also have some test SFF files here (see the README file for details):
> 
> http://github.com/biopython/biopython/tree/master/Tests/Roche/
> 
> Peter


From hlapp at drycafe.net  Thu Nov  4 12:12:04 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 4 Nov 2010 12:12:04 -0400
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>

I agree - Bio:: isn't exclusive to BioPerl, but in choosing module  
name and namespace, as well as in documentation, try to minimize  
potential confusion for users.

	-hilmar
On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:

> Miguel,
>
> (Caveat: You should also ask this on the perl module-authors list,  
> just in case: http://lists.perl.org/list/module-authors.html)
>
> Not sure how the other devs feel, but I personally don't think the  
> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo,  
> for example).  It's a fairly generic top-level name.  The only worry  
> I have is if these are too similar to current BioPerl modules;  
> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN  
> related to BioPerl modules.
>
> Saying that, tagging them as *::Lite might be fine, as long as the  
> documentation indicated these are not related to BioPerl.  Anyone  
> else want to chime in?  Maybe releasing them as a top-level Taxonomy?
>
> chris
>
> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>
>> Hi all,
>>
>> I have written a couple of modules that overlap certain  
>> functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write  
>> them because certain constraints in the environment I had to run it  
>> (GRID) made impossible to use a bioperl based solution.
>>
>>
>> The main features of these modules are:
>>
>> + No dependencies of non-standard Perl modules
>> + NCBI and RDP based taxonomies supported
>> + Very fast and low memory footprint -- orders of magnitude faster  
>> than Bioperl modules (for the tasks they are designed for --).
>>
>> Of course, they do not compete with Bio::DB::Taxonomy and  
>> Bio::Taxon in completeness or integration with other tools (e.g.  
>> rest of bioperl suit) but they are handy for mapping very large  
>> datasets (for example blast results) with the NCBI or RDP Taxonomy.
>>
>> The modules are:
>>
>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>                 names, ranks and IDs, etc...
>>
>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>
>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>                 (nodes.dmp and names.dmp)
>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>
>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>                           NCBI GIs to Taxids.
>>                           Uses a binary lookup table.
>>
>> These modules are being used by several groups now -- mainly  
>> working with large metagenomics datasets -- and I am considering  
>> uploading them to CPAN, but I am not clear on where these modules  
>> should be placed there.
>>
>> How do you think I should name these modules? (e.g. where these  
>> modules should live in CPAN?) Their natural place could be under  
>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite /  
>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and  
>> convenient) without being part of Bioperl? Any other suggestions?
>>
>> Thank you very much in advance,
>>
>> M;
>>
>> ----------------------------------------------------
>> _______________________________________________
>> 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

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From kellert at ohsu.edu  Thu Nov  4 20:45:25 2010
From: kellert at ohsu.edu (Tom Keller)
Date: Thu, 4 Nov 2010 17:45:25 -0700
Subject: [Bioperl-l] parsing PubMed retrievals
Message-ID: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>

Greetings,
I'm getting the following error from the bioplerl 1.6.1 example

$ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.


Any suggestions for getting this to work?

thanks,


Tom
MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
503-494-2442
kellert at ohsu.edu<mailto:kellert at ohsu.edu>
Office: 6588 RJH (CROET/BasicScience)








From cjfields at illinois.edu  Fri Nov  5 00:28:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 4 Nov 2010 23:28:01 -0500
Subject: [Bioperl-l] parsing PubMed retrievals
In-Reply-To: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <EA90A6B2-7D87-4CC0-B4FB-D8A00FD5C77D@illinois.edu>

It seems that in some cases a webenv/querykey are not returned.  I have committed a fix to github for this which seems to fix the problem from our end.

https://github.com/bioperl/bioperl-live/commit/7c64e8410d291dbd7097b2cd8fc948d95063d153

chris

On Nov 4, 2010, at 7:45 PM, Tom Keller wrote:

> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> 
> Tom
> MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert at ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From miguel.pignatelli at uv.es  Fri Nov  5 05:31:46 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Fri, 05 Nov 2010 10:31:46 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
Message-ID: <4CD3CF02.9010608@uv.es>

Hi all,

In the perl module-authors list I have been suggested two nice alternatives:

Bio::Lite::Taxonomy::*
BioX::Taxonomy::*

If the devs don't have any objection/preference I will follow the first one.

Regards,

M;


Hilmar Lapp wrote:
> I agree - Bio:: isn't exclusive to BioPerl, but in choosing module name 
> and namespace, as well as in documentation, try to minimize potential 
> confusion for users.
> 
>     -hilmar
> On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:
> 
>> Miguel,
>>
>> (Caveat: You should also ask this on the perl module-authors list, 
>> just in case: http://lists.perl.org/list/module-authors.html)
>>
>> Not sure how the other devs feel, but I personally don't think the 
>> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, 
>> for example).  It's a fairly generic top-level name.  The only worry I 
>> have is if these are too similar to current BioPerl modules; 
>> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN 
>> related to BioPerl modules.
>>
>> Saying that, tagging them as *::Lite might be fine, as long as the 
>> documentation indicated these are not related to BioPerl.  Anyone else 
>> want to chime in?  Maybe releasing them as a top-level Taxonomy?
>>
>> chris
>>
>> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>>
>>> Hi all,
>>>
>>> I have written a couple of modules that overlap certain functionality 
>>> with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
>>> certain constraints in the environment I had to run it (GRID) made 
>>> impossible to use a bioperl based solution.
>>>
>>>
>>> The main features of these modules are:
>>>
>>> + No dependencies of non-standard Perl modules
>>> + NCBI and RDP based taxonomies supported
>>> + Very fast and low memory footprint -- orders of magnitude faster 
>>> than Bioperl modules (for the tasks they are designed for --).
>>>
>>> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon 
>>> in completeness or integration with other tools (e.g. rest of bioperl 
>>> suit) but they are handy for mapping very large datasets (for example 
>>> blast results) with the NCBI or RDP Taxonomy.
>>>
>>> The modules are:
>>>
>>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>>                 names, ranks and IDs, etc...
>>>
>>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>>
>>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>>                 (nodes.dmp and names.dmp)
>>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>>
>>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>>                           NCBI GIs to Taxids.
>>>                           Uses a binary lookup table.
>>>
>>> These modules are being used by several groups now -- mainly working 
>>> with large metagenomics datasets -- and I am considering uploading 
>>> them to CPAN, but I am not clear on where these modules should be 
>>> placed there.
>>>
>>> How do you think I should name these modules? (e.g. where these 
>>> modules should live in CPAN?) Their natural place could be under 
>>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
>>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
>>> convenient) without being part of Bioperl? Any other suggestions?
>>>
>>> Thank you very much in advance,
>>>
>>> M;
>>>
>>> ----------------------------------------------------
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From David.Messina at sbc.su.se  Fri Nov  5 06:36:38 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 11:36:38 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD3CF02.9010608@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
	<4CD3CF02.9010608@uv.es>
Message-ID: <5E0858F2-3957-46E1-BCD7-0F75FF44DE7D@sbc.su.se>

> Bio::Lite::Taxonomy::*
> BioX::Taxonomy::*

Either works for me.

Thanks for asking, Miguel, and I'm looking forward to checking them out!

Dave


From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 07:33:44 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 12:33:44 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
Message-ID: <4CD3EB98.3050508@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi folks,

https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser
contains my attempt to get a hmmer parser that is able to detect which
hmmer version output it's given and which parser to call in turn.

I chose to sneak in a Bio::SearchIO::hmmer class into the object
hierarchy that the hmmer2 parser (renamed to Bio::SearchIO::hmmer2) and
the hmmer3 parser subclass from.

I'm not sure if this is the best way to go, though, and I'd like to get
some feedback on the implementation.
The last six patches on
https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser are
the full changeset, the core of the change is in
https://github.com/kblin/bioperl-live/commit/2d4816f1d67880c69948b2ce529fdeb52e0d843f

Thanks in advance for your time,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From David.Messina at sbc.su.se  Fri Nov  5 08:35:32 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 13:35:32 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
Message-ID: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>

I may have missed some recent off-list discussion, but I thought we explicitly talked about *not* merging these since it will complicate future maintenance and Hmmer2 will be obsolete in the near future.


Dave




From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 08:56:23 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 13:56:23 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
Message-ID: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 13:35, Dave Messina wrote:
> I may have missed some recent off-list discussion, but I thought we
> explicitly talked about *not* merging these since it will complicate
> future maintenance and Hmmer2 will be obsolete in the near future.

Yes, that's what I thought until about last week. Then I was bitten by
the fact that Hmmer3 can't do global alignments, so you can't reliably
use Hmmer3 to extract protein domains using the domain's motif. As this
seems to be a common use case, I think we'll end up supporting hmmer2
for quite a while now.

There's currently no plans by the Hmmer authors to add globlal and
glocal (whole profile alignments against parts of the sequence)
alignments to hmmer3. They suggested to keep using hmmer2 for now.

For this reason I decided to try and merge the two parsers to a point
where users don't have to care which version of hmmer their file is.

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 10:17:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 09:17:03 -0500
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
Message-ID: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>

On Nov 5, 2010, at 7:56 AM, Kai Blin wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On 2010-11-05 13:35, Dave Messina wrote:
>> I may have missed some recent off-list discussion, but I thought we
>> explicitly talked about *not* merging these since it will complicate
>> future maintenance and Hmmer2 will be obsolete in the near future.
> 
> Yes, that's what I thought until about last week. Then I was bitten by
> the fact that Hmmer3 can't do global alignments, so you can't reliably
> use Hmmer3 to extract protein domains using the domain's motif. As this
> seems to be a common use case, I think we'll end up supporting hmmer2
> for quite a while now.
> 
> There's currently no plans by the Hmmer authors to add globlal and
> glocal (whole profile alignments against parts of the sequence)
> alignments to hmmer3. They suggested to keep using hmmer2 for now.
> 
> For this reason I decided to try and merge the two parsers to a point
> where users don't have to care which version of hmmer their file is.
> 
> Cheers,
> Kai

Makes sense to me.  We're tackling some Bio::Tree revisions next week, my guess is we can also get this added in.  I'm really keen on getting 1.6.2 out sometime soon, before things get really crazy for me this spring.

Key things to test: can specify the exact hmmer2/3 parser directly?  

   my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

Can one explicitly specify the hmmer parser variant?

   my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file => 'foo')

This will more than likely pop up.  I did something with Bio::SeqIO::fastq to allow specifying sanger/illumina/solexa variants, this would be similar in respect.

chris


From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 10:53:24 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 15:53:24 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
	<283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
Message-ID: <4CD41A64.4070104@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 15:17, Chris Fields wrote:

> Makes sense to me.  We're tackling some Bio::Tree revisions next
> week, my guess is we can also get this added in.  I'm really keen on
> getting 1.6.2 out sometime soon, before things get really crazy for
> me this spring.

I changed my mind about the hmmer parser just in time then, I guess. :)

> Key things to test: can specify the exact hmmer2/3 parser directly?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

That's how I started the development. But I just see I changed all tests
over, so I can't prove it. I've added some tests to show this is
equivalent. (907b7d0a2b93d4961f64)

> Can one explicitly specify the hmmer parser variant?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file
> => 'foo')

I didn't think about this, but that certainly seems reasonable. If
somebody specifies a format explicitly, we can short-circuit the other
detection code. I've added code and a couple of tests to support this.
See c9cd75df492dbef90fff.

Thanks for the input,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 11:06:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:06:01 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
Message-ID: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>

All,

I have a local Blat wrapper refactoring that I had to quickly write up for some local work.  Unfortunately, the original Blat wrapper in BioPerl-Run (Bio::Tools::Run::Alignment::Blat) had parameters that weren't compatible with more recent versions of Blat, and which didn't even use most passed parameters, so it was unfortunately pretty much useless in my hands (one couldn't designate whether the query/db was dna, prot, dnax, etc).

Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?  I plan on having it pass the original tests and adding a bit more.

As a small semi-'bonus', along with this I am also writing up additional code for Bio::SearchIO::psl that allows switching parsing logic to cluster distinct regional hits; basically, same query = Result, each Hit = distinct region, each set of blocks = HSP.  This is in response from some users here to making the bp_search2gff.pl script work with PSL a little better.  Should be added in over the next few weeks.

chris


From cjfields at illinois.edu  Fri Nov  5 11:43:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:43:13 -0500
Subject: [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utility GEO Database
	name change
References: <A9D8BF3D8A74DF4A925FB541C0F39D2A14C4E64EE2@NIHMLBX15.nih.gov>
Message-ID: <0831372A-B40C-4B62-B423-5BEB7B5D3543@illinois.edu>

FYI, for those GEO users out there.

-c

Begin forwarded message:

> From: <utilities-announce at ncbi.nlm.nih.gov>
> Date: November 5, 2010 10:39:27 AM CDT
> To: NLM/NCBI List utilities-announce <utilities-announce at ncbi.nlm.nih.gov>
> Subject: [Utilities-announce] NCBI E-Utility GEO Database name change
> Reply-To: utilities-announce at ncbi.nlm.nih.gov
> 
> Dear E-Utility Users,
>  
> Recently the name of the GEO Profiles database used within the E-utilities changed from 'geo' to 'geoprofiles'. While the old name (&db=geo) will still function, users are encouraged to change their requests to use the new name (db=geoprofiles). ELink users should be aware that all linknames including 'geo' will no longer function. Instead, these names should include 'geoprofiles' rather than 'geo'. For example, the linkname of links from Gene to GEO Profiles is now &linkname=gene_geoprofiles.
>  
> Thank you.
>  
> 
>  
> _______________________________________________
> Utilities-announce mailing list
> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce




From David.Messina at sbc.su.se  Fri Nov  5 12:11:41 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 17:11:41 +0100
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
Message-ID: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>

On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:

> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?


Sounds great! Go for it.


Dave




From njauxiongjie at gmail.com  Fri Nov  5 05:12:33 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Fri, 05 Nov 2010 02:12:33 -0700 (PDT)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd3ca81.123f970a.39e2.ffff8e89@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  



From alpita at uvigo.es  Fri Nov  5 11:52:58 2010
From: alpita at uvigo.es (alpita at uvigo.es)
Date: Fri, 05 Nov 2010 16:52:58 +0100
Subject: [Bioperl-l] Primer3
Message-ID: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>

Hi

I am a PhD-student working with EST sequences. I have got an input  
file for Primer3 and the program does not run. I try directly in the  
windows console and with Bioperl. I suppose the problem is with the  
syntax, because I have never used these tools, so I would appreciate  
some help.

How can I invoked my input file in primer 3? If it is easy to run it  
with BioPerl, tell me

Thank you very much


From cjfields at illinois.edu  Fri Nov  5 13:27:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 12:27:13 -0500
Subject: [Bioperl-l] Primer3
In-Reply-To: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
References: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
Message-ID: <8BBED864-BB9A-4FF7-9B09-2549D927F858@illinois.edu>

This all depends on what version of Primer3 you are using; the Primer3 tools in bioperl-live and bioperl-run do not work with primer3 v2 due to significant changes in the primer3 API.  However, I wrote up a full refactor of these tools, along with tests, here:

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

This includes both the wrapper and the parser (see the test files for examples on how to run them).  They have been renamed because of a change in the module API.  Let me know if they work for you.

chris

On Nov 5, 2010, at 10:52 AM, alpita at uvigo.es wrote:

> Hi
> 
> I am a PhD-student working with EST sequences. I have got an input file for Primer3 and the program does not run. I try directly in the windows console and with Bioperl. I suppose the problem is with the syntax, because I have never used these tools, so I would appreciate some help.
> 
> How can I invoked my input file in primer 3? If it is easy to run it with BioPerl, tell me
> 
> Thank you very much
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Fri Nov  5 16:57:56 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 15:57:56 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
	<D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
Message-ID: <374003E7-0F9F-466F-99D9-89F85F22CFF9@illinois.edu>


On Nov 5, 2010, at 11:11 AM, Dave Messina wrote:

> On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?
> 
> 
> Sounds great! Go for it.
> 
> 
> Dave

Okay, now in bioperl-run, master branch.  This passes all prior tests; I added a few more.

chris


From gabbyteku at gmail.com  Fri Nov  5 17:17:55 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Fri, 5 Nov 2010 23:17:55 +0200
Subject: [Bioperl-l] Bad request from efetch Bio::DB::EUtilities
Message-ID: <AANLkTimT2-K7cA3N1esBQSHb9Q8btUy3572y6L0rv5J=@mail.gmail.com>

Hi
I don't know what the problem is, but the efetch code snippet throws a Bad
request error,

while( my $id = <$in> ){           # $in, file contains list of uids
                chomp $id;

                my $eut_obj = Bio::DB::EUtilities->new(   -eutil      =>
'efetch',
                                                          -email      => '
myemail at gmail.com',
                                                          -db         =>
'geoprofile',
                                                          -id         =>
$id,
                                                      );

                open( my $tmpOut, '>' ,'doc' ) or die "Can't open doc: $!";

                eval{
                        $eut_obj->get_Response(-cb => sub {my ($data) = @_;
print $tmpOut $data );
                };
                .....
}

What is wrong with the request?

Thanks in advance


From cselig01 at students.poly.edu  Sat Nov  6 00:07:16 2010
From: cselig01 at students.poly.edu (Chet Seligman)
Date: Sat, 6 Nov 2010 04:07:16 +0000
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
 Graphics in perl 5.8 in windows 7
Message-ID: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>


I'd like to use ppm or cpan.
Does anyone know which repositories to use for the modules in the subject line?

Chet Seligman
 		 	   		  


From Kevin.M.Brown at asu.edu  Mon Nov  8 10:35:56 2010
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Mon, 8 Nov 2010 08:35:56 -0700
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
	Graphics in perl 5.8 in windows 7
In-Reply-To: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
References: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
Message-ID: <1A4207F8295607498283FE9E93B775B4072A9051@EX02.asurite.ad.asu.edu>

Follow the directions at:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
To get the main parts of BioPerl installed.

Bio::Graphics is now a separate module
http://search.cpan.org/~lds/Bio-Graphics-2.15/


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Chet Seligman
> Sent: Friday, November 05, 2010 9:07 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Problem installing Bio::SeqIO, 
> ::SearchIO, ; ; Graphics in perl 5.8 in windows 7
> 
> 
> I'd like to use ppm or cpan.
> Does anyone know which repositories to use for the modules in 
> the subject line?
> 
> Chet Seligman
>  		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From dan.bolser at gmail.com  Tue Nov  9 05:41:53 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 9 Nov 2010 10:41:53 +0000
Subject: [Bioperl-l] BP reports "All tests successful.", but some failed ...
Message-ID: <AANLkTing=D4xRTV6Lxzz6z0m=ap7-a7H5jO7eKhev7FK@mail.gmail.com>

I see the following error in the output of ./Build test:

...
t/LocalDB/SeqFeature_BDB.t ................... ok
t/LocalDB/SeqFeature_mysql.t ................. 1/84 DBI
connect('database=test','',...) failed: Can't connect to local MySQL
server through socket '/var/lib/mysql/mysql.sock' (2) at
Bio/DB/SeqFeature/Store/DBI/mysql.pm line 217
sh: -user: command not found
t/LocalDB/SeqFeature_mysql.t ................. ok
...


Related to a bug I filed a while back:
http://bugzilla.open-bio.org/show_bug.cgi?id=2899

IIRC there are a few bugs in Bio::SeqFeature::Store that are hidden
due to this initial failure.


Anyway, the point is that later I see:

All tests successful.
Files=348, Tests=24136, 249 wallclock secs ( 8.99 usr  2.04 sys +
197.16 cusr 26.85 csys = 235.04 CPU)
Result: PASS


How come we get "All tests successful." when there has clearly been an
error in "t/LocalDB/SeqFeature_mysql.t"?



BioPerl version is git bcd3b66f0422493e5f1d7c05220a4e58cced6313


Cheers,
Dan.

# The place to be
irc://irc.freenode.net/#BioPerl

# Sometimes good
irc://irc.perl.org/#gmod


From cjfields at illinois.edu  Tue Nov  9 07:58:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 06:58:40 -0600
Subject: [Bioperl-l] bioperl-primer3
In-Reply-To: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
References: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
Message-ID: <532C3550-5AA1-4A47-9C8D-82899E78B7E5@illinois.edu>

On Nov 9, 2010, at 6:05 AM, alpita at uvigo.es wrote:

> Hi Chris
> 
> As I wrote last day, I have never used bioperl and Primer3. All of this is completely new for me. It seems very interesting but I am in a student exchange, so I have got no-time to deep into it now (I will do this in the future, because I think it is very interesting to my work).
> 
> I want to design some primers, so I have used the tools of Thomas Thiel (MISA and p3_in) to obtain the input file of primer3 software. The next step would be to invoked the primer3 in the windows console (directly with the primer3 software or with bioperl tools) but I always have got problems with error messages. I suppose that I am writting some errors.
> 
> If you can, I would greatly appreciate you to tell me what tool to use and how to write it in the windows console.
> 
> Thank you very much for you effort. I hope to be improving slowly in this task
> Regards

Please make responses to the main bioperl list.  

I rewrote the main set of tools for Primer3, which I believe i pointed out to you previously (unless I'm mistaken):

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

I can't tell you what to use for Windows: I don't develop on that platform.  Any patches are welcome in case you find problems there and fix them.

chris





From njauxiongjie at gmail.com  Tue Nov  9 04:05:04 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Tue, 09 Nov 2010 01:05:04 -0800 (PST)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  



From singh.amarv at epa.gov  Tue Nov  9 13:38:18 2010
From: singh.amarv at epa.gov (Amar Singh)
Date: Tue, 9 Nov 2010 18:38:18 +0000 (UTC)
Subject: [Bioperl-l] parsing PubMed retrievals
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <loom.20101109T193516-922@post.gmane.org>

Tom Keller <kellert <at> ohsu.edu> writes:

> 
> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at
/Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> Tom
> MMI DNA Services Core
Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert <at> ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 


Tom,

I am also facing the same problem. This was working a month back and now when I
wanted to test new thing it is giving me the same error. I think this is due to
some changes in the way we access the data. Will keep updated if I find a
solution and same way you too. 

Thanks,

Amar



From Russell.Smithies at agresearch.co.nz  Tue Nov  9 15:08:23 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 10 Nov 2010 09:08:23 +1300
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313BCA1138@exchsth.agresearch.co.nz>

Not sure if this will work but have you tried using STDOUT as the filename then piping all the output to a single file?
The other (much simpler) option is just concatenate all the outputs into a single file when it's finished.

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of njauxiongjie
Sent: Tuesday, 9 November 2010 10:05 p.m.
To: bioperl-l
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
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taking of any action in reliance upon, this information by persons or
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From florent.angly at gmail.com  Tue Nov  9 19:54:58 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 10 Nov 2010 10:54:58 +1000
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <4CD9ED62.50102@gmail.com>

Wouldn't using a single filename be the way to go?
> my $filename = "blast_ressults.out";
>            $factory->save_output($filename);
Florent


On 09/11/10 19:05, njauxiongjie wrote:
> Hi,
>
> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>
> there are two line of the code like below:
> my $filename = $result->query_name()."\.out";
>            $factory->save_output($filename);
> this saved the blast result in separated files by the query name.
>
> my question is: how can i save the blast results of all querys in one file?
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Tue Nov  9 22:46:00 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 21:46:00 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4CD9ED62.50102@gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
Message-ID: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>

Only if the output appends to that file (I don't recall personally, so it's worth a try).

chris

On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:

> Wouldn't using a single filename be the way to go?
>> my $filename = "blast_ressults.out";
>>           $factory->save_output($filename);
> Florent
> 
> 
> On 09/11/10 19:05, njauxiongjie wrote:
>> Hi,
>> 
>> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>> 
>> there are two line of the code like below:
>> my $filename = $result->query_name()."\.out";
>>           $factory->save_output($filename);
>> this saved the blast result in separated files by the query name.
>> 
>> my question is: how can i save the blast results of all querys in one file?
>> 
>> 
>> 
>> _______________________________________________
>> 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 roy.chaudhuri at gmail.com  Wed Nov 10 11:11:27 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 10 Nov 2010 16:11:27 +0000
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
In-Reply-To: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
References: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
Message-ID: <4CDAC42F.9020708@gmail.com>

Hi Jim,

I don't think you ever got a reply to this. I think you want 
$tree->splice() rather than $tree->remove_Node().

Cheers,
Roy.

On 21/10/2010 18:52, Jim Hu wrote:
> I'm trying to take an unreadable tree from PFAM and prune it down to
> just show the paralogs from E. coli.
>
> When you run remove_Node on an internal node, is it supposed to
> reconnect the ancestors to the descendants?  This seems to be way to
> aggressive in what it's removing.
>
> while( my $tree = $treeio->next_tree ) { for my $node (
> $tree->get_nodes ) { if ($node->id =~ m/_ECOLI/){ #	leave this node
> alone #	print $node->id."\n"; }else{ if ($node->is_Leaf){
> $tree->remove_Node($node); }else{ my $num_children =
> scalar($node->each_Descendent); if ($num_children == 1){ print
> "removing ".$node->id."\n"; $tree->remove_Node($node); } } } }
> $treeio_out->write_tree($tree); }
>
> The idea is that when I've pruned the non-ECOLI leaves, some internal
> nodes will not be branches anymore.  But at the end, all the ECOLI
> nodes are gone, presumably because an ancestor got removed and the
> whole branch was lost.  Is there a way to remove just a node and
> graft the tree back together?  My plan, once I get that working is to
> repeat the traversal until the output stops changing.
>
> Jim
>
>
> ===================================== Jim Hu Associate 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 chandan.kr.singh at gmail.com  Thu Nov 11 06:10:25 2010
From: chandan.kr.singh at gmail.com (CHANDAN SINGH)
Date: Thu, 11 Nov 2010 16:40:25 +0530
Subject: [Bioperl-l] each_gene_symbol() is missing from
	Bio::Phenotype::OMIM::OMIMentry
Message-ID: <AANLkTinSX5oUFNYJFZwos2ODfsXFLj=xntxg43umfxs9@mail.gmail.com>

Hi Christian

The implementation of each_gene_symbol() is missing from
Bio::Phenotype::OMIM::OMIMentry even though the method has been referred in
the module and also in OMIMparser. I'm sure it was just a overlook; in which
case will you be implementing the method in the near future.

Thanks
Chandan


From cjfields at illinois.edu  Sun Nov 14 16:49:52 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 14 Nov 2010 15:49:52 -0600
Subject: [Bioperl-l] GitHub down
Message-ID: <E008728D-057A-415F-9415-EFD68F5F2B6F@illinois.edu>

Just a note that GitHub (and the main bioperl repo) appear to be down at the moment with a major disruption of service.  If anyone absolutely needs code, we have a synced repo set up here:

http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-db.git
http://repo.or.cz/w/bioperl-run.git
http://repo.or.cz/w/bioperl-network.git

chris


From maj at fortinbras.us  Mon Nov 15 20:08:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 15 Nov 2010 20:08:25 -0500
Subject: [Bioperl-l] use Bio::Search::Tiling::MapTiling
In-Reply-To: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
References: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
Message-ID: <E703F129EE074EFD9ACA421FED2A87F2@NewLife>

Hi Wei, 
You'll need to install the trunk code to access this method; the "release" is woefully out of date (not that I'm helping much on that these days). Use git to obtain the latests bioperl-live and bioperl-run from https://github.com/bioperl/, or the synchronized repos
http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-run.git
cheers, 
MAJ
----- Original Message ----- 
  From: Shao, Wei (NIH/NCI) [C] 
  To: Mark A Jensen 
  Sent: Monday, November 15, 2010 10:47 AM
  Subject: use Bio::Search::Tiling::MapTiling


Dear Dr. Jensen, I am looking for a bioperl module that can be used to concatenate HSP from a blast into a sequence. I found that your Bio::Search::Tiling::MapTilingcan do exactly that. I used your example script to test it. I got an error message:?Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::MapTiling" at get_hsp.pl line 29, <GEN1> line 2630?.It seems that method ?get_tiled_alns? is not in the bioperl we installed. Is that possible? The script I used is this one:  use Bio::SearchIO;use Bio::Search::Tiling::MapTiling # Note that to get one hit, the user first blasts# the set of contigs against single sequence, the reference sequence.# The result of this BLAST run is in 'contig_tile.bls' $blio = Bio::SearchIO->new( -file => 'contig_tile.bls');$result = $blio->next_result;$hit = $result->next_hit;$tiling = Bio::Search::Tiling::MapTiling->new($hit);@alns = $tiling->get_tiled_alns('query'); # here's the concatenation:$concat_seq_obj = $alns[0]->get_seq_by_id('query'); 

  Best regards,

   

   

  Wei Shao, Ph.D. [Contractor] 
  Bioinformatics Analyst IV

  Advanced Biomedical Computing Center/HIV Drug Resistance Program
  SAIC-Frederick, Inc. 

  National Cancer Institute at Frederick
  P.O. Box B, Frederick, MD 21702
  Phone: 301/846-6021

  Fax:  301/846-6013
  Email:  shaow at mail.nih.gov


  NOTICE:  This communication may contain privileged or other confidential information.  If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information.  Please indicate to the sender that you have received this email in error and delete the copy you received.

   



From dimitark at bii.a-star.edu.sg  Mon Nov 15 21:44:15 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 16 Nov 2010 10:44:15 +0800
Subject: [Bioperl-l] about tblastn and strand
Message-ID: <4CE1EFFF.70304@bii.a-star.edu.sg>

Hi guys,
i have a simple question. How exactly is defined on which strand is 
located a certain HSP in tblastn? I know it is used the strand function 
but i would like to know how is implemented. I ask cos here i made a 
perl script using bioperl but other people want to implement it in Java.

In the output of tblastn there is no strand string only frame+ or 
frame-. Do you just take the + or - to determine on which strand is the HSP?

Thank you for your time and help.

Dimitar


From mmuratet at hudsonalpha.org  Tue Nov 16 16:56:08 2010
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Tue, 16 Nov 2010 15:56:08 -0600
Subject: [Bioperl-l] Obtaining Refseq status with eutils
Message-ID: <EEABA734-39A8-44B4-9540-A20FE1BC575E@hudsonalpha.org>

Greetings

I have been trying to get to the Refseq status info that shows up NCBI  
gene webpage. My latest attempt is:

my @accs = qw(SAAV_0049);

my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -email => 'mmuratet at hudsonalpha.org 
',
                                        -db    => 'gene',
                                        -term  => join(',', at accs));

my @uids = $factory->get_ids;

$factory->reset_parameters(-eutil => 'elink',
                            -dbfrom => 'gene',
                            -db => 'nuccore',
                            -linkname => 'gene_nuccore_refseqgene',
                            -id    => \@uids);

$factory->get_Response(-file => 'temp.txt');

All I get back is the ID number I gave it. Also, $factory->next_DocSum  
returns nothing.

A big part of the problem is that I don't know what field I'm looking  
for. I am also unsure that I am using the elink interface properly.

Does anyone know how to get to the Refseq data for a gene? I am  
looking for evidence of expression of gene models--is there a better  
annotation to use?

Thanks

Mike


Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806







From pcantalupo at gmail.com  Wed Nov 17 12:38:05 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 12:38:05 -0500
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
Message-ID: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>

Hi,

Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm


---
 Bio/SeqIO.pm |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
index fe49822..cf6d3a2 100644
--- a/Bio/SeqIO.pm
+++ b/Bio/SeqIO.pm
@@ -651,6 +651,7 @@ sub _guess_format {
    return 'phd'     if /\.(phd|phred)$/i;
    return 'pir'     if /\.pir$/i;
    return 'pln'     if /\.pln$/i;
+   return 'qual'    if /\.qual$/i;
    return 'raw'     if /\.(txt)$/i;
    return 'scf'     if /\.scf$/i;
    return 'swiss'   if /\.(swiss|sp)$/i;
-- 
1.6.4.2



Paul

Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260


From maj at fortinbras.us  Wed Nov 17 17:59:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 17 Nov 2010 22:59:25 +0000
Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] GO annotation
Message-ID: <W347038377283011290034765@webmail27>


redirect to list
-----Original Message-----
From: Christos Noutsos [mailto:cnoutsos at cshl.edu]
Sent: Wednesday, November 17, 2010 05:35 PM
To: bioperl-guts-l at lists.open-bio.org
Subject: [Bioperl-guts-l] GO annotation

Hi all,
I have several clusters of coregulated genes from Arabidopsis and I would like to check  their GO annotation? Is there a module in bioperl which I can use? 
Thank you for your help
Christos


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





From lskatz at gatech.edu  Wed Nov 17 22:20:03 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Wed, 17 Nov 2010 22:20:03 -0500
Subject: [Bioperl-l] Status of assembly modules
Message-ID: <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc@mail.gmail.com>

I have read on the BioPerl site that a 454 ace is not standardized due to
its coordinate system.  How can I convert it to the standard ace file?

When I run this code either by using contig or assembly objects, I get an
error.
Can't call method "get_consensus_sequence" on an undefined value at
Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.

    sub _newblerAceToAce($args){
      my($self,$args)=@_;
      my
$ace454=Bio::Assembly::IO->new(-file=>$$args{ace454Path},-format=>"ace",-variant=>'454');
      my
$ace=Bio::Assembly::IO->new(-file=>">$$args{acePath}",-format=>"ace");
      #while(my $contig=$ace454->next_contig){
      while(my $scaffold=$ace454->next_assembly){
        print Dumper $scaffold;
      }
      return $$args{acePath};
    }


On Fri, Jun 18, 2010 at 5:59 AM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 13
> Date: Fri, 18 Jun 2010 15:39:39 +1000
> From: Florent Angly <florent.angly at gmail.com>
> Subject: [Bioperl-l] Status of assembly modules
> To: Joshua Udall <jaudall at gmail.com>,   bioperl-l List
>        <bioperl-l at lists.open-bio.org>
> Message-ID: <4C1B069B.5020105 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Joshua,
>
> Yes, there have been interesting improvements in the assembly BioPerl
> module since v1.6.1. You can find these changes in the development
> version of BioPerl at http://github.com/bioperl/. I'll take this
> opportunity to introduce people who don't follow the commit messages to
> the new features that have been introduced:
>
> First, there is support for more file formats from high-throughput
> platforms, including those generated by de novo assembly and comparative
> assembly tools, such as:
>     * Roche 454 GS Assembler, aka Newbler (the ACE-454 variant)
>     * Maq
>     * Sam
>     * Bowtie
> There is support for running a lot more of these tools in Bioperl-run
> Bio::Tools::Run :
>     * Roche 454 GS Assembler, aka Newbler
>     * Minimo
>     * Maq
>     * Samtools
>     * Bowtie
> In terms of writing assembly file, I added the option to write ACE
> files, which is quite useful because maybe assembly programs recognize
> this format. So now you can read assemblies, modify them as you see fit
> and exporting them to other programs by writing the modified assembly in
> an ACE file.
> The internals of the IO parsers have acquired some granularity as it is
> now possible to read/write assembly files entirely, or one contig at a
> time. This is terrific to reduce memory usage.
>
> That's about it...
>
> Regards,
>
> Florent
>
> PS/ Josh, you filed bug reports related to several of these issues
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2726,
> http://bugzilla.open-bio.org/show_bug.cgi?id=2483). I am closing the
> ones that were not closed yet and thank you for submitting patches.
>
>
> On 18/06/10 14:00, Joshua Udall wrote:
> > Florent -
> >
> > I didn't want to ask a direct question on-list to perhaps avoid
> > confusion.  Were you able to improve/submit a ContigIO to bioperl that
> > works with one entry at a time (instead of slurping the entire ace
> > file)?
> >
> >
>



-- 
Lee Katz
http://leeskatz.com


From rmb32 at cornell.edu  Thu Nov 18 02:03:46 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 17 Nov 2010 23:03:46 -0800
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
In-Reply-To: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
References: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
Message-ID: <4CE4CFD2.3000901@cornell.edu>

Applied!  Thanks Paul!

Rob

Paul Cantalupo wrote:
> Hi,
> 
> Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm
> 
> 
> ---
>  Bio/SeqIO.pm |    1 +
>  1 files changed, 1 insertions(+), 0 deletions(-)
> 
> diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
> index fe49822..cf6d3a2 100644
> --- a/Bio/SeqIO.pm
> +++ b/Bio/SeqIO.pm
> @@ -651,6 +651,7 @@ sub _guess_format {
>     return 'phd'     if /\.(phd|phred)$/i;
>     return 'pir'     if /\.pir$/i;
>     return 'pln'     if /\.pln$/i;
> +   return 'qual'    if /\.qual$/i;
>     return 'raw'     if /\.(txt)$/i;
>     return 'scf'     if /\.scf$/i;
>     return 'swiss'   if /\.(swiss|sp)$/i;



From pcantalupo at gmail.com  Thu Nov 18 10:15:04 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 18 Nov 2010 10:15:04 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTikW_cKGovyGyKLZMxAeP1E6Vs8P=KOzAXQsKBxK@mail.gmail.com>

Hi,

I'm resending this to the list (without an attachment) since it got
flagged as having a suspicious header.


I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string":

---
 Bio/Seq/PrimaryQual.pm |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/Bio/Seq/PrimaryQual.pm b/Bio/Seq/PrimaryQual.pm
index 4935639..30383fc 100644
--- a/Bio/Seq/PrimaryQual.pm
+++ b/Bio/Seq/PrimaryQual.pm
@@ -461,7 +461,7 @@ sub qualat {
 sub to_string {
     my ($self,$out,$result) = shift;
     $out = "qual: ".join(',',@{$self->qual()});
-    foreach (qw(display_id accession_number primary_id desc id)) {
+    foreach (qw(display_id accession_number primary_id desc id length)) {
 	$result = $self->$_();
 	if (!$result) { $result = "<unset>"; }
 	$out .= "$_: $result\n";
-- 
1.6.4.2






Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260


From pcantalupo at gmail.com  Wed Nov 17 10:55:52 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 10:55:52 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>

Hi,

I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string"

Paul


Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260
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From twaddlac at gmail.com  Fri Nov 19 15:03:14 2010
From: twaddlac at gmail.com (Alan Twaddle)
Date: Fri, 19 Nov 2010 15:03:14 -0500
Subject: [Bioperl-l] bioperl-ext package installation error
Message-ID: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>

Hello all,

     I am trying to write a simple script to parse an ABI file into usable
data which requires the staden io_lib of which I installed. However, am
receiving an error message when trying to run my script that says the
following:
------------- EXCEPTION: Bio::Root::SystemException -------------
MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
package has been installed successfully!
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
abi.pm:100
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
STACK: AB1_parser.pl:10

I didn't receive any error messages when installing the staden package so
I'm assuming that there's some path specified in some file that is pointing
to the wrong place. I don't know if this is the case but if you have any
suggestions about how to fix this I would greatly appreciate it! Thank you
very much!

-- 

Alan Twaddle, B.S.
MUC class of 2010


From cjfields at illinois.edu  Fri Nov 19 23:33:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:33:14 -0600
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
In-Reply-To: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
References: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
Message-ID: <644615D3-8F59-4E59-B7A1-6BCE6159E9C9@illinois.edu>

Paul, 

Committed this to github master branch.  Thanks for pointing that out.

chris

On Nov 17, 2010, at 9:55 AM, Paul Cantalupo wrote:

> Hi,
> 
> I simply added "length" to the foreach loop in sub "to_string" of
> Bio/Seq/PrimaryQual.pm to match documentation of "to_string"
> 
> Paul
> 
> 
> Paul Cantalupo
> Research Specialist/Systems Programmer
> University of Pittsburgh
> Pittsburgh, PA 15260
> <0001-Added-length-to-foreach-loop-to-match-documentation-.patch>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Fri Nov 19 23:50:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:50:17 -0600
Subject: [Bioperl-l] bioperl-ext package installation error
In-Reply-To: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
References: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
Message-ID: <D0C6F261-EFF7-46D3-823D-171BAA240A91@illinois.edu>

Alan, 

You need to install the bioperl-ext module Bio::SeqIO::staden::read, which uses XS bindings to io_lib, but there's a bit of a caveat: we're not really maintaining that code anymore.  Saying that, it does work using io_lib version 1.12.2 (my local version). 

Here's the code, please make sure to note the README (specifically, the version of io_lib you will need and the problems you may run into):

https://github.com/bioperl/bioperl-ext/tree/master/Bio/SeqIO/staden/

chris

On Nov 19, 2010, at 2:03 PM, Alan Twaddle wrote:

> Hello all,
> 
>     I am trying to write a simple script to parse an ABI file into usable
> data which requires the staden io_lib of which I installed. However, am
> receiving an error message when trying to run my script that says the
> following:
> ------------- EXCEPTION: Bio::Root::SystemException -------------
> MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
> package has been installed successfully!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
> abi.pm:100
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
> STACK: AB1_parser.pl:10
> 
> I didn't receive any error messages when installing the staden package so
> I'm assuming that there's some path specified in some file that is pointing
> to the wrong place. I don't know if this is the case but if you have any
> suggestions about how to fix this I would greatly appreciate it! Thank you
> very much!
> 
> -- 
> 
> Alan Twaddle, B.S.
> MUC class of 2010
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jordi.durban at gmail.com  Mon Nov 22 15:01:34 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Mon, 22 Nov 2010 21:01:34 +0100
Subject: [Bioperl-l] parse multi xml
Message-ID: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>

Hi all,
I'm a newbie in the list although I've been using bioperl for 2 years.
Now I have a problem with a XML file and I don't know how to parse it.
That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
resulted from  Blast2go software the usage and I suppose the file is the
outcome of multiple blast results concatenation.
Well, I would like to split all 795 different xml chunks in 795 different
files in order to parse them looking for the best hit.
The problem appears using the blastxml parse
(*Bio::SearchIO::blastxml) *because
(and that's a personal opinion) there's another top tag not expected and I
get a error message once the first blast result was parsed.
How can I do that split function?
I hope I was clear
Thanks




-- 
Jordi


From biopython at maubp.freeserve.co.uk  Mon Nov 22 15:23:29 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Nov 2010 20:23:29 +0000
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
Message-ID: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>

On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
> Hi all,
> I'm a newbie in the list although I've been using bioperl for 2 years.
> Now I have a problem with a XML file and I don't know how to parse it.
> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
> resulted from ?Blast2go software the usage and I suppose the file is the
> outcome of multiple blast results concatenation.

Such a file is NOT a valid XML file (but see below), you can't just
concatenate XML files. I'm pretty sure people have posted scripts
to fix such files on the blast2go mailing list.

> Well, I would like to split all 795 different xml chunks in 795 different
> files in order to parse them looking for the best hit.
> The problem appears using the blastxml parse
> (*Bio::SearchIO::blastxml) *because
> (and that's a personal opinion) there's another top tag not expected
> and I get a error message once the first blast result was parsed.
> How can I do that split function?
> I hope I was clear
> Thanks

Historically the NCBI standalone BLAST used to create these
concatenated XML files when used on multiple queries. It has
since been fixed, but perhaps BioPerl has code still in it to
handle these legacy invalid XML files?

My suggestion (until a BioPerl guru speaks up) would be to
split the file into chunks (in memory) by looking for the string
<?xml version="1.0">, and parsing each chunk individually.
Each chunk should be a valid XML file on its own.

Peter



From lskatz at gatech.edu  Mon Nov 22 15:18:10 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Mon, 22 Nov 2010 15:18:10 -0500
Subject: [Bioperl-l] Re(2): Status of assembly modules
Message-ID: <AANLkTi=JShCLsHDxHK4eeWD3Da=vWmRkGN2rkuLwCjxn@mail.gmail.com>

I figured it out (I haven't tested much though).

To whoever works on Assembly::IO::ace.pm:
I changed a regular expression on line 231 because the contig object was not
initializing properly.  For some reason the 454 ace file had adopted the
reference assembly's ID and therefore there was a GI number followed by a
pipe.  The pipe was not captured with \w+.  I think that the regex will be
safe with \s(\S+)\s.

 if (/^CO\s(\S+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!
#if (/^CO\s(\w+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!

On Thu, Nov 18, 2010 at 12:04 PM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 3
> Date: Wed, 17 Nov 2010 22:20:03 -0500
> From: Lee Katz <lskatz at gatech.edu>
> Subject: Re: [Bioperl-l] Status of assembly modules
> To: bioperl-l at lists.open-bio.org
> Message-ID:
>        <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I have read on the BioPerl site that a 454 ace is not standardized due to
> its coordinate system.  How can I convert it to the standard ace file?
>
> When I run this code either by using contig or assembly objects, I get an
> error.
> Can't call method "get_consensus_sequence" on an undefined value at
> Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.
>
>    sub _newblerAceToAce($args){
>      my($self,$args)=@_;
>      my
>
> $ace454=Bio::Assembly::IO->new(-file=>$args{ace454Path},-format=>"ace",-variant=>'454');
>      my
> $ace=Bio::Assembly::IO->new(-file=>">$args{acePath}",-format=>"ace");
>      #while(my $contig=$ace454->next_contig){
>      while(my $scaffold=$ace454->next_assembly){
>        print Dumper $scaffold;
>      }
>      return $args{acePath};
>    }
>



-- 
Lee Katz
http://leeskatz.com


From thomas.sharpton at gmail.com  Mon Nov 22 17:28:52 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 22 Nov 2010 14:28:52 -0800
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
Message-ID: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>

Hi Evan,

Glad to hear this software is a promising solution to your needs. I  
just tried running the test script under Bio/t/SearchIO/hmmer3.t and  
everything passed. Can you verify that you are using an up-to-date  
version of bioperl-live? You can grab a snapshot from github if you  
haven't already:

https://github.com/bioperl/bioperl-live

Also, I'm cc'ing this to the bioperl list so that others may benefit  
from our discourse (and chime in - Kai Blin, who created the test  
tools, and others have made substantial contributions and improvements  
to the original code and they might have good suggestions).

T



On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:

> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3  
> reports. Everything seems to be working nicely with the test data  
> and my own reports except for getting the $hsp->query_string and  
> $hsp->hit_string. I noticed that these HSP routines were not working  
> with the test script/data (for me anyway) so I thought I would ask  
> before spending days trying to solve this one.
>
> Thanks,
>
> Evan
>
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602



From jordi.durban at gmail.com  Mon Nov 22 18:34:03 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Tue, 23 Nov 2010 00:34:03 +0100
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <AANLkTi=RBBL1vC4XRQM=_gf+5CPLiw2+6xdtwzZjFy6a@mail.gmail.com>

Thanks Peter.
That's exactly what I was looking for but so far I've not been able to do
that properly.
Any ideas??


2010/11/22 Peter <biopython at maubp.freeserve.co.uk>

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com>
> wrote:
> > Hi all,
> > I'm a newbie in the list although I've been using bioperl for 2 years.
> > Now I have a problem with a XML file and I don't know how to parse it.
> > That file has 795 xml top tags (thta's is <?xml version="1.0">) because
> they
> > resulted from  Blast2go software the usage and I suppose the file is the
> > outcome of multiple blast results concatenation.
>
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
>
> > Well, I would like to split all 795 different xml chunks in 795 different
> > files in order to parse them looking for the best hit.
> > The problem appears using the blastxml parse
> > (*Bio::SearchIO::blastxml) *because
> > (and that's a personal opinion) there's another top tag not expected
> > and I get a error message once the first blast result was parsed.
> > How can I do that split function?
> > I hope I was clear
> > Thanks
>
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?
>
> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
>
> Peter
>



-- 
Jordi


From cjfields at illinois.edu  Mon Nov 22 19:27:43 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 22 Nov 2010 18:27:43 -0600
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <348A592A-D634-4C1C-9F05-DB20FE87F61C@illinois.edu>

On Nov 22, 2010, at 2:23 PM, Peter wrote:

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
>> Hi all,
>> I'm a newbie in the list although I've been using bioperl for 2 years.
>> Now I have a problem with a XML file and I don't know how to parse it.
>> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
>> resulted from  Blast2go software the usage and I suppose the file is the
>> outcome of multiple blast results concatenation.
> 
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
> 
>> Well, I would like to split all 795 different xml chunks in 795 different
>> files in order to parse them looking for the best hit.
>> The problem appears using the blastxml parse
>> (*Bio::SearchIO::blastxml) *because
>> (and that's a personal opinion) there's another top tag not expected
>> and I get a error message once the first blast result was parsed.
>> How can I do that split function?
>> I hope I was clear
>> Thanks
> 
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?

It does (last I looked).

> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
> 
> Peter

Or, better yet, push the blast2go folks to create valid XML output or use an updated version of BLAST.  This bug was fixed about 3 years ago.

chris





From statonse at uga.edu  Mon Nov 22 18:41:26 2010
From: statonse at uga.edu (Evan Staton)
Date: Mon, 22 Nov 2010 18:41:26 -0500
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
Message-ID: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>

Hi Thomas,

Everything works with the latest release of bioperl-live. My bioperl was
1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
did not realize it had been incorporated into the latest distribution). All
the tests passed and all the routines worked before except for the
$hsp->query_string and $hsp->hit_string, but that is resolved now.

Thanks for the quick response, it saved me a lot of time.

Evan

On Mon, Nov 22, 2010 at 5:28 PM, Thomas Sharpton
<thomas.sharpton at gmail.com>wrote:

> Hi Evan,
>
> Glad to hear this software is a promising solution to your needs. I just
> tried running the test script under Bio/t/SearchIO/hmmer3.t and everything
> passed. Can you verify that you are using an up-to-date version of
> bioperl-live? You can grab a snapshot from github if you haven't already:
>
> https://github.com/bioperl/bioperl-live
>
> Also, I'm cc'ing this to the bioperl list so that others may benefit from
> our discourse (and chime in - Kai Blin, who created the test tools, and
> others have made substantial contributions and improvements to the original
> code and they might have good suggestions).
>
> T
>
>
>
> On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:
>
> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3 reports.
> Everything seems to be working nicely with the test data and my own reports
> except for getting the $hsp->query_string and $hsp->hit_string. I noticed
> that these HSP routines were not working with the test script/data (for me
> anyway) so I thought I would ask before spending days trying to solve this
> one.
>
> Thanks,
>
> Evan
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602
>
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
S. Evan Staton
PhD Student - Burke Lab
University of Georgia
Department of Genetics
3507 Miller Plant Sciences
Athens, GA 30602


From kris.richardson at tufts.edu  Tue Nov 23 12:10:56 2010
From: kris.richardson at tufts.edu (kris richardson)
Date: Tue, 23 Nov 2010 12:10:56 -0500
Subject: [Bioperl-l] GeneMapper
Message-ID: <BA6B80D7-732A-4333-83AD-54AB14BF334D@tufts.edu>

Dear Members,

 I have a list mRNA target positions,  for various mRNAs and  I also have the RefSeq accession NM_#s for their genes  and mRNA (ex; gene: NM_198155 --- mRNA positions: NM_004649: 800-890).   

I would like to use this info to pull the chromosomal coordinates of NM_198155 corresponding to the resulting transcript positions NM:_004649:800-890.  I am familiarizing myself with bioperl and GeneMapper seems like it can provide this info.  However, the documentation on the module code is sparse, and there are no examples.  I was wondering if anyone has experience with this and could point me in the right direction, or perhaps provide some example code?  

Regards,

Kris







From kai.blin at biotech.uni-tuebingen.de  Wed Nov 24 01:24:22 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Wed, 24 Nov 2010 07:24:22 +0100
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
	<AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
Message-ID: <4CECAF96.7010706@biotech.uni-tuebingen.de>

On 2010-11-23 00:41, Evan Staton wrote:

Hi Evan,

> Everything works with the latest release of bioperl-live. My bioperl was
> 1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
> did not realize it had been incorporated into the latest distribution). All
> the tests passed and all the routines worked before except for the
> $hsp->query_string and $hsp->hit_string, but that is resolved now.

I recently fixed this in bioperl-live when I bumped into that feature
missing. I didn't bother to update the bioperl-hmmer3 repository.
Perhaps it should be deleted to avoid the confusion.

Also, in bioperl-live, the Bio::SearchIO::hmmer parser now supports
hmmer2 and hmmer3 parsing, but by all means go for the specific parser
class if you know the version of hmmer result you're loading. :)

On a side note, even though you're probably aware of this... HMMer3 only
does local alignments, so it's not really good for domain extraction. It
is very fast, but if your software uses a profile based search to
extract specific amino acid motifs HMMer3 might let you down.
Just as a caveat that has bitten me recently.

Cheers,
Kai

-- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-University of T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Deutschland
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben


From dimitark at bii.a-star.edu.sg  Wed Nov 24 21:38:52 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:38:52 +0800
Subject: [Bioperl-l] update: genpept module
Message-ID: <4CEDCC3C.9070707@bii.a-star.edu.sg>

Hi guys,
just managed to get GenPept to give me the fasta in the full form. I 
modified GenPept in this way:

sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); 
#DIMITAR
   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
   $self->request_format($self->default_format($format));
   return $self;
}

Cheers
Dimitar


From cjfields at illinois.edu  Wed Nov 24 22:24:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 24 Nov 2010 21:24:40 -0600
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDCC3C.9070707@bii.a-star.edu.sg>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
Message-ID: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>

Dimitar,

Missed your original post, but was it reported as a bug?  

chris

On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:

> Hi guys,
> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
> 
> sub new {
>  my($class, @args) = @_;
>  my $self = $class->SUPER::new(@args);
>  my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>  $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>  $self->request_format($self->default_format($format));
>  return $self;
> }
> 
> Cheers
> Dimitar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jason at bioperl.org  Wed Nov 24 22:57:11 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Nov 2010 19:57:11 -0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
Message-ID: <4CEDDE97.5020406@bioperl.org>

This doesn't seem like the right fix -- you don't want to updated a 
default variable -- why didn't you just use it like this: ?

my $db = new Bio::DB::GenPept->new(-format => 'fasta');



Chris Fields wrote, On 11/24/10 7:24 PM:
> Dimitar,
>
> Missed your original post, but was it reported as a bug?
>
> chris
>
> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>
>> Hi guys,
>> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
>>
>> sub new {
>>   my($class, @args) = @_;
>>   my $self = $class->SUPER::new(@args);
>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>   $self->request_format($self->default_format($format));
>>   return $self;
>> }
>>
>> Cheers
>> Dimitar
>> _______________________________________________
>> 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 at bioperl.org



From dimitark at bii.a-star.edu.sg  Thu Nov 25 00:34:39 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 13:34:39 +0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDDE97.5020406@bioperl.org>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
	<4CEDDE97.5020406@bioperl.org>
Message-ID: <4CEDF56F.3020409@bii.a-star.edu.sg>

I used it like this in the script:

if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


}

i added $retformat to getoptlong as well. but that didnt work well as 
did for GenBank. May be GenBank and GenPept should be made to work in 
the same way. Now they are a bit different. I tried to see why they 
react different but i couldnt understand why.

now my GenPept new method looks like this:
sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
FORMAT)], at args);#dimitar
   $DEFAULTFORMAT=$format if (defined $format);#dimitar
   $self->request_format($self->default_format($format));
   return $self;
}

this way i can get sequences in any format which Eutils is allowing.

On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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
>



On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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 dimitark at bii.a-star.edu.sg  Thu Nov 25 02:05:36 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 15:05:36 +0800
Subject: [Bioperl-l] about NCBI seq reports
Message-ID: <4CEE0AC0.6050104@bii.a-star.edu.sg>

Hi again,
now i can get the sequences in full fasta as NCBI provides them. But can 
I also get and the GenPept reports in some way?
I tried using 'download_query_genbank.pl' but i always get some fasta 
seq but not the GenPept report even though the generated by the script 
request is valid. When i put it in browser i get the report file but the 
script itself returns fasta. I think is limitation of the modules which 
the scripts uses, right? Or am i mistaken.

Cheers
Dimitar


From Marc.Perry at oicr.on.ca  Fri Nov 26 23:53:48 2010
From: Marc.Perry at oicr.on.ca (Marc Perry)
Date: Fri, 26 Nov 2010 23:53:48 -0500
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm; 'sizes' method is broken
Message-ID: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>

Hi,

I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:

=+=+=+=
#!/usr/bin/perl

use strict;
use warnings;
use Bio::SeqIO;
use Bio::Restriction::Analysis;
use Bio::Restriction::Enzyme;
use Bio::Restriction::EnzymeCollection;

my $input = shift or die "No fasta file on command line.";

my $seqio_obj = Bio::SeqIO->new(-file   => $input,
                                                -format => "fasta" );

my $seq = $seqio_obj->next_seq;

my $all_enz = Bio::Restriction::EnzymeCollection->new();

my $h3 = $all_enz->get_enzyme('HindIII');

my $ra = Bio::Restriction::Analysis->new(-seq => $seq);

print join "\n", $ra->sizes($h3), "\n\n";
print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
print join "\n", $ra->sizes($h3, 1, 1), "\n\n";

exit;
=+=+=+=

And here is the output:

48502


48502


48.502

As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:


sub sizes {

    my ($self, $enz, $kb, $sort) = @_;

    $self->throw('no enzyme selected to get fragments for')

        unless $enz;

    $self->cut unless $self->{'_cut'};

    my @frag; my $lastsite=0;

    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG

      $kb ? push (@frag, (int($site-($lastsite))/100)/10)

          : push (@frag, $site-($lastsite));

      $lastsite=$site;

    }

    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)

        : push (@frag, $self->{'_seq'}->length-($lastsite));

    if ($self->{'_seq'}->is_circular) {

       my $first=shift @frag;

       my $last=pop @frag;

       push @frag, ($first+$last);

    }

    $sort ? @frag = sort {$b <=> $a} @frag : 1;



    return @frag;

}


I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:

my $name = $enz->{_seq}->{display_id};
foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {

And now my script yields this output:

23130
2027
2322
9416
564
6682
4361


23130
9416
6682
4361
2322
2027
564


23.13
9.416
6.682
4.361
2.322
2.027
0.564

which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:


You should be able to do these:



  # to see all the fragment sizes,

  print join "\n", @{$re->sizes($enz)}, "\n";

  # to see all the fragment sizes sorted

  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";

  # to see all the fragment sizes in kb sorted

  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";

--Marc

Marc Perry
Scientific Associate

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:       416-673-8593
Toll-free:  1-866-678-6427
Cell:      416-904-8037
www.oicr.on.ca<http://www.oicr.on.ca/>

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all




From cjfields at illinois.edu  Sat Nov 27 00:15:46 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 26 Nov 2010 23:15:46 -0600
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm;
	'sizes' method is broken
In-Reply-To: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
References: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
Message-ID: <66A351B0-D483-490A-90CC-BF7C596D6505@illinois.edu>

Marc,

I've entered this into bugzilla for tracking (the best place for this, BTW).  I can't promise when we'll get to it, but since there is a proposed fix it may be handled fairly soon.  Thanks for pointing this out!

chris

On Nov 26, 2010, at 10:53 PM, Marc Perry wrote:

> Hi,
> 
> I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:
> 
> =+=+=+=
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::SeqIO;
> use Bio::Restriction::Analysis;
> use Bio::Restriction::Enzyme;
> use Bio::Restriction::EnzymeCollection;
> 
> my $input = shift or die "No fasta file on command line.";
> 
> my $seqio_obj = Bio::SeqIO->new(-file   => $input,
>                                                -format => "fasta" );
> 
> my $seq = $seqio_obj->next_seq;
> 
> my $all_enz = Bio::Restriction::EnzymeCollection->new();
> 
> my $h3 = $all_enz->get_enzyme('HindIII');
> 
> my $ra = Bio::Restriction::Analysis->new(-seq => $seq);
> 
> print join "\n", $ra->sizes($h3), "\n\n";
> print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
> print join "\n", $ra->sizes($h3, 1, 1), "\n\n";
> 
> exit;
> =+=+=+=
> 
> And here is the output:
> 
> 48502
> 
> 
> 48502
> 
> 
> 48.502
> 
> As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:
> 
> 
> sub sizes {
> 
>    my ($self, $enz, $kb, $sort) = @_;
> 
>    $self->throw('no enzyme selected to get fragments for')
> 
>        unless $enz;
> 
>    $self->cut unless $self->{'_cut'};
> 
>    my @frag; my $lastsite=0;
> 
>    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG
> 
>      $kb ? push (@frag, (int($site-($lastsite))/100)/10)
> 
>          : push (@frag, $site-($lastsite));
> 
>      $lastsite=$site;
> 
>    }
> 
>    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)
> 
>        : push (@frag, $self->{'_seq'}->length-($lastsite));
> 
>    if ($self->{'_seq'}->is_circular) {
> 
>       my $first=shift @frag;
> 
>       my $last=pop @frag;
> 
>       push @frag, ($first+$last);
> 
>    }
> 
>    $sort ? @frag = sort {$b <=> $a} @frag : 1;
> 
> 
> 
>    return @frag;
> 
> }
> 
> 
> I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:
> 
> my $name = $enz->{_seq}->{display_id};
> foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {
> 
> And now my script yields this output:
> 
> 23130
> 2027
> 2322
> 9416
> 564
> 6682
> 4361
> 
> 
> 23130
> 9416
> 6682
> 4361
> 2322
> 2027
> 564
> 
> 
> 23.13
> 9.416
> 6.682
> 4.361
> 2.322
> 2.027
> 0.564
> 
> which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:
> 
> 
> You should be able to do these:
> 
> 
> 
>  # to see all the fragment sizes,
> 
>  print join "\n", @{$re->sizes($enz)}, "\n";
> 
>  # to see all the fragment sizes sorted
> 
>  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";
> 
>  # to see all the fragment sizes in kb sorted
> 
>  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";
> 
> --Marc
> 
> Marc Perry
> Scientific Associate
> 
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
> 
> Tel:       416-673-8593
> Toll-free:  1-866-678-6427
> Cell:      416-904-8037
> www.oicr.on.ca<http://www.oicr.on.ca/>
> 
> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dimitark at bii.a-star.edu.sg  Mon Nov 29 04:35:26 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 17:35:26 +0800
Subject: [Bioperl-l] genbank
Message-ID: <4CF373DE.4070902@bii.a-star.edu.sg>

Hi again,
it seems that when i download (with 'download_query_genbank.pl') the 
whole proteome from NCBI in fasta format it is first being downloaded 
and from it is being created some kind of SeqFastaSpeedFactory and after 
that from it is being copied to the output file. But i want to download 
and write to output file one by one so i can see the download 
progress(which is working for genbank data).

Its frustrating :)

Any ideas where to look for solution
Cheers
Dimitar




From cjfields at illinois.edu  Mon Nov 29 09:39:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 08:39:16 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF373DE.4070902@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
Message-ID: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>

On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:

> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
> 
> Its frustrating :)
> 
> Any ideas where to look for solution
> Cheers
> Dimitar

You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:

my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
	$out->write_seq($seq);
}

insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.

If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.

chris


From dimitark at bii.a-star.edu.sg  Wed Nov 24 21:20:28 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:20:28 +0800
Subject: [Bioperl-l] question about GenPept.pm
Message-ID: <4CEDC7EC.1000903@bii.a-star.edu.sg>

Hi guys,
i want to get some genomes and proteomes from NCBI in fasta format. I 
found i have to use 'download_query_genbank.pl' for that. It works but 
not as i would like. It uses the modules GenPept and GenBank. They 
retrieve the data in fasta but in different format than i want.

Example:
a) i want the fasta to be like the following:
 >gi|5834889|ref|NP_006959.1|COX3_10021 cytochrome c oxidase subunit III 
[Caenorhabditis elegans]
here sequense...

b) but it comes like this:
 >COX3_10021 cytochrome c oxidase subunit III [Caenorhabditis elegans]
here sequense...

But i need the gi and NP as well. So i dug up a bit and after playing 
with 'download_query_genbank.pl' i managed to make GenBank to give the 
fasta seqs in the format i want.
I made the following changes:
1. added $retformat option for Getopt
2.modified this section:
if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


} else {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenBank->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenBank->new(-verbose => $debug);
     }
}

But i go problem with GenPept. I still cant get the seqs in full fasta 
format as i explained above. Its interesting cos both modules GenPept 
and GenBank are almost identical except that GenBank uses the new method 
of NCBIHelper while GenPept has its own which still uses the 
NCBIHelper's as well.

With my modification i pass the format i want but then somehow it 
reverts to the default set in GenPept which is 'gp' while i need it to 
be 'fasta'.

If i change the defaultformat in GenPept to fasta it works but thats 
just doing the job without adding the needed flexibility.

Any help would be appreciated. I will try to find solution as well.
Cheers

PS: i attache the modified 'download_query_genbank.pl'
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From dimitark at bii.a-star.edu.sg  Mon Nov 29 02:17:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 15:17:50 +0800
Subject: [Bioperl-l] about genpept and genbank
Message-ID: <4CF3539E.8030002@bii.a-star.edu.sg>

hi guys,
i dug up a bit more and found a solution. i think the problem is that in 
'download_query_genbank.pl' there is the 'format' option which only is 
responsible for the format of the output file to which seqs are 
downloaded. While i need 'ret_type' format option according to NCBI 
Eutils. So now i found that i can use GenBank.pm for all DBs in NCBI. I 
restored the GenPept as it was in original but i do not use it, its more 
tricky than GenBank.pm. Now modified 'download_query_genbank.pl' to use 
only GenBank and added one more option 'retformat' which can be set 
according to NCBI 'rettype'. Also added a simple progress bar to follow 
the download. Unfortunately it is working only if im downloading genbank 
data(Bio::SeqIO::genbank) when i download fasta(Bio::SeqIO::fasta) i 
cant use it. Seems that the fasta stream is a big chunk or somewhere the 
flush is set to zero. I dont know yet, still trying to figgure that out.

The modified script is attached.

Cheers
Dimitar


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From lsbrath at gmail.com  Mon Nov 29 16:22:09 2010
From: lsbrath at gmail.com (Mgavi Brathwaite)
Date: Mon, 29 Nov 2010 16:22:09 -0500
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
Message-ID: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>

Hello,

When I run
Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
package but can't figure out what the deal is. Any suggestions.

LomSpace

On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Only if the output appends to that file (I don't recall personally, so it's
> worth a try).
>
> chris
>
> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>
> > Wouldn't using a single filename be the way to go?
> >> my $filename = "blast_ressults.out";
> >>           $factory->save_output($filename);
> > Florent
> >
> >
> > On 09/11/10 19:05, njauxiongjie wrote:
> >> Hi,
> >>
> >> I have used the scripts list in section of "SYNOPSIS" in th webpage
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
> .
> >>
> >> there are two line of the code like below:
> >> my $filename = $result->query_name()."\.out";
> >>           $factory->save_output($filename);
> >> this saved the blast result in separated files by the query name.
> >>
> >> my question is: how can i save the blast results of all querys in one
> file?
> >>
> >>
> >>
> >> _______________________________________________
> >> 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 cjfields at illinois.edu  Mon Nov 29 16:40:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 15:40:08 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
	<AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
Message-ID: <EE86D059-1DAF-478B-9610-0821D6D239E7@illinois.edu>

You haven't installed BioPerl (you need more than Bio::Tools::Run::RemoteBlast).  Please see bioperl.org for installation instructions.

chris

On Nov 29, 2010, at 3:22 PM, Mgavi Brathwaite wrote:

> Hello,
> 
> When I run
> Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
> Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
> package but can't figure out what the deal is. Any suggestions.
> 
> LomSpace
> 
> On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Only if the output appends to that file (I don't recall personally, so it's
>> worth a try).
>> 
>> chris
>> 
>> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>> 
>>> Wouldn't using a single filename be the way to go?
>>>> my $filename = "blast_ressults.out";
>>>>          $factory->save_output($filename);
>>> Florent
>>> 
>>> 
>>> On 09/11/10 19:05, njauxiongjie wrote:
>>>> Hi,
>>>> 
>>>> I have used the scripts list in section of "SYNOPSIS" in th webpage
>> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
>> .
>>>> 
>>>> there are two line of the code like below:
>>>> my $filename = $result->query_name()."\.out";
>>>>          $factory->save_output($filename);
>>>> this saved the blast result in separated files by the query name.
>>>> 
>>>> my question is: how can i save the blast results of all querys in one
>> file?
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jason at bioperl.org  Mon Nov 29 21:19:56 2010
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 29 Nov 2010 18:19:56 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45F4C.7050102@bioperl.org>

Dimitar -

In terms of your question - a GenBank db query previously (ie 4-5 years 
ago when this was written) WOULD NOT return a sequence if a GenPept ID 
was specified so we had to have a separate module for GenBank and 
GenPept db querying since there was a different set of parameters - I 
think that changed so that most of the queries can run through GenBank

I see that must have been improved at NCBI.  For the record if you want 
the full GenPept record with features and annotations you just request a 
different db, in this case 'gb' for genbank instead of the fasta source
As in: http://gist.github.com/721012

But maybe you already figured it out?

-jason
Chris Fields wrote, On 11/29/10 6:39 AM:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org



From dimitark at bii.a-star.edu.sg  Mon Nov 29 21:54:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 10:54:50 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF45F4C.7050102@bioperl.org>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org>
Message-ID: <4CF4677A.5010604@bii.a-star.edu.sg>

On 11/30/2010 10:19 AM, Jason Stajich wrote:
> Dimitar -
>
> In terms of your question - a GenBank db query previously (ie 4-5 
> years ago when this was written) WOULD NOT return a sequence if a 
> GenPept ID was specified so we had to have a separate module for 
> GenBank and GenPept db querying since there was a different set of 
> parameters - I think that changed so that most of the queries can run 
> through GenBank
>
> I see that must have been improved at NCBI.  For the record if you 
> want the full GenPept record with features and annotations you just 
> request a different db, in this case 'gb' for genbank instead of the 
> fasta source
> As in: http://gist.github.com/721012
>
> But maybe you already figured it out?
>
> -jason
> Chris Fields wrote, On 11/29/10 6:39 AM:
>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>
>>> Hi again,
>>> it seems that when i download (with 'download_query_genbank.pl') the 
>>> whole proteome from NCBI in fasta format it is first being 
>>> downloaded and from it is being created some kind of 
>>> SeqFastaSpeedFactory and after that from it is being copied to the 
>>> output file. But i want to download and write to output file one by 
>>> one so i can see the download progress(which is working for genbank 
>>> data).
>>>
>>> Its frustrating :)
>>>
>>> Any ideas where to look for solution
>>> Cheers
>>> Dimitar
>>
>> You can't do this with the default script, but you can use a modified 
>> version and, where you are retrieving a sequence stream, in the last 
>> four lines:
>>
>> my $stream = $dbh->get_Stream_by_query($query);
>> while( my $seq = $stream->next_seq ) {
>>     $out->write_seq($seq);
>> }
>>
>> insert an iterator in the loop that indicates progress.  Realize the 
>> sequence data is processed through Bio::SeqIO, so it won't be exactly 
>> the same as what is retrieved from GenBank, but it should be very close.
>>
>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a 
>> bit more complicated.
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Thank you Jason,
i figured that out yes :)
I know am wandering how to get the GI list so i can download by ID or 
ACC and not by query when i download fasta. I have the simple code:
-------------
my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
                                        -query=>$query_str);

my $count=$query->count;
my @ids=$query->ids; <------- error msg here
------------
but i get an error msg:

MSG: Id list has been truncated even after maxids requested.

How can i get the ID/ACC? Any idea?

Thank you
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg



From dimitark at bii.a-star.edu.sg  Mon Nov 29 20:39:07 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:39:07 +0800
Subject: [Bioperl-l] Bioperl-l Digest, Vol 91, Issue 20
In-Reply-To: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
References: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
Message-ID: <4CF455BB.4060608@bii.a-star.edu.sg>

On 11/30/2010 01:00 AM, 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
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
>
>
> Today's Topics:
>
>     1.  genbank (Dimitar Kenanov)
>     2. Re:  genbank (Chris Fields)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Nov 2010 17:35:26 +0800
> From: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Subject: [Bioperl-l] genbank
> To: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<4CF373DE.4070902 at bii.a-star.edu.sg>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the
> whole proteome from NCBI in fasta format it is first being downloaded
> and from it is being created some kind of SeqFastaSpeedFactory and after
> that from it is being copied to the output file. But i want to download
> and write to output file one by one so i can see the download
> progress(which is working for genbank data).
>
> Its frustrating :)
>
> Any ideas where to look for solution
> Cheers
> Dimitar
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 29 Nov 2010 08:39:16 -0600
> From: Chris Fields<cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] genbank
> To: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Cc: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<F3C80557-52DE-4D60-9E72-0660031D8F46 at illinois.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>
>
> ------------------------------
>
> _______________________________________________
> 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 91, Issue 20
> *****************************************
>
>    

Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

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From dimitark at bii.a-star.edu.sg  Mon Nov 29 20:50:42 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:50:42 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45872.1060405@bii.a-star.edu.sg>

On 11/29/2010 10:39 PM, Chris Fields wrote:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>    
Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

-------------- next part --------------
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From cjfields at illinois.edu  Mon Nov 29 22:42:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 21:42:14 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4677A.5010604@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
Message-ID: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>

On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:

> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>> Dimitar -
>> 
>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>> 
>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>> As in: http://gist.github.com/721012
>> 
>> But maybe you already figured it out?
>> 
>> -jason
>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>> 
>>>> Hi again,
>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>> 
>>>> Its frustrating :)
>>>> 
>>>> Any ideas where to look for solution
>>>> Cheers
>>>> Dimitar
>>> 
>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>> 
>>> my $stream = $dbh->get_Stream_by_query($query);
>>> while( my $seq = $stream->next_seq ) {
>>>    $out->write_seq($seq);
>>> }
>>> 
>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>> 
>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>> 
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> Thank you Jason,
> i figured that out yes :)
> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
> -------------
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>                                       -query=>$query_str);
> 
> my $count=$query->count;
> my @ids=$query->ids; <------- error msg here
> ------------
> but i get an error msg:
> 
> MSG: Id list has been truncated even after maxids requested.
> 
> How can i get the ID/ACC? Any idea?
> 
> Thank you
> Dimitar

Dimitar, 

You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:

----------------------------------------------
use Bio::DB::Query::GenBank;

my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-maxids => 40000,
                                       -db=>'protein',
                                      -query=>$query_str);

my $count=$query->count;
say "Count: $count";

my @ids=$query->ids;
say scalar(@ids); # equal to $count
----------------------------------------------

Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.

chris






From dimitark at bii.a-star.edu.sg  Tue Nov 30 04:04:30 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 17:04:30 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
Message-ID: <4CF4BE1E.6090100@bii.a-star.edu.sg>

On 11/30/2010 11:42 AM, Chris Fields wrote:
> On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:
>
>    
>> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>>      
>>> Dimitar -
>>>
>>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>>>
>>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>>> As in: http://gist.github.com/721012
>>>
>>> But maybe you already figured it out?
>>>
>>> -jason
>>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>>        
>>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>>>
>>>>          
>>>>> Hi again,
>>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>>>
>>>>> Its frustrating :)
>>>>>
>>>>> Any ideas where to look for solution
>>>>> Cheers
>>>>> Dimitar
>>>>>            
>>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>>>
>>>> my $stream = $dbh->get_Stream_by_query($query);
>>>> while( my $seq = $stream->next_seq ) {
>>>>     $out->write_seq($seq);
>>>> }
>>>>
>>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>>>
>>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>>>
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>          
>>>        
>> Thank you Jason,
>> i figured that out yes :)
>> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
>> -------------
>> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
>> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>>                                        -query=>$query_str);
>>
>> my $count=$query->count;
>> my @ids=$query->ids;<------- error msg here
>> ------------
>> but i get an error msg:
>>
>> MSG: Id list has been truncated even after maxids requested.
>>
>> How can i get the ID/ACC? Any idea?
>>
>> Thank you
>> Dimitar
>>      
> Dimitar,
>
> You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:
>
> ----------------------------------------------
> use Bio::DB::Query::GenBank;
>
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-maxids =>  40000,
>                                         -db=>'protein',
>                                        -query=>$query_str);
>
> my $count=$query->count;
> say "Count: $count";
>
> my @ids=$query->ids;
> say scalar(@ids); # equal to $count
> ----------------------------------------------
>
> Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.
>
> chris
>
>
>
>    
Hi again,
i managed to solve my problem. It may be dirty but it works the way i 
want :)
I reworked the 'download_query_genbank.pl' (attached). Now i can get the 
seqs in full fasta for proteomes and genomes and the genpept report 
files for the proteomes.
For DB handle i only use GenPept now cos it gives me stream which i can 
track with term::progressbar.

For the output i use 2 cases:
-----------------
while( my $seq = $stream->next_seq ) {
     #DIMITAR
     my($gi,$locus,$refnum,$desc,$seqstr);
     if($retformat eq 'fasta'){ <-------------------------| for the 
fasta as i want it
         check_progress($prgs,$seqnum,$count);
         $locus=$seq->display_id;
         $refnum=$seq->accession_number;
         $gi=$seq->primary_id;
         $desc=$seq->desc;
         $desc=~s/\.$//;
         $seqstr=$seq->seq;
         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
     }else{
         check_progress($prgs,$seqnum,$count);
         $out->write_seq($seq); <--------------------------| for the 
genbank reports
     }
     $seqnum++;
     #DIMITAR

#    $out->write_seq($seq);#original

}
------------------

Thank you for your help and time.

Cheers
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

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From jason at bioperl.org  Tue Nov 30 12:06:08 2010
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Nov 2010 09:06:08 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4BE1E.6090100@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
	<4CF4BE1E.6090100@bii.a-star.edu.sg>
Message-ID: <4CF52F00.5000803@bioperl.org>

great - the whole point of the scripts are as examples really, not that 
you need to send patches back to show everything that you modified, but 
that you modify to use modules and code to do whatever special thing you 
want. The hope is that the modules are flexible enough that you can 
write the script to accomplish your goal.

BTW - the one thing you can't recover from the GBK version of the file 
is the source of the accession number -- you have hardcoded in 'ref' but 
it can be 'gb', 'emb', 'sp' etc this field isn't part of the genbank 
record unfortunately -- one can come up with a pattern based on 
knowledge of accession number formats but I don't know that anyone has 
really been that worried about that sort of thing to try and write 
something for it.

>>
> Hi again,
> i managed to solve my problem. It may be dirty but it works the way i 
> want :)
> I reworked the 'download_query_genbank.pl' (attached). Now i can get 
> the seqs in full fasta for proteomes and genomes and the genpept 
> report files for the proteomes.
> For DB handle i only use GenPept now cos it gives me stream which i 
> can track with term::progressbar.
>
> For the output i use 2 cases:
> -----------------
> while( my $seq = $stream->next_seq ) {
>     #DIMITAR
>     my($gi,$locus,$refnum,$desc,$seqstr);
>     if($retformat eq 'fasta'){ <-------------------------| for the 
> fasta as i want it
>         check_progress($prgs,$seqnum,$count);
>         $locus=$seq->display_id;
>         $refnum=$seq->accession_number;
>         $gi=$seq->primary_id;
>         $desc=$seq->desc;
>         $desc=~s/\.$//;
>         $seqstr=$seq->seq;
>         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
>     }else{
>         check_progress($prgs,$seqnum,$count);
>         $out->write_seq($seq); <--------------------------| for the 
> genbank reports
>     }
>     $seqnum++;
>     #DIMITAR
>
> #    $out->write_seq($seq);#original
>
> }
> ------------------
>
> Thank you for your help and time.
>
> Cheers
> Dimitar
>

-- 
Jason Stajich
jason at bioperl.org



From chiragmatkarbioinfo at gmail.com  Mon Nov  1 02:58:55 2010
From: chiragmatkarbioinfo at gmail.com (chirag matkar)
Date: Mon, 1 Nov 2010 13:58:55 +0700
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
Message-ID: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar


From Russell.Smithies at agresearch.co.nz  Tue Nov  2 22:11:36 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Nov 2010 15:11:36 +1300
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313A9B7D7C@exchsth.agresearch.co.nz>

Seems a bit like overkill, what's wrong with wget?

wget -i <list_of_urls.txt>

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
Sent: Monday, 1 November 2010 7:59 p.m.
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to download PDB files using Bioperl script

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar
_______________________________________________
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 miguel.pignatelli at uv.es  Wed Nov  3 05:42:49 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 10:42:49 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4C8606FA.3000509@fmi.ch>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch>
Message-ID: <4CD12E99.7080701@uv.es>

Hi all,

I have written a couple of modules that overlap certain functionality 
with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
certain constraints in the environment I had to run it (GRID) made 
impossible to use a bioperl based solution.


The main features of these modules are:

+ No dependencies of non-standard Perl modules
+ NCBI and RDP based taxonomies supported
+ Very fast and low memory footprint -- orders of magnitude faster than 
Bioperl modules (for the tasks they are designed for --).

Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in 
completeness or integration with other tools (e.g. rest of bioperl suit) 
but they are handy for mapping very large datasets (for example blast 
results) with the NCBI or RDP Taxonomy.

The modules are:

Taxonomy::Base -- Finds ancestors, ranks, converts between
                   names, ranks and IDs, etc...

Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file

Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
                   (nodes.dmp and names.dmp)
                   (Similar to Bio::DB::Taxonomy::flatfile)

Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
                             NCBI GIs to Taxids.
                             Uses a binary lookup table.

These modules are being used by several groups now -- mainly working 
with large metagenomics datasets -- and I am considering uploading them 
to CPAN, but I am not clear on where these modules should be placed there.

How do you think I should name these modules? (e.g. where these modules 
should live in CPAN?) Their natural place could be under 
Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
convenient) without being part of Bioperl? Any other suggestions?

Thank you very much in advance,

M;

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


From gabbyteku at gmail.com  Wed Nov  3 07:53:42 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Wed, 3 Nov 2010 13:53:42 +0200
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
Message-ID: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>

I can't get my esearch to work. It's as follows:

my $eut_obj = Bio::DB::EUtilities->new(   -eutil      => 'esearch',
                                                  -email      => '
myemail at gmail.com',
                                                  -term       =>
'$genename[SYMB] AND homo_sapiens[ORGN]',
                                                  -db         => 'geo',
                                                  -usehistory => 'y'
                                              );

When I run this using a gene symbol, it works fine.
But then when I run it as it is with a gene's symbol changed to
$genename(stores the gene's symbol/name), it fails.
How can this be fixed?

Thanks


From miguel.pignatelli at uv.es  Wed Nov  3 09:51:18 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 14:51:18 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>
Message-ID: <4CD168D6.8030100@uv.es>

Hi all,

I have seen in the Nextgen section of the bioperl wiki 
(http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in 
the wish list. I have some code written for parsing SFF files that I can 
refactor and contribute with it.

Does anyone already took this?

Best regards,

M;



From biopython at maubp.freeserve.co.uk  Wed Nov  3 10:28:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 3 Nov 2010 14:28:56 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <AANLkTikAAz5FP3kiN0U6dtnvpgWAHtLu5DoEBcm_yzVD@mail.gmail.com>

On 2010/11/3 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Hi all,
>
> I have seen in the Nextgen section of the bioperl wiki
> (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the
> wish list. I have some code written for parsing SFF files that I can
> refactor and contribute with it.
>
> Does anyone already took this?
>
> Best regards,
>
> M;

Hi,

This sounds like a good thing for BioPerl.

If you hook this up into Bio::SeqIO then for consistency with
Biopython for the format name note we use "sff" as the full
reads, and "sff-trim" for the reads with the quality trimming
applied. If BioPerl has some built in way to hold a trimmed
sequence (with the head/tail still accessible) then this may
not be a good solution.

Peter


From scott at scottcain.net  Wed Nov  3 10:59:12 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 10:59:12 -0400
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
In-Reply-To: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
References: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
Message-ID: <AANLkTi=VgyrfZPPt+--pVJxfgh9QRsh_OLpsBq79F8z1@mail.gmail.com>

Hi Gabriel,

It looks to me like you've got a few things going wrong.  First, you
are using single quotes for the right hand side of the -term value.
In perl, single quotes are non-interpolating, which means variables
won't be substituted in.  However, if you switch to double quotes,
you'll still have a problem, because this:

  $genename[SYMB]

looks like you are trying to access an element of an array called
genename with a constant called SYMB, which of course you aren't, so
the perl interpreter will die with that.  You can rewrite that section
like this:

  $genename . '[SYMB] AND homo_sapiens[ORGN]'

so that the variable interpolation is moved out of the single quotes.

Scott




On Wed, Nov 3, 2010 at 7:53 AM, gabriel teku <gabbyteku at gmail.com> wrote:
> I can't get my esearch to work. It's as follows:
>
> my $eut_obj = Bio::DB::EUtilities->new( ? -eutil ? ? ?=> 'esearch',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-email ? ? ?=> '
> myemail at gmail.com',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-term ? ? ? =>
> '$genename[SYMB] AND homo_sapiens[ORGN]',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-db ? ? ? ? => 'geo',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-usehistory => 'y'
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> When I run this using a gene symbol, it works fine.
> But then when I run it as it is with a gene's symbol changed to
> $genename(stores the gene's symbol/name), it fails.
> How can this be fixed?
>
> Thanks
> _______________________________________________
> 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 cseligman at earthlink.net  Wed Nov  3 12:07:05 2010
From: cseligman at earthlink.net (Chet Seligman)
Date: Wed, 3 Nov 2010 09:07:05 -0700
Subject: [Bioperl-l] BioPerl installation was incomplete
Message-ID: <001001cb7b71$294f12c0$7bed3840$@earthlink.net>

My perl is ActiveState 5.10.1

I installed with PPM using the following repositories:

BioPerl-Regular Releases

BioPerl-Release Candidates

Kobes

Bribes

Trouchelle

 

I got the following warnings:

Can't find any package that provides DB_File:: for Bundle-BioPerl-Core

WARNING: Can't find any package that provides IPC::Run for GraphViz

WARNING: Can't find any package that provides Apache:: for SOAP-Lite

 

I do have DB_File installed but do not have:

IPC::Run or,

Apache:: for SOAP-Lite

 

I did try to install SOAP-Lite according to the instructions in the Wiki but
no luck.

In PPM-edit repositories I saw that Kobes, Bribes & Trouchelle all showed
"0"

So how do I get SOAP-Lite, Apache and IPC::Run?

 

Chet Seligman



From cjfields at illinois.edu  Wed Nov  3 13:18:38 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 12:18:38 -0500
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>

Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  

I suggest, though, for long-term maintenance you could be added as a collaborator.  

chris

On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
> 
> Does anyone already took this?
> 
> Best regards,
> 
> M;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hanbobio at 126.com  Tue Nov  2 01:29:50 2010
From: hanbobio at 126.com (hanbobio)
Date: Tue, 2 Nov 2010 13:29:50 +0800 (CST)
Subject: [Bioperl-l] bioperl modules
Message-ID: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>

Hi, all.
 I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:

liaoy at linux:~/nd-hn> perl nd-hn.pl

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.

BEGIN failed--compilation aborted at nd-hn.pl line 26.
 The detail of this script in two ways: the attached file and the following script.
Would you be kindly to test my script and give me some modification or suggestion?
 I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
Thank you very much for your advice.
 
Best regards
Yusheng Liao 2010-11-02
 
# retrive sequence from Genbank
use strict;
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;
open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
my $query = Bio::DB::Query::GenBank->new
    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
   -db      => 'nucleotide');
my $seqio = $gb->get_Stream_by_query($query);
my $i=0;
while( defined (my $seq = $seqio->next_seq )) {
$seqout->write_seq($seq);
$i++;
print ".";
}
print "$i \n";
# run multi sequence alignment
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::SimpleAlign;
use Bio::AlignIO::clustalw;
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $ktuple = 3;
$factory->ktuple($ktuple); 
my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
my $aln = $factory->align($inputfilename);
my $alignout->write_aln(my $aln);

my $line;
my @array=('A','C','G','T','-');
my @arrayX=('a','c','g','t','-');
my @arrayA;
my @arrayB;
my ($i,$j,$k);
my (@a, at b);
my %hash;
open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
while($line=<FILE>){
      chomp;
      if($line=~ /CLUSTAL/){
            next;
      }elsif($line=~ /^[A-Za-z0-9]/){
            @a=split /\s+/,$line;
            if(defined($hash{$a[0]})){
                  push @{$hash{$a[0]}}, $line;
            }else{
                  ${$hash{$a[0]}}[0]=$line;
                  push @b,$a[0];
            }
       }
}
for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
      for(my $l=0;$l<=$#b;$l++){
            print OUT ${$hash{$b[$l]}}[$k];
            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
            @arrayA=split //,$seq;
            for($i=0;$i<=$#arrayA;$i++){
                  if($arrayA[$i] =~ /A/i){
                        $arrayB[0][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /C/i){
                        $arrayB[1][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /G/i){
                        $arrayB[2][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /T/i){
                        $arrayB[3][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\./i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\-/i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
            }
       }
       for($j=0;$j<=$#arrayA;$j++){
              my $large=0;my $pos=0;
              for($i=0;$i<=4;$i++){
                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
                    if($arrayB[$i][$j]>$large){
                          $large=$arrayB[$i][$j];
                          $pos=$i;
                    }
              }
                    if($large>0.5){
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]=$array[$pos];
                    }else{
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]='N';
                    }
       }
       for($i=0;$i<=5;$i++){
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                    if($arrayB[$i][$j]>0){
                           printf OUT "%.2f\t",$arrayB[$i][$j];
                    }else{
                           print OUT "0\t";
                    }
              }
              print OUT "\n";
        }
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUT "$arrayB[6][$j]\t";
              }
              print OUT "\n";
              for($j=0;$j<=15;$j++){
                    print OUTA " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUTA "$arrayB[6][$j]";
              }
              print OUTA "\n";
        @arrayB=undef;
}
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From daniel.standage at gmail.com  Wed Nov  3 14:42:07 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 13:42:07 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
Message-ID: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>

Hi

I've got a simple script that is filtering some GFF3 data. The
Bio::Tools::GFF class has methods for reading and writing features and
reading regions (segments), but I cannot find a method for writing regions.
It's not hard to just print out the sequence-region line from the
LocatableSeq object, but then these lines are printed out before the
gff-version line (which is a no-no). Any suggestions about how to handle
this?

Thanks.

-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From scott at scottcain.net  Wed Nov  3 16:09:45 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:09:45 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
Message-ID: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>

Hi Daniel,

Why do you need the sequence-region line?  It is mostly just
informational.  If you want to define the reference sequence for the
features in the GFF file, I would suggest printing out a full GFF line
for the reference sequence instead anyway.  That way, it can have all
the information that a GFF line can encode, like a source and type, as
well as information in the ninth column.

That said, Bio::Tools::GFF probably does lack that method.  The code
in it is probably a little outdated.

Scott


On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> Hi
>
> I've got a simple script that is filtering some GFF3 data. The
> Bio::Tools::GFF class has methods for reading and writing features and
> reading regions (segments), but I cannot find a method for writing regions.
> It's not hard to just print out the sequence-region line from the
> LocatableSeq object, but then these lines are printed out before the
> gff-version line (which is a no-no). Any suggestions about how to handle
> this?
>
> Thanks.
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> 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 scott at scottcain.net  Wed Nov  3 16:19:07 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:19:07 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
Message-ID: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>

Ah, I see.  Well, you should complain to the authors that
sequence-region isn't a required directive (though if you made that
complaint to me, I'd say "well, it is for this tool" :-)

Of course, you could also use Bio::Graphics or GBrowse to do the
drawing, then I could do more to help. :-)

Scott


On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I'm using a tool called AnnotationSketch (part of the GenomeTools package)
> to create graphics from my GFF3 files. It complains when sequence-region
> lines are not included, even when the reference is printed as a feature.
> That's what got me interested in the problem in the first place.
>
> Thanks for the info, I'll figure something out.
>
> Daniel
>
> On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> Why do you need the sequence-region line? ?It is mostly just
>> informational. ?If you want to define the reference sequence for the
>> features in the GFF file, I would suggest printing out a full GFF line
>> for the reference sequence instead anyway. ?That way, it can have all
>> the information that a GFF line can encode, like a source and type, as
>> well as information in the ninth column.
>>
>> That said, Bio::Tools::GFF probably does lack that method. ?The code
>> in it is probably a little outdated.
>>
>> Scott
>>
>>
>> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > Hi
>> >
>> > I've got a simple script that is filtering some GFF3 data. The
>> > Bio::Tools::GFF class has methods for reading and writing features and
>> > reading regions (segments), but I cannot find a method for writing
>> > regions.
>> > It's not hard to just print out the sequence-region line from the
>> > LocatableSeq object, but then these lines are printed out before the
>> > gff-version line (which is a no-no). Any suggestions about how to handle
>> > this?
>> >
>> > Thanks.
>> >
>> > --
>> > Daniel S. Standage
>> > Graduate Research Assistant
>> > Bioinformatics and Computational Biology Program
>> > Iowa State University
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



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



From daniel.standage at gmail.com  Wed Nov  3 16:14:02 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:14:02 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
Message-ID: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>

I'm using a tool called AnnotationSketch (part of the GenomeTools package)
to create graphics from my GFF3 files. It complains when sequence-region
lines are not included, even when the reference is printed as a feature.
That's what got me interested in the problem in the first place.

Thanks for the info, I'll figure something out.

Daniel

On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Daniel,
>
> Why do you need the sequence-region line?  It is mostly just
> informational.  If you want to define the reference sequence for the
> features in the GFF file, I would suggest printing out a full GFF line
> for the reference sequence instead anyway.  That way, it can have all
> the information that a GFF line can encode, like a source and type, as
> well as information in the ninth column.
>
> That said, Bio::Tools::GFF probably does lack that method.  The code
> in it is probably a little outdated.
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > Hi
> >
> > I've got a simple script that is filtering some GFF3 data. The
> > Bio::Tools::GFF class has methods for reading and writing features and
> > reading regions (segments), but I cannot find a method for writing
> regions.
> > It's not hard to just print out the sequence-region line from the
> > LocatableSeq object, but then these lines are printed out before the
> > gff-version line (which is a no-no). Any suggestions about how to handle
> > this?
> >
> > Thanks.
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > 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
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From daniel.standage at gmail.com  Wed Nov  3 16:29:29 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:29:29 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
	<AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
Message-ID: <AANLkTikv-N-45cgapmZ_yHqHLFtNroBm9KU+ehXn=qad@mail.gmail.com>

Yeah, I guess it's not a show stopper, since it still generates the graphics
fine. The output that clutters the terminal is still annoying, but I can
live with that. Thanks!

Daniel

On Wed, Nov 3, 2010 at 3:19 PM, Scott Cain <scott at scottcain.net> wrote:

> Ah, I see.  Well, you should complain to the authors that
> sequence-region isn't a required directive (though if you made that
> complaint to me, I'd say "well, it is for this tool" :-)
>
> Of course, you could also use Bio::Graphics or GBrowse to do the
> drawing, then I could do more to help. :-)
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > I'm using a tool called AnnotationSketch (part of the GenomeTools
> package)
> > to create graphics from my GFF3 files. It complains when sequence-region
> > lines are not included, even when the reference is printed as a feature.
> > That's what got me interested in the problem in the first place.
> >
> > Thanks for the info, I'll figure something out.
> >
> > Daniel
> >
> > On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Daniel,
> >>
> >> Why do you need the sequence-region line?  It is mostly just
> >> informational.  If you want to define the reference sequence for the
> >> features in the GFF file, I would suggest printing out a full GFF line
> >> for the reference sequence instead anyway.  That way, it can have all
> >> the information that a GFF line can encode, like a source and type, as
> >> well as information in the ninth column.
> >>
> >> That said, Bio::Tools::GFF probably does lack that method.  The code
> >> in it is probably a little outdated.
> >>
> >> Scott
> >>
> >>
> >> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> >> <daniel.standage at gmail.com> wrote:
> >> > Hi
> >> >
> >> > I've got a simple script that is filtering some GFF3 data. The
> >> > Bio::Tools::GFF class has methods for reading and writing features and
> >> > reading regions (segments), but I cannot find a method for writing
> >> > regions.
> >> > It's not hard to just print out the sequence-region line from the
> >> > LocatableSeq object, but then these lines are printed out before the
> >> > gff-version line (which is a no-no). Any suggestions about how to
> handle
> >> > this?
> >> >
> >> > Thanks.
> >> >
> >> > --
> >> > Daniel S. Standage
> >> > Graduate Research Assistant
> >> > Bioinformatics and Computational Biology Program
> >> > Iowa State University
> >> > _______________________________________________
> >> > 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
> >
> >
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From cjfields at illinois.edu  Wed Nov  3 17:27:28 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 16:27:28 -0500
Subject: [Bioperl-l] bioperl modules
In-Reply-To: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
References: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
Message-ID: <2A3F6A7D-CF80-4C6D-8BE2-EEDA873BCC3D@illinois.edu>

You need to install bioperl-run to get Bio::Tools::Run::Alignment::Clustalw.

chris

On Nov 2, 2010, at 12:29 AM, hanbobio wrote:

> Hi, all.
> I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:
> 
> liaoy at linux:~/nd-hn> perl nd-hn.pl
> 
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.
> 
> BEGIN failed--compilation aborted at nd-hn.pl line 26.
> The detail of this script in two ways: the attached file and the following script.
> Would you be kindly to test my script and give me some modification or suggestion?
> I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
> Thank you very much for your advice.
> 
> Best regards
> Yusheng Liao 2010-11-02
> 
> # retrive sequence from Genbank
> use strict;
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> my $gb = new Bio::DB::GenBank;
> open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
> my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
> my $query = Bio::DB::Query::GenBank->new
>    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
>   -db      => 'nucleotide');
> my $seqio = $gb->get_Stream_by_query($query);
> my $i=0;
> while( defined (my $seq = $seqio->next_seq )) {
> $seqout->write_seq($seq);
> $i++;
> print ".";
> }
> print "$i \n";
> # run multi sequence alignment
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::SimpleAlign;
> use Bio::AlignIO::clustalw;
> my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
> my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> my $ktuple = 3;
> $factory->ktuple($ktuple); 
> my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
> my $aln = $factory->align($inputfilename);
> my $alignout->write_aln(my $aln);
> 
> my $line;
> my @array=('A','C','G','T','-');
> my @arrayX=('a','c','g','t','-');
> my @arrayA;
> my @arrayB;
> my ($i,$j,$k);
> my (@a, at b);
> my %hash;
> open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
> open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
> open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
> while($line=<FILE>){
>      chomp;
>      if($line=~ /CLUSTAL/){
>            next;
>      }elsif($line=~ /^[A-Za-z0-9]/){
>            @a=split /\s+/,$line;
>            if(defined($hash{$a[0]})){
>                  push @{$hash{$a[0]}}, $line;
>            }else{
>                  ${$hash{$a[0]}}[0]=$line;
>                  push @b,$a[0];
>            }
>       }
> }
> for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
>      for(my $l=0;$l<=$#b;$l++){
>            print OUT ${$hash{$b[$l]}}[$k];
>            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
>            @arrayA=split //,$seq;
>            for($i=0;$i<=$#arrayA;$i++){
>                  if($arrayA[$i] =~ /A/i){
>                        $arrayB[0][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /C/i){
>                        $arrayB[1][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /G/i){
>                        $arrayB[2][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /T/i){
>                        $arrayB[3][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\./i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\-/i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>            }
>       }
>       for($j=0;$j<=$#arrayA;$j++){
>              my $large=0;my $pos=0;
>              for($i=0;$i<=4;$i++){
>                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
>                    if($arrayB[$i][$j]>$large){
>                          $large=$arrayB[$i][$j];
>                          $pos=$i;
>                    }
>              }
>                    if($large>0.5){
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]=$array[$pos];
>                    }else{
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]='N';
>                    }
>       }
>       for($i=0;$i<=5;$i++){
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                    if($arrayB[$i][$j]>0){
>                           printf OUT "%.2f\t",$arrayB[$i][$j];
>                    }else{
>                           print OUT "0\t";
>                    }
>              }
>              print OUT "\n";
>        }
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUT "$arrayB[6][$j]\t";
>              }
>              print OUT "\n";
>              for($j=0;$j<=15;$j++){
>                    print OUTA " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUTA "$arrayB[6][$j]";
>              }
>              print OUTA "\n";
>        @arrayB=undef;
> }
> <Moduletest.pl.pl>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Wed Nov  3 22:34:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 21:34:30 -0500
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
Message-ID: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>

Miguel,

(Caveat: You should also ask this on the perl module-authors list, just in case: http://lists.perl.org/list/module-authors.html)

Not sure how the other devs feel, but I personally don't think the Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, for example).  It's a fairly generic top-level name.  The only worry I have is if these are too similar to current BioPerl modules; Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN related to BioPerl modules.   

Saying that, tagging them as *::Lite might be fine, as long as the documentation indicated these are not related to BioPerl.  Anyone else want to chime in?  Maybe releasing them as a top-level Taxonomy?  

chris

On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have written a couple of modules that overlap certain functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because certain constraints in the environment I had to run it (GRID) made impossible to use a bioperl based solution.
> 
> 
> The main features of these modules are:
> 
> + No dependencies of non-standard Perl modules
> + NCBI and RDP based taxonomies supported
> + Very fast and low memory footprint -- orders of magnitude faster than Bioperl modules (for the tasks they are designed for --).
> 
> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in completeness or integration with other tools (e.g. rest of bioperl suit) but they are handy for mapping very large datasets (for example blast results) with the NCBI or RDP Taxonomy.
> 
> The modules are:
> 
> Taxonomy::Base -- Finds ancestors, ranks, converts between
>                  names, ranks and IDs, etc...
> 
> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
> 
> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>                  (nodes.dmp and names.dmp)
>                  (Similar to Bio::DB::Taxonomy::flatfile)
> 
> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>                            NCBI GIs to Taxids.
>                            Uses a binary lookup table.
> 
> These modules are being used by several groups now -- mainly working with large metagenomics datasets -- and I am considering uploading them to CPAN, but I am not clear on where these modules should be placed there.
> 
> How do you think I should name these modules? (e.g. where these modules should live in CPAN?) Their natural place could be under Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and convenient) without being part of Bioperl? Any other suggestions?
> 
> Thank you very much in advance,
> 
> M;
> 
> ----------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Thu Nov  4 04:54:33 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 4 Nov 2010 09:54:33 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <4F9F218F-22EC-46B8-8BAB-82BD0956FB76@sbc.su.se>

I agree with Chris. You're welcome to put your code in the Bio:: namespace ? it's not reserved for BioPerl ? but since there are already modules with Taxonomy in their names, it would be likely to cause confusion.

So, if your modules are renamed to be sufficiently distinguishable from existing Taxonomy modules, putting them under Bio:: should be no problem.

Otherwise, I would go whatever the modules list folks recommend.

Dave



From miguel.pignatelli at uv.es  Thu Nov  4 07:13:20 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:13:20 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>
	<4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
Message-ID: <4CD29550.6030005@uv.es>

Thanks Chris,

I will get in touch again when I am able to hook a working module (I 
will check Biopython's Bio.Seq.SffIO)

M;


Chris Fields wrote:
> Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  
> 
> I suggest, though, for long-term maintenance you could be added as a collaborator.  
> 
> chris
> 
> On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:
> 
>> Hi all,
>>
>> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
>>
>> Does anyone already took this?
>>
>> Best regards,
>>
>> M;
>>
>> _______________________________________________
>> 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 biopython at maubp.freeserve.co.uk  Thu Nov  4 07:40:13 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 4 Nov 2010 11:40:13 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD29550.6030005@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
	<4CD29550.6030005@uv.es>
Message-ID: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>

2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Thanks Chris,
>
> I will get in touch again when I am able to hook a working module (I will
> check Biopython's Bio.Seq.SffIO)
>
> M;

Hi Miguel,

In case it helps, the Biopython SFF code is here - this includes embedded
documentation with test examples:

http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

We also have some test SFF files here (see the README file for details):

http://github.com/biopython/biopython/tree/master/Tests/Roche/

Peter


From pignatelli_mig at gva.es  Thu Nov  4 07:49:07 2010
From: pignatelli_mig at gva.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:49:07 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>	<4CD168D6.8030100@uv.es>	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>	<4CD29550.6030005@uv.es>
	<AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
Message-ID: <4CD29DB3.9010805@gva.es>

Thanks Peter, I have already took a look at the module. It will 
certainly help a lot. I also have some real SFF files from different 
collaborations that I can use for testing.

Let's roll up the sleeves...

M;


Peter wrote:
> 2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
>> Thanks Chris,
>>
>> I will get in touch again when I am able to hook a working module (I will
>> check Biopython's Bio.Seq.SffIO)
>>
>> M;
> 
> Hi Miguel,
> 
> In case it helps, the Biopython SFF code is here - this includes embedded
> documentation with test examples:
> 
> http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
> 
> We also have some test SFF files here (see the README file for details):
> 
> http://github.com/biopython/biopython/tree/master/Tests/Roche/
> 
> Peter


From hlapp at drycafe.net  Thu Nov  4 12:12:04 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 4 Nov 2010 12:12:04 -0400
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>

I agree - Bio:: isn't exclusive to BioPerl, but in choosing module  
name and namespace, as well as in documentation, try to minimize  
potential confusion for users.

	-hilmar
On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:

> Miguel,
>
> (Caveat: You should also ask this on the perl module-authors list,  
> just in case: http://lists.perl.org/list/module-authors.html)
>
> Not sure how the other devs feel, but I personally don't think the  
> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo,  
> for example).  It's a fairly generic top-level name.  The only worry  
> I have is if these are too similar to current BioPerl modules;  
> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN  
> related to BioPerl modules.
>
> Saying that, tagging them as *::Lite might be fine, as long as the  
> documentation indicated these are not related to BioPerl.  Anyone  
> else want to chime in?  Maybe releasing them as a top-level Taxonomy?
>
> chris
>
> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>
>> Hi all,
>>
>> I have written a couple of modules that overlap certain  
>> functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write  
>> them because certain constraints in the environment I had to run it  
>> (GRID) made impossible to use a bioperl based solution.
>>
>>
>> The main features of these modules are:
>>
>> + No dependencies of non-standard Perl modules
>> + NCBI and RDP based taxonomies supported
>> + Very fast and low memory footprint -- orders of magnitude faster  
>> than Bioperl modules (for the tasks they are designed for --).
>>
>> Of course, they do not compete with Bio::DB::Taxonomy and  
>> Bio::Taxon in completeness or integration with other tools (e.g.  
>> rest of bioperl suit) but they are handy for mapping very large  
>> datasets (for example blast results) with the NCBI or RDP Taxonomy.
>>
>> The modules are:
>>
>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>                 names, ranks and IDs, etc...
>>
>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>
>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>                 (nodes.dmp and names.dmp)
>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>
>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>                           NCBI GIs to Taxids.
>>                           Uses a binary lookup table.
>>
>> These modules are being used by several groups now -- mainly  
>> working with large metagenomics datasets -- and I am considering  
>> uploading them to CPAN, but I am not clear on where these modules  
>> should be placed there.
>>
>> How do you think I should name these modules? (e.g. where these  
>> modules should live in CPAN?) Their natural place could be under  
>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite /  
>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and  
>> convenient) without being part of Bioperl? Any other suggestions?
>>
>> Thank you very much in advance,
>>
>> M;
>>
>> ----------------------------------------------------
>> _______________________________________________
>> 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

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From kellert at ohsu.edu  Thu Nov  4 20:45:25 2010
From: kellert at ohsu.edu (Tom Keller)
Date: Thu, 4 Nov 2010 17:45:25 -0700
Subject: [Bioperl-l] parsing PubMed retrievals
Message-ID: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>

Greetings,
I'm getting the following error from the bioplerl 1.6.1 example

$ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.


Any suggestions for getting this to work?

thanks,


Tom
MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
503-494-2442
kellert at ohsu.edu<mailto:kellert at ohsu.edu>
Office: 6588 RJH (CROET/BasicScience)








From cjfields at illinois.edu  Fri Nov  5 00:28:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 4 Nov 2010 23:28:01 -0500
Subject: [Bioperl-l] parsing PubMed retrievals
In-Reply-To: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <EA90A6B2-7D87-4CC0-B4FB-D8A00FD5C77D@illinois.edu>

It seems that in some cases a webenv/querykey are not returned.  I have committed a fix to github for this which seems to fix the problem from our end.

https://github.com/bioperl/bioperl-live/commit/7c64e8410d291dbd7097b2cd8fc948d95063d153

chris

On Nov 4, 2010, at 7:45 PM, Tom Keller wrote:

> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> 
> Tom
> MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert at ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From miguel.pignatelli at uv.es  Fri Nov  5 05:31:46 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Fri, 05 Nov 2010 10:31:46 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
Message-ID: <4CD3CF02.9010608@uv.es>

Hi all,

In the perl module-authors list I have been suggested two nice alternatives:

Bio::Lite::Taxonomy::*
BioX::Taxonomy::*

If the devs don't have any objection/preference I will follow the first one.

Regards,

M;


Hilmar Lapp wrote:
> I agree - Bio:: isn't exclusive to BioPerl, but in choosing module name 
> and namespace, as well as in documentation, try to minimize potential 
> confusion for users.
> 
>     -hilmar
> On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:
> 
>> Miguel,
>>
>> (Caveat: You should also ask this on the perl module-authors list, 
>> just in case: http://lists.perl.org/list/module-authors.html)
>>
>> Not sure how the other devs feel, but I personally don't think the 
>> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, 
>> for example).  It's a fairly generic top-level name.  The only worry I 
>> have is if these are too similar to current BioPerl modules; 
>> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN 
>> related to BioPerl modules.
>>
>> Saying that, tagging them as *::Lite might be fine, as long as the 
>> documentation indicated these are not related to BioPerl.  Anyone else 
>> want to chime in?  Maybe releasing them as a top-level Taxonomy?
>>
>> chris
>>
>> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>>
>>> Hi all,
>>>
>>> I have written a couple of modules that overlap certain functionality 
>>> with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
>>> certain constraints in the environment I had to run it (GRID) made 
>>> impossible to use a bioperl based solution.
>>>
>>>
>>> The main features of these modules are:
>>>
>>> + No dependencies of non-standard Perl modules
>>> + NCBI and RDP based taxonomies supported
>>> + Very fast and low memory footprint -- orders of magnitude faster 
>>> than Bioperl modules (for the tasks they are designed for --).
>>>
>>> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon 
>>> in completeness or integration with other tools (e.g. rest of bioperl 
>>> suit) but they are handy for mapping very large datasets (for example 
>>> blast results) with the NCBI or RDP Taxonomy.
>>>
>>> The modules are:
>>>
>>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>>                 names, ranks and IDs, etc...
>>>
>>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>>
>>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>>                 (nodes.dmp and names.dmp)
>>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>>
>>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>>                           NCBI GIs to Taxids.
>>>                           Uses a binary lookup table.
>>>
>>> These modules are being used by several groups now -- mainly working 
>>> with large metagenomics datasets -- and I am considering uploading 
>>> them to CPAN, but I am not clear on where these modules should be 
>>> placed there.
>>>
>>> How do you think I should name these modules? (e.g. where these 
>>> modules should live in CPAN?) Their natural place could be under 
>>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
>>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
>>> convenient) without being part of Bioperl? Any other suggestions?
>>>
>>> Thank you very much in advance,
>>>
>>> M;
>>>
>>> ----------------------------------------------------
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From David.Messina at sbc.su.se  Fri Nov  5 06:36:38 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 11:36:38 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD3CF02.9010608@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
	<4CD3CF02.9010608@uv.es>
Message-ID: <5E0858F2-3957-46E1-BCD7-0F75FF44DE7D@sbc.su.se>

> Bio::Lite::Taxonomy::*
> BioX::Taxonomy::*

Either works for me.

Thanks for asking, Miguel, and I'm looking forward to checking them out!

Dave


From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 07:33:44 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 12:33:44 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
Message-ID: <4CD3EB98.3050508@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi folks,

https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser
contains my attempt to get a hmmer parser that is able to detect which
hmmer version output it's given and which parser to call in turn.

I chose to sneak in a Bio::SearchIO::hmmer class into the object
hierarchy that the hmmer2 parser (renamed to Bio::SearchIO::hmmer2) and
the hmmer3 parser subclass from.

I'm not sure if this is the best way to go, though, and I'd like to get
some feedback on the implementation.
The last six patches on
https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser are
the full changeset, the core of the change is in
https://github.com/kblin/bioperl-live/commit/2d4816f1d67880c69948b2ce529fdeb52e0d843f

Thanks in advance for your time,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From David.Messina at sbc.su.se  Fri Nov  5 08:35:32 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 13:35:32 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
Message-ID: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>

I may have missed some recent off-list discussion, but I thought we explicitly talked about *not* merging these since it will complicate future maintenance and Hmmer2 will be obsolete in the near future.


Dave




From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 08:56:23 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 13:56:23 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
Message-ID: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 13:35, Dave Messina wrote:
> I may have missed some recent off-list discussion, but I thought we
> explicitly talked about *not* merging these since it will complicate
> future maintenance and Hmmer2 will be obsolete in the near future.

Yes, that's what I thought until about last week. Then I was bitten by
the fact that Hmmer3 can't do global alignments, so you can't reliably
use Hmmer3 to extract protein domains using the domain's motif. As this
seems to be a common use case, I think we'll end up supporting hmmer2
for quite a while now.

There's currently no plans by the Hmmer authors to add globlal and
glocal (whole profile alignments against parts of the sequence)
alignments to hmmer3. They suggested to keep using hmmer2 for now.

For this reason I decided to try and merge the two parsers to a point
where users don't have to care which version of hmmer their file is.

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 10:17:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 09:17:03 -0500
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
Message-ID: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>

On Nov 5, 2010, at 7:56 AM, Kai Blin wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On 2010-11-05 13:35, Dave Messina wrote:
>> I may have missed some recent off-list discussion, but I thought we
>> explicitly talked about *not* merging these since it will complicate
>> future maintenance and Hmmer2 will be obsolete in the near future.
> 
> Yes, that's what I thought until about last week. Then I was bitten by
> the fact that Hmmer3 can't do global alignments, so you can't reliably
> use Hmmer3 to extract protein domains using the domain's motif. As this
> seems to be a common use case, I think we'll end up supporting hmmer2
> for quite a while now.
> 
> There's currently no plans by the Hmmer authors to add globlal and
> glocal (whole profile alignments against parts of the sequence)
> alignments to hmmer3. They suggested to keep using hmmer2 for now.
> 
> For this reason I decided to try and merge the two parsers to a point
> where users don't have to care which version of hmmer their file is.
> 
> Cheers,
> Kai

Makes sense to me.  We're tackling some Bio::Tree revisions next week, my guess is we can also get this added in.  I'm really keen on getting 1.6.2 out sometime soon, before things get really crazy for me this spring.

Key things to test: can specify the exact hmmer2/3 parser directly?  

   my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

Can one explicitly specify the hmmer parser variant?

   my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file => 'foo')

This will more than likely pop up.  I did something with Bio::SeqIO::fastq to allow specifying sanger/illumina/solexa variants, this would be similar in respect.

chris


From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 10:53:24 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 15:53:24 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
	<283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
Message-ID: <4CD41A64.4070104@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 15:17, Chris Fields wrote:

> Makes sense to me.  We're tackling some Bio::Tree revisions next
> week, my guess is we can also get this added in.  I'm really keen on
> getting 1.6.2 out sometime soon, before things get really crazy for
> me this spring.

I changed my mind about the hmmer parser just in time then, I guess. :)

> Key things to test: can specify the exact hmmer2/3 parser directly?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

That's how I started the development. But I just see I changed all tests
over, so I can't prove it. I've added some tests to show this is
equivalent. (907b7d0a2b93d4961f64)

> Can one explicitly specify the hmmer parser variant?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file
> => 'foo')

I didn't think about this, but that certainly seems reasonable. If
somebody specifies a format explicitly, we can short-circuit the other
detection code. I've added code and a couple of tests to support this.
See c9cd75df492dbef90fff.

Thanks for the input,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 11:06:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:06:01 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
Message-ID: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>

All,

I have a local Blat wrapper refactoring that I had to quickly write up for some local work.  Unfortunately, the original Blat wrapper in BioPerl-Run (Bio::Tools::Run::Alignment::Blat) had parameters that weren't compatible with more recent versions of Blat, and which didn't even use most passed parameters, so it was unfortunately pretty much useless in my hands (one couldn't designate whether the query/db was dna, prot, dnax, etc).

Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?  I plan on having it pass the original tests and adding a bit more.

As a small semi-'bonus', along with this I am also writing up additional code for Bio::SearchIO::psl that allows switching parsing logic to cluster distinct regional hits; basically, same query = Result, each Hit = distinct region, each set of blocks = HSP.  This is in response from some users here to making the bp_search2gff.pl script work with PSL a little better.  Should be added in over the next few weeks.

chris


From cjfields at illinois.edu  Fri Nov  5 11:43:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:43:13 -0500
Subject: [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utility GEO Database
	name change
References: <A9D8BF3D8A74DF4A925FB541C0F39D2A14C4E64EE2@NIHMLBX15.nih.gov>
Message-ID: <0831372A-B40C-4B62-B423-5BEB7B5D3543@illinois.edu>

FYI, for those GEO users out there.

-c

Begin forwarded message:

> From: <utilities-announce at ncbi.nlm.nih.gov>
> Date: November 5, 2010 10:39:27 AM CDT
> To: NLM/NCBI List utilities-announce <utilities-announce at ncbi.nlm.nih.gov>
> Subject: [Utilities-announce] NCBI E-Utility GEO Database name change
> Reply-To: utilities-announce at ncbi.nlm.nih.gov
> 
> Dear E-Utility Users,
>  
> Recently the name of the GEO Profiles database used within the E-utilities changed from 'geo' to 'geoprofiles'. While the old name (&db=geo) will still function, users are encouraged to change their requests to use the new name (db=geoprofiles). ELink users should be aware that all linknames including 'geo' will no longer function. Instead, these names should include 'geoprofiles' rather than 'geo'. For example, the linkname of links from Gene to GEO Profiles is now &linkname=gene_geoprofiles.
>  
> Thank you.
>  
> 
>  
> _______________________________________________
> Utilities-announce mailing list
> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce




From David.Messina at sbc.su.se  Fri Nov  5 12:11:41 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 17:11:41 +0100
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
Message-ID: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>

On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:

> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?


Sounds great! Go for it.


Dave




From njauxiongjie at gmail.com  Fri Nov  5 05:12:33 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Fri, 05 Nov 2010 02:12:33 -0700 (PDT)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd3ca81.123f970a.39e2.ffff8e89@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  



From alpita at uvigo.es  Fri Nov  5 11:52:58 2010
From: alpita at uvigo.es (alpita at uvigo.es)
Date: Fri, 05 Nov 2010 16:52:58 +0100
Subject: [Bioperl-l] Primer3
Message-ID: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>

Hi

I am a PhD-student working with EST sequences. I have got an input  
file for Primer3 and the program does not run. I try directly in the  
windows console and with Bioperl. I suppose the problem is with the  
syntax, because I have never used these tools, so I would appreciate  
some help.

How can I invoked my input file in primer 3? If it is easy to run it  
with BioPerl, tell me

Thank you very much


From cjfields at illinois.edu  Fri Nov  5 13:27:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 12:27:13 -0500
Subject: [Bioperl-l] Primer3
In-Reply-To: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
References: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
Message-ID: <8BBED864-BB9A-4FF7-9B09-2549D927F858@illinois.edu>

This all depends on what version of Primer3 you are using; the Primer3 tools in bioperl-live and bioperl-run do not work with primer3 v2 due to significant changes in the primer3 API.  However, I wrote up a full refactor of these tools, along with tests, here:

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

This includes both the wrapper and the parser (see the test files for examples on how to run them).  They have been renamed because of a change in the module API.  Let me know if they work for you.

chris

On Nov 5, 2010, at 10:52 AM, alpita at uvigo.es wrote:

> Hi
> 
> I am a PhD-student working with EST sequences. I have got an input file for Primer3 and the program does not run. I try directly in the windows console and with Bioperl. I suppose the problem is with the syntax, because I have never used these tools, so I would appreciate some help.
> 
> How can I invoked my input file in primer 3? If it is easy to run it with BioPerl, tell me
> 
> Thank you very much
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Fri Nov  5 16:57:56 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 15:57:56 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
	<D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
Message-ID: <374003E7-0F9F-466F-99D9-89F85F22CFF9@illinois.edu>


On Nov 5, 2010, at 11:11 AM, Dave Messina wrote:

> On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?
> 
> 
> Sounds great! Go for it.
> 
> 
> Dave

Okay, now in bioperl-run, master branch.  This passes all prior tests; I added a few more.

chris


From gabbyteku at gmail.com  Fri Nov  5 17:17:55 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Fri, 5 Nov 2010 23:17:55 +0200
Subject: [Bioperl-l] Bad request from efetch Bio::DB::EUtilities
Message-ID: <AANLkTimT2-K7cA3N1esBQSHb9Q8btUy3572y6L0rv5J=@mail.gmail.com>

Hi
I don't know what the problem is, but the efetch code snippet throws a Bad
request error,

while( my $id = <$in> ){           # $in, file contains list of uids
                chomp $id;

                my $eut_obj = Bio::DB::EUtilities->new(   -eutil      =>
'efetch',
                                                          -email      => '
myemail at gmail.com',
                                                          -db         =>
'geoprofile',
                                                          -id         =>
$id,
                                                      );

                open( my $tmpOut, '>' ,'doc' ) or die "Can't open doc: $!";

                eval{
                        $eut_obj->get_Response(-cb => sub {my ($data) = @_;
print $tmpOut $data );
                };
                .....
}

What is wrong with the request?

Thanks in advance


From cselig01 at students.poly.edu  Sat Nov  6 00:07:16 2010
From: cselig01 at students.poly.edu (Chet Seligman)
Date: Sat, 6 Nov 2010 04:07:16 +0000
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
 Graphics in perl 5.8 in windows 7
Message-ID: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>


I'd like to use ppm or cpan.
Does anyone know which repositories to use for the modules in the subject line?

Chet Seligman
 		 	   		  


From Kevin.M.Brown at asu.edu  Mon Nov  8 10:35:56 2010
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Mon, 8 Nov 2010 08:35:56 -0700
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
	Graphics in perl 5.8 in windows 7
In-Reply-To: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
References: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
Message-ID: <1A4207F8295607498283FE9E93B775B4072A9051@EX02.asurite.ad.asu.edu>

Follow the directions at:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
To get the main parts of BioPerl installed.

Bio::Graphics is now a separate module
http://search.cpan.org/~lds/Bio-Graphics-2.15/


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Chet Seligman
> Sent: Friday, November 05, 2010 9:07 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Problem installing Bio::SeqIO, 
> ::SearchIO, ; ; Graphics in perl 5.8 in windows 7
> 
> 
> I'd like to use ppm or cpan.
> Does anyone know which repositories to use for the modules in 
> the subject line?
> 
> Chet Seligman
>  		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From dan.bolser at gmail.com  Tue Nov  9 05:41:53 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 9 Nov 2010 10:41:53 +0000
Subject: [Bioperl-l] BP reports "All tests successful.", but some failed ...
Message-ID: <AANLkTing=D4xRTV6Lxzz6z0m=ap7-a7H5jO7eKhev7FK@mail.gmail.com>

I see the following error in the output of ./Build test:

...
t/LocalDB/SeqFeature_BDB.t ................... ok
t/LocalDB/SeqFeature_mysql.t ................. 1/84 DBI
connect('database=test','',...) failed: Can't connect to local MySQL
server through socket '/var/lib/mysql/mysql.sock' (2) at
Bio/DB/SeqFeature/Store/DBI/mysql.pm line 217
sh: -user: command not found
t/LocalDB/SeqFeature_mysql.t ................. ok
...


Related to a bug I filed a while back:
http://bugzilla.open-bio.org/show_bug.cgi?id=2899

IIRC there are a few bugs in Bio::SeqFeature::Store that are hidden
due to this initial failure.


Anyway, the point is that later I see:

All tests successful.
Files=348, Tests=24136, 249 wallclock secs ( 8.99 usr  2.04 sys +
197.16 cusr 26.85 csys = 235.04 CPU)
Result: PASS


How come we get "All tests successful." when there has clearly been an
error in "t/LocalDB/SeqFeature_mysql.t"?



BioPerl version is git bcd3b66f0422493e5f1d7c05220a4e58cced6313


Cheers,
Dan.

# The place to be
irc://irc.freenode.net/#BioPerl

# Sometimes good
irc://irc.perl.org/#gmod


From cjfields at illinois.edu  Tue Nov  9 07:58:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 06:58:40 -0600
Subject: [Bioperl-l] bioperl-primer3
In-Reply-To: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
References: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
Message-ID: <532C3550-5AA1-4A47-9C8D-82899E78B7E5@illinois.edu>

On Nov 9, 2010, at 6:05 AM, alpita at uvigo.es wrote:

> Hi Chris
> 
> As I wrote last day, I have never used bioperl and Primer3. All of this is completely new for me. It seems very interesting but I am in a student exchange, so I have got no-time to deep into it now (I will do this in the future, because I think it is very interesting to my work).
> 
> I want to design some primers, so I have used the tools of Thomas Thiel (MISA and p3_in) to obtain the input file of primer3 software. The next step would be to invoked the primer3 in the windows console (directly with the primer3 software or with bioperl tools) but I always have got problems with error messages. I suppose that I am writting some errors.
> 
> If you can, I would greatly appreciate you to tell me what tool to use and how to write it in the windows console.
> 
> Thank you very much for you effort. I hope to be improving slowly in this task
> Regards

Please make responses to the main bioperl list.  

I rewrote the main set of tools for Primer3, which I believe i pointed out to you previously (unless I'm mistaken):

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

I can't tell you what to use for Windows: I don't develop on that platform.  Any patches are welcome in case you find problems there and fix them.

chris





From njauxiongjie at gmail.com  Tue Nov  9 04:05:04 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Tue, 09 Nov 2010 01:05:04 -0800 (PST)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  



From singh.amarv at epa.gov  Tue Nov  9 13:38:18 2010
From: singh.amarv at epa.gov (Amar Singh)
Date: Tue, 9 Nov 2010 18:38:18 +0000 (UTC)
Subject: [Bioperl-l] parsing PubMed retrievals
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <loom.20101109T193516-922@post.gmane.org>

Tom Keller <kellert <at> ohsu.edu> writes:

> 
> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at
/Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> Tom
> MMI DNA Services Core
Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert <at> ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 


Tom,

I am also facing the same problem. This was working a month back and now when I
wanted to test new thing it is giving me the same error. I think this is due to
some changes in the way we access the data. Will keep updated if I find a
solution and same way you too. 

Thanks,

Amar



From Russell.Smithies at agresearch.co.nz  Tue Nov  9 15:08:23 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 10 Nov 2010 09:08:23 +1300
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313BCA1138@exchsth.agresearch.co.nz>

Not sure if this will work but have you tried using STDOUT as the filename then piping all the output to a single file?
The other (much simpler) option is just concatenate all the outputs into a single file when it's finished.

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of njauxiongjie
Sent: Tuesday, 9 November 2010 10:05 p.m.
To: bioperl-l
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
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taking of any action in reliance upon, this information by persons or
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From florent.angly at gmail.com  Tue Nov  9 19:54:58 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 10 Nov 2010 10:54:58 +1000
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <4CD9ED62.50102@gmail.com>

Wouldn't using a single filename be the way to go?
> my $filename = "blast_ressults.out";
>            $factory->save_output($filename);
Florent


On 09/11/10 19:05, njauxiongjie wrote:
> Hi,
>
> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>
> there are two line of the code like below:
> my $filename = $result->query_name()."\.out";
>            $factory->save_output($filename);
> this saved the blast result in separated files by the query name.
>
> my question is: how can i save the blast results of all querys in one file?
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Tue Nov  9 22:46:00 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 21:46:00 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4CD9ED62.50102@gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
Message-ID: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>

Only if the output appends to that file (I don't recall personally, so it's worth a try).

chris

On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:

> Wouldn't using a single filename be the way to go?
>> my $filename = "blast_ressults.out";
>>           $factory->save_output($filename);
> Florent
> 
> 
> On 09/11/10 19:05, njauxiongjie wrote:
>> Hi,
>> 
>> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>> 
>> there are two line of the code like below:
>> my $filename = $result->query_name()."\.out";
>>           $factory->save_output($filename);
>> this saved the blast result in separated files by the query name.
>> 
>> my question is: how can i save the blast results of all querys in one file?
>> 
>> 
>> 
>> _______________________________________________
>> 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 roy.chaudhuri at gmail.com  Wed Nov 10 11:11:27 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 10 Nov 2010 16:11:27 +0000
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
In-Reply-To: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
References: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
Message-ID: <4CDAC42F.9020708@gmail.com>

Hi Jim,

I don't think you ever got a reply to this. I think you want 
$tree->splice() rather than $tree->remove_Node().

Cheers,
Roy.

On 21/10/2010 18:52, Jim Hu wrote:
> I'm trying to take an unreadable tree from PFAM and prune it down to
> just show the paralogs from E. coli.
>
> When you run remove_Node on an internal node, is it supposed to
> reconnect the ancestors to the descendants?  This seems to be way to
> aggressive in what it's removing.
>
> while( my $tree = $treeio->next_tree ) { for my $node (
> $tree->get_nodes ) { if ($node->id =~ m/_ECOLI/){ #	leave this node
> alone #	print $node->id."\n"; }else{ if ($node->is_Leaf){
> $tree->remove_Node($node); }else{ my $num_children =
> scalar($node->each_Descendent); if ($num_children == 1){ print
> "removing ".$node->id."\n"; $tree->remove_Node($node); } } } }
> $treeio_out->write_tree($tree); }
>
> The idea is that when I've pruned the non-ECOLI leaves, some internal
> nodes will not be branches anymore.  But at the end, all the ECOLI
> nodes are gone, presumably because an ancestor got removed and the
> whole branch was lost.  Is there a way to remove just a node and
> graft the tree back together?  My plan, once I get that working is to
> repeat the traversal until the output stops changing.
>
> Jim
>
>
> ===================================== Jim Hu Associate 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 chandan.kr.singh at gmail.com  Thu Nov 11 06:10:25 2010
From: chandan.kr.singh at gmail.com (CHANDAN SINGH)
Date: Thu, 11 Nov 2010 16:40:25 +0530
Subject: [Bioperl-l] each_gene_symbol() is missing from
	Bio::Phenotype::OMIM::OMIMentry
Message-ID: <AANLkTinSX5oUFNYJFZwos2ODfsXFLj=xntxg43umfxs9@mail.gmail.com>

Hi Christian

The implementation of each_gene_symbol() is missing from
Bio::Phenotype::OMIM::OMIMentry even though the method has been referred in
the module and also in OMIMparser. I'm sure it was just a overlook; in which
case will you be implementing the method in the near future.

Thanks
Chandan


From cjfields at illinois.edu  Sun Nov 14 16:49:52 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 14 Nov 2010 15:49:52 -0600
Subject: [Bioperl-l] GitHub down
Message-ID: <E008728D-057A-415F-9415-EFD68F5F2B6F@illinois.edu>

Just a note that GitHub (and the main bioperl repo) appear to be down at the moment with a major disruption of service.  If anyone absolutely needs code, we have a synced repo set up here:

http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-db.git
http://repo.or.cz/w/bioperl-run.git
http://repo.or.cz/w/bioperl-network.git

chris


From maj at fortinbras.us  Mon Nov 15 20:08:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 15 Nov 2010 20:08:25 -0500
Subject: [Bioperl-l] use Bio::Search::Tiling::MapTiling
In-Reply-To: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
References: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
Message-ID: <E703F129EE074EFD9ACA421FED2A87F2@NewLife>

Hi Wei, 
You'll need to install the trunk code to access this method; the "release" is woefully out of date (not that I'm helping much on that these days). Use git to obtain the latests bioperl-live and bioperl-run from https://github.com/bioperl/, or the synchronized repos
http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-run.git
cheers, 
MAJ
----- Original Message ----- 
  From: Shao, Wei (NIH/NCI) [C] 
  To: Mark A Jensen 
  Sent: Monday, November 15, 2010 10:47 AM
  Subject: use Bio::Search::Tiling::MapTiling


Dear Dr. Jensen, I am looking for a bioperl module that can be used to concatenate HSP from a blast into a sequence. I found that your Bio::Search::Tiling::MapTilingcan do exactly that. I used your example script to test it. I got an error message:?Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::MapTiling" at get_hsp.pl line 29, <GEN1> line 2630?.It seems that method ?get_tiled_alns? is not in the bioperl we installed. Is that possible? The script I used is this one:  use Bio::SearchIO;use Bio::Search::Tiling::MapTiling # Note that to get one hit, the user first blasts# the set of contigs against single sequence, the reference sequence.# The result of this BLAST run is in 'contig_tile.bls' $blio = Bio::SearchIO->new( -file => 'contig_tile.bls');$result = $blio->next_result;$hit = $result->next_hit;$tiling = Bio::Search::Tiling::MapTiling->new($hit);@alns = $tiling->get_tiled_alns('query'); # here's the concatenation:$concat_seq_obj = $alns[0]->get_seq_by_id('query'); 

  Best regards,

   

   

  Wei Shao, Ph.D. [Contractor] 
  Bioinformatics Analyst IV

  Advanced Biomedical Computing Center/HIV Drug Resistance Program
  SAIC-Frederick, Inc. 

  National Cancer Institute at Frederick
  P.O. Box B, Frederick, MD 21702
  Phone: 301/846-6021

  Fax:  301/846-6013
  Email:  shaow at mail.nih.gov


  NOTICE:  This communication may contain privileged or other confidential information.  If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information.  Please indicate to the sender that you have received this email in error and delete the copy you received.

   



From dimitark at bii.a-star.edu.sg  Mon Nov 15 21:44:15 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 16 Nov 2010 10:44:15 +0800
Subject: [Bioperl-l] about tblastn and strand
Message-ID: <4CE1EFFF.70304@bii.a-star.edu.sg>

Hi guys,
i have a simple question. How exactly is defined on which strand is 
located a certain HSP in tblastn? I know it is used the strand function 
but i would like to know how is implemented. I ask cos here i made a 
perl script using bioperl but other people want to implement it in Java.

In the output of tblastn there is no strand string only frame+ or 
frame-. Do you just take the + or - to determine on which strand is the HSP?

Thank you for your time and help.

Dimitar


From mmuratet at hudsonalpha.org  Tue Nov 16 16:56:08 2010
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Tue, 16 Nov 2010 15:56:08 -0600
Subject: [Bioperl-l] Obtaining Refseq status with eutils
Message-ID: <EEABA734-39A8-44B4-9540-A20FE1BC575E@hudsonalpha.org>

Greetings

I have been trying to get to the Refseq status info that shows up NCBI  
gene webpage. My latest attempt is:

my @accs = qw(SAAV_0049);

my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -email => 'mmuratet at hudsonalpha.org 
',
                                        -db    => 'gene',
                                        -term  => join(',', at accs));

my @uids = $factory->get_ids;

$factory->reset_parameters(-eutil => 'elink',
                            -dbfrom => 'gene',
                            -db => 'nuccore',
                            -linkname => 'gene_nuccore_refseqgene',
                            -id    => \@uids);

$factory->get_Response(-file => 'temp.txt');

All I get back is the ID number I gave it. Also, $factory->next_DocSum  
returns nothing.

A big part of the problem is that I don't know what field I'm looking  
for. I am also unsure that I am using the elink interface properly.

Does anyone know how to get to the Refseq data for a gene? I am  
looking for evidence of expression of gene models--is there a better  
annotation to use?

Thanks

Mike


Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806







From pcantalupo at gmail.com  Wed Nov 17 12:38:05 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 12:38:05 -0500
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
Message-ID: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>

Hi,

Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm


---
 Bio/SeqIO.pm |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
index fe49822..cf6d3a2 100644
--- a/Bio/SeqIO.pm
+++ b/Bio/SeqIO.pm
@@ -651,6 +651,7 @@ sub _guess_format {
    return 'phd'     if /\.(phd|phred)$/i;
    return 'pir'     if /\.pir$/i;
    return 'pln'     if /\.pln$/i;
+   return 'qual'    if /\.qual$/i;
    return 'raw'     if /\.(txt)$/i;
    return 'scf'     if /\.scf$/i;
    return 'swiss'   if /\.(swiss|sp)$/i;
-- 
1.6.4.2



Paul

Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260


From maj at fortinbras.us  Wed Nov 17 17:59:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 17 Nov 2010 22:59:25 +0000
Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] GO annotation
Message-ID: <W347038377283011290034765@webmail27>


redirect to list
-----Original Message-----
From: Christos Noutsos [mailto:cnoutsos at cshl.edu]
Sent: Wednesday, November 17, 2010 05:35 PM
To: bioperl-guts-l at lists.open-bio.org
Subject: [Bioperl-guts-l] GO annotation

Hi all,
I have several clusters of coregulated genes from Arabidopsis and I would like to check  their GO annotation? Is there a module in bioperl which I can use? 
Thank you for your help
Christos


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





From lskatz at gatech.edu  Wed Nov 17 22:20:03 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Wed, 17 Nov 2010 22:20:03 -0500
Subject: [Bioperl-l] Status of assembly modules
Message-ID: <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc@mail.gmail.com>

I have read on the BioPerl site that a 454 ace is not standardized due to
its coordinate system.  How can I convert it to the standard ace file?

When I run this code either by using contig or assembly objects, I get an
error.
Can't call method "get_consensus_sequence" on an undefined value at
Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.

    sub _newblerAceToAce($args){
      my($self,$args)=@_;
      my
$ace454=Bio::Assembly::IO->new(-file=>$$args{ace454Path},-format=>"ace",-variant=>'454');
      my
$ace=Bio::Assembly::IO->new(-file=>">$$args{acePath}",-format=>"ace");
      #while(my $contig=$ace454->next_contig){
      while(my $scaffold=$ace454->next_assembly){
        print Dumper $scaffold;
      }
      return $$args{acePath};
    }


On Fri, Jun 18, 2010 at 5:59 AM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 13
> Date: Fri, 18 Jun 2010 15:39:39 +1000
> From: Florent Angly <florent.angly at gmail.com>
> Subject: [Bioperl-l] Status of assembly modules
> To: Joshua Udall <jaudall at gmail.com>,   bioperl-l List
>        <bioperl-l at lists.open-bio.org>
> Message-ID: <4C1B069B.5020105 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Joshua,
>
> Yes, there have been interesting improvements in the assembly BioPerl
> module since v1.6.1. You can find these changes in the development
> version of BioPerl at http://github.com/bioperl/. I'll take this
> opportunity to introduce people who don't follow the commit messages to
> the new features that have been introduced:
>
> First, there is support for more file formats from high-throughput
> platforms, including those generated by de novo assembly and comparative
> assembly tools, such as:
>     * Roche 454 GS Assembler, aka Newbler (the ACE-454 variant)
>     * Maq
>     * Sam
>     * Bowtie
> There is support for running a lot more of these tools in Bioperl-run
> Bio::Tools::Run :
>     * Roche 454 GS Assembler, aka Newbler
>     * Minimo
>     * Maq
>     * Samtools
>     * Bowtie
> In terms of writing assembly file, I added the option to write ACE
> files, which is quite useful because maybe assembly programs recognize
> this format. So now you can read assemblies, modify them as you see fit
> and exporting them to other programs by writing the modified assembly in
> an ACE file.
> The internals of the IO parsers have acquired some granularity as it is
> now possible to read/write assembly files entirely, or one contig at a
> time. This is terrific to reduce memory usage.
>
> That's about it...
>
> Regards,
>
> Florent
>
> PS/ Josh, you filed bug reports related to several of these issues
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2726,
> http://bugzilla.open-bio.org/show_bug.cgi?id=2483). I am closing the
> ones that were not closed yet and thank you for submitting patches.
>
>
> On 18/06/10 14:00, Joshua Udall wrote:
> > Florent -
> >
> > I didn't want to ask a direct question on-list to perhaps avoid
> > confusion.  Were you able to improve/submit a ContigIO to bioperl that
> > works with one entry at a time (instead of slurping the entire ace
> > file)?
> >
> >
>



-- 
Lee Katz
http://leeskatz.com


From rmb32 at cornell.edu  Thu Nov 18 02:03:46 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 17 Nov 2010 23:03:46 -0800
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
In-Reply-To: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
References: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
Message-ID: <4CE4CFD2.3000901@cornell.edu>

Applied!  Thanks Paul!

Rob

Paul Cantalupo wrote:
> Hi,
> 
> Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm
> 
> 
> ---
>  Bio/SeqIO.pm |    1 +
>  1 files changed, 1 insertions(+), 0 deletions(-)
> 
> diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
> index fe49822..cf6d3a2 100644
> --- a/Bio/SeqIO.pm
> +++ b/Bio/SeqIO.pm
> @@ -651,6 +651,7 @@ sub _guess_format {
>     return 'phd'     if /\.(phd|phred)$/i;
>     return 'pir'     if /\.pir$/i;
>     return 'pln'     if /\.pln$/i;
> +   return 'qual'    if /\.qual$/i;
>     return 'raw'     if /\.(txt)$/i;
>     return 'scf'     if /\.scf$/i;
>     return 'swiss'   if /\.(swiss|sp)$/i;



From pcantalupo at gmail.com  Thu Nov 18 10:15:04 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 18 Nov 2010 10:15:04 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTikW_cKGovyGyKLZMxAeP1E6Vs8P=KOzAXQsKBxK@mail.gmail.com>

Hi,

I'm resending this to the list (without an attachment) since it got
flagged as having a suspicious header.


I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string":

---
 Bio/Seq/PrimaryQual.pm |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/Bio/Seq/PrimaryQual.pm b/Bio/Seq/PrimaryQual.pm
index 4935639..30383fc 100644
--- a/Bio/Seq/PrimaryQual.pm
+++ b/Bio/Seq/PrimaryQual.pm
@@ -461,7 +461,7 @@ sub qualat {
 sub to_string {
     my ($self,$out,$result) = shift;
     $out = "qual: ".join(',',@{$self->qual()});
-    foreach (qw(display_id accession_number primary_id desc id)) {
+    foreach (qw(display_id accession_number primary_id desc id length)) {
 	$result = $self->$_();
 	if (!$result) { $result = "<unset>"; }
 	$out .= "$_: $result\n";
-- 
1.6.4.2






Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260


From pcantalupo at gmail.com  Wed Nov 17 10:55:52 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 10:55:52 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>

Hi,

I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string"

Paul


Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260
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From twaddlac at gmail.com  Fri Nov 19 15:03:14 2010
From: twaddlac at gmail.com (Alan Twaddle)
Date: Fri, 19 Nov 2010 15:03:14 -0500
Subject: [Bioperl-l] bioperl-ext package installation error
Message-ID: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>

Hello all,

     I am trying to write a simple script to parse an ABI file into usable
data which requires the staden io_lib of which I installed. However, am
receiving an error message when trying to run my script that says the
following:
------------- EXCEPTION: Bio::Root::SystemException -------------
MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
package has been installed successfully!
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
abi.pm:100
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
STACK: AB1_parser.pl:10

I didn't receive any error messages when installing the staden package so
I'm assuming that there's some path specified in some file that is pointing
to the wrong place. I don't know if this is the case but if you have any
suggestions about how to fix this I would greatly appreciate it! Thank you
very much!

-- 

Alan Twaddle, B.S.
MUC class of 2010


From cjfields at illinois.edu  Fri Nov 19 23:33:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:33:14 -0600
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
In-Reply-To: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
References: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
Message-ID: <644615D3-8F59-4E59-B7A1-6BCE6159E9C9@illinois.edu>

Paul, 

Committed this to github master branch.  Thanks for pointing that out.

chris

On Nov 17, 2010, at 9:55 AM, Paul Cantalupo wrote:

> Hi,
> 
> I simply added "length" to the foreach loop in sub "to_string" of
> Bio/Seq/PrimaryQual.pm to match documentation of "to_string"
> 
> Paul
> 
> 
> Paul Cantalupo
> Research Specialist/Systems Programmer
> University of Pittsburgh
> Pittsburgh, PA 15260
> <0001-Added-length-to-foreach-loop-to-match-documentation-.patch>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Fri Nov 19 23:50:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:50:17 -0600
Subject: [Bioperl-l] bioperl-ext package installation error
In-Reply-To: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
References: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
Message-ID: <D0C6F261-EFF7-46D3-823D-171BAA240A91@illinois.edu>

Alan, 

You need to install the bioperl-ext module Bio::SeqIO::staden::read, which uses XS bindings to io_lib, but there's a bit of a caveat: we're not really maintaining that code anymore.  Saying that, it does work using io_lib version 1.12.2 (my local version). 

Here's the code, please make sure to note the README (specifically, the version of io_lib you will need and the problems you may run into):

https://github.com/bioperl/bioperl-ext/tree/master/Bio/SeqIO/staden/

chris

On Nov 19, 2010, at 2:03 PM, Alan Twaddle wrote:

> Hello all,
> 
>     I am trying to write a simple script to parse an ABI file into usable
> data which requires the staden io_lib of which I installed. However, am
> receiving an error message when trying to run my script that says the
> following:
> ------------- EXCEPTION: Bio::Root::SystemException -------------
> MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
> package has been installed successfully!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
> abi.pm:100
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
> STACK: AB1_parser.pl:10
> 
> I didn't receive any error messages when installing the staden package so
> I'm assuming that there's some path specified in some file that is pointing
> to the wrong place. I don't know if this is the case but if you have any
> suggestions about how to fix this I would greatly appreciate it! Thank you
> very much!
> 
> -- 
> 
> Alan Twaddle, B.S.
> MUC class of 2010
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jordi.durban at gmail.com  Mon Nov 22 15:01:34 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Mon, 22 Nov 2010 21:01:34 +0100
Subject: [Bioperl-l] parse multi xml
Message-ID: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>

Hi all,
I'm a newbie in the list although I've been using bioperl for 2 years.
Now I have a problem with a XML file and I don't know how to parse it.
That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
resulted from  Blast2go software the usage and I suppose the file is the
outcome of multiple blast results concatenation.
Well, I would like to split all 795 different xml chunks in 795 different
files in order to parse them looking for the best hit.
The problem appears using the blastxml parse
(*Bio::SearchIO::blastxml) *because
(and that's a personal opinion) there's another top tag not expected and I
get a error message once the first blast result was parsed.
How can I do that split function?
I hope I was clear
Thanks




-- 
Jordi


From biopython at maubp.freeserve.co.uk  Mon Nov 22 15:23:29 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Nov 2010 20:23:29 +0000
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
Message-ID: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>

On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
> Hi all,
> I'm a newbie in the list although I've been using bioperl for 2 years.
> Now I have a problem with a XML file and I don't know how to parse it.
> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
> resulted from ?Blast2go software the usage and I suppose the file is the
> outcome of multiple blast results concatenation.

Such a file is NOT a valid XML file (but see below), you can't just
concatenate XML files. I'm pretty sure people have posted scripts
to fix such files on the blast2go mailing list.

> Well, I would like to split all 795 different xml chunks in 795 different
> files in order to parse them looking for the best hit.
> The problem appears using the blastxml parse
> (*Bio::SearchIO::blastxml) *because
> (and that's a personal opinion) there's another top tag not expected
> and I get a error message once the first blast result was parsed.
> How can I do that split function?
> I hope I was clear
> Thanks

Historically the NCBI standalone BLAST used to create these
concatenated XML files when used on multiple queries. It has
since been fixed, but perhaps BioPerl has code still in it to
handle these legacy invalid XML files?

My suggestion (until a BioPerl guru speaks up) would be to
split the file into chunks (in memory) by looking for the string
<?xml version="1.0">, and parsing each chunk individually.
Each chunk should be a valid XML file on its own.

Peter



From lskatz at gatech.edu  Mon Nov 22 15:18:10 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Mon, 22 Nov 2010 15:18:10 -0500
Subject: [Bioperl-l] Re(2): Status of assembly modules
Message-ID: <AANLkTi=JShCLsHDxHK4eeWD3Da=vWmRkGN2rkuLwCjxn@mail.gmail.com>

I figured it out (I haven't tested much though).

To whoever works on Assembly::IO::ace.pm:
I changed a regular expression on line 231 because the contig object was not
initializing properly.  For some reason the 454 ace file had adopted the
reference assembly's ID and therefore there was a GI number followed by a
pipe.  The pipe was not captured with \w+.  I think that the regex will be
safe with \s(\S+)\s.

 if (/^CO\s(\S+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!
#if (/^CO\s(\w+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!

On Thu, Nov 18, 2010 at 12:04 PM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 3
> Date: Wed, 17 Nov 2010 22:20:03 -0500
> From: Lee Katz <lskatz at gatech.edu>
> Subject: Re: [Bioperl-l] Status of assembly modules
> To: bioperl-l at lists.open-bio.org
> Message-ID:
>        <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I have read on the BioPerl site that a 454 ace is not standardized due to
> its coordinate system.  How can I convert it to the standard ace file?
>
> When I run this code either by using contig or assembly objects, I get an
> error.
> Can't call method "get_consensus_sequence" on an undefined value at
> Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.
>
>    sub _newblerAceToAce($args){
>      my($self,$args)=@_;
>      my
>
> $ace454=Bio::Assembly::IO->new(-file=>$args{ace454Path},-format=>"ace",-variant=>'454');
>      my
> $ace=Bio::Assembly::IO->new(-file=>">$args{acePath}",-format=>"ace");
>      #while(my $contig=$ace454->next_contig){
>      while(my $scaffold=$ace454->next_assembly){
>        print Dumper $scaffold;
>      }
>      return $args{acePath};
>    }
>



-- 
Lee Katz
http://leeskatz.com


From thomas.sharpton at gmail.com  Mon Nov 22 17:28:52 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 22 Nov 2010 14:28:52 -0800
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
Message-ID: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>

Hi Evan,

Glad to hear this software is a promising solution to your needs. I  
just tried running the test script under Bio/t/SearchIO/hmmer3.t and  
everything passed. Can you verify that you are using an up-to-date  
version of bioperl-live? You can grab a snapshot from github if you  
haven't already:

https://github.com/bioperl/bioperl-live

Also, I'm cc'ing this to the bioperl list so that others may benefit  
from our discourse (and chime in - Kai Blin, who created the test  
tools, and others have made substantial contributions and improvements  
to the original code and they might have good suggestions).

T



On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:

> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3  
> reports. Everything seems to be working nicely with the test data  
> and my own reports except for getting the $hsp->query_string and  
> $hsp->hit_string. I noticed that these HSP routines were not working  
> with the test script/data (for me anyway) so I thought I would ask  
> before spending days trying to solve this one.
>
> Thanks,
>
> Evan
>
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602



From jordi.durban at gmail.com  Mon Nov 22 18:34:03 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Tue, 23 Nov 2010 00:34:03 +0100
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <AANLkTi=RBBL1vC4XRQM=_gf+5CPLiw2+6xdtwzZjFy6a@mail.gmail.com>

Thanks Peter.
That's exactly what I was looking for but so far I've not been able to do
that properly.
Any ideas??


2010/11/22 Peter <biopython at maubp.freeserve.co.uk>

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com>
> wrote:
> > Hi all,
> > I'm a newbie in the list although I've been using bioperl for 2 years.
> > Now I have a problem with a XML file and I don't know how to parse it.
> > That file has 795 xml top tags (thta's is <?xml version="1.0">) because
> they
> > resulted from  Blast2go software the usage and I suppose the file is the
> > outcome of multiple blast results concatenation.
>
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
>
> > Well, I would like to split all 795 different xml chunks in 795 different
> > files in order to parse them looking for the best hit.
> > The problem appears using the blastxml parse
> > (*Bio::SearchIO::blastxml) *because
> > (and that's a personal opinion) there's another top tag not expected
> > and I get a error message once the first blast result was parsed.
> > How can I do that split function?
> > I hope I was clear
> > Thanks
>
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?
>
> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
>
> Peter
>



-- 
Jordi


From cjfields at illinois.edu  Mon Nov 22 19:27:43 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 22 Nov 2010 18:27:43 -0600
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <348A592A-D634-4C1C-9F05-DB20FE87F61C@illinois.edu>

On Nov 22, 2010, at 2:23 PM, Peter wrote:

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
>> Hi all,
>> I'm a newbie in the list although I've been using bioperl for 2 years.
>> Now I have a problem with a XML file and I don't know how to parse it.
>> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
>> resulted from  Blast2go software the usage and I suppose the file is the
>> outcome of multiple blast results concatenation.
> 
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
> 
>> Well, I would like to split all 795 different xml chunks in 795 different
>> files in order to parse them looking for the best hit.
>> The problem appears using the blastxml parse
>> (*Bio::SearchIO::blastxml) *because
>> (and that's a personal opinion) there's another top tag not expected
>> and I get a error message once the first blast result was parsed.
>> How can I do that split function?
>> I hope I was clear
>> Thanks
> 
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?

It does (last I looked).

> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
> 
> Peter

Or, better yet, push the blast2go folks to create valid XML output or use an updated version of BLAST.  This bug was fixed about 3 years ago.

chris





From statonse at uga.edu  Mon Nov 22 18:41:26 2010
From: statonse at uga.edu (Evan Staton)
Date: Mon, 22 Nov 2010 18:41:26 -0500
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
Message-ID: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>

Hi Thomas,

Everything works with the latest release of bioperl-live. My bioperl was
1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
did not realize it had been incorporated into the latest distribution). All
the tests passed and all the routines worked before except for the
$hsp->query_string and $hsp->hit_string, but that is resolved now.

Thanks for the quick response, it saved me a lot of time.

Evan

On Mon, Nov 22, 2010 at 5:28 PM, Thomas Sharpton
<thomas.sharpton at gmail.com>wrote:

> Hi Evan,
>
> Glad to hear this software is a promising solution to your needs. I just
> tried running the test script under Bio/t/SearchIO/hmmer3.t and everything
> passed. Can you verify that you are using an up-to-date version of
> bioperl-live? You can grab a snapshot from github if you haven't already:
>
> https://github.com/bioperl/bioperl-live
>
> Also, I'm cc'ing this to the bioperl list so that others may benefit from
> our discourse (and chime in - Kai Blin, who created the test tools, and
> others have made substantial contributions and improvements to the original
> code and they might have good suggestions).
>
> T
>
>
>
> On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:
>
> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3 reports.
> Everything seems to be working nicely with the test data and my own reports
> except for getting the $hsp->query_string and $hsp->hit_string. I noticed
> that these HSP routines were not working with the test script/data (for me
> anyway) so I thought I would ask before spending days trying to solve this
> one.
>
> Thanks,
>
> Evan
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602
>
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
S. Evan Staton
PhD Student - Burke Lab
University of Georgia
Department of Genetics
3507 Miller Plant Sciences
Athens, GA 30602


From kris.richardson at tufts.edu  Tue Nov 23 12:10:56 2010
From: kris.richardson at tufts.edu (kris richardson)
Date: Tue, 23 Nov 2010 12:10:56 -0500
Subject: [Bioperl-l] GeneMapper
Message-ID: <BA6B80D7-732A-4333-83AD-54AB14BF334D@tufts.edu>

Dear Members,

 I have a list mRNA target positions,  for various mRNAs and  I also have the RefSeq accession NM_#s for their genes  and mRNA (ex; gene: NM_198155 --- mRNA positions: NM_004649: 800-890).   

I would like to use this info to pull the chromosomal coordinates of NM_198155 corresponding to the resulting transcript positions NM:_004649:800-890.  I am familiarizing myself with bioperl and GeneMapper seems like it can provide this info.  However, the documentation on the module code is sparse, and there are no examples.  I was wondering if anyone has experience with this and could point me in the right direction, or perhaps provide some example code?  

Regards,

Kris







From kai.blin at biotech.uni-tuebingen.de  Wed Nov 24 01:24:22 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Wed, 24 Nov 2010 07:24:22 +0100
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
	<AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
Message-ID: <4CECAF96.7010706@biotech.uni-tuebingen.de>

On 2010-11-23 00:41, Evan Staton wrote:

Hi Evan,

> Everything works with the latest release of bioperl-live. My bioperl was
> 1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
> did not realize it had been incorporated into the latest distribution). All
> the tests passed and all the routines worked before except for the
> $hsp->query_string and $hsp->hit_string, but that is resolved now.

I recently fixed this in bioperl-live when I bumped into that feature
missing. I didn't bother to update the bioperl-hmmer3 repository.
Perhaps it should be deleted to avoid the confusion.

Also, in bioperl-live, the Bio::SearchIO::hmmer parser now supports
hmmer2 and hmmer3 parsing, but by all means go for the specific parser
class if you know the version of hmmer result you're loading. :)

On a side note, even though you're probably aware of this... HMMer3 only
does local alignments, so it's not really good for domain extraction. It
is very fast, but if your software uses a profile based search to
extract specific amino acid motifs HMMer3 might let you down.
Just as a caveat that has bitten me recently.

Cheers,
Kai

-- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-University of T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Deutschland
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben


From dimitark at bii.a-star.edu.sg  Wed Nov 24 21:38:52 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:38:52 +0800
Subject: [Bioperl-l] update: genpept module
Message-ID: <4CEDCC3C.9070707@bii.a-star.edu.sg>

Hi guys,
just managed to get GenPept to give me the fasta in the full form. I 
modified GenPept in this way:

sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); 
#DIMITAR
   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
   $self->request_format($self->default_format($format));
   return $self;
}

Cheers
Dimitar


From cjfields at illinois.edu  Wed Nov 24 22:24:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 24 Nov 2010 21:24:40 -0600
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDCC3C.9070707@bii.a-star.edu.sg>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
Message-ID: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>

Dimitar,

Missed your original post, but was it reported as a bug?  

chris

On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:

> Hi guys,
> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
> 
> sub new {
>  my($class, @args) = @_;
>  my $self = $class->SUPER::new(@args);
>  my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>  $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>  $self->request_format($self->default_format($format));
>  return $self;
> }
> 
> Cheers
> Dimitar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jason at bioperl.org  Wed Nov 24 22:57:11 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Nov 2010 19:57:11 -0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
Message-ID: <4CEDDE97.5020406@bioperl.org>

This doesn't seem like the right fix -- you don't want to updated a 
default variable -- why didn't you just use it like this: ?

my $db = new Bio::DB::GenPept->new(-format => 'fasta');



Chris Fields wrote, On 11/24/10 7:24 PM:
> Dimitar,
>
> Missed your original post, but was it reported as a bug?
>
> chris
>
> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>
>> Hi guys,
>> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
>>
>> sub new {
>>   my($class, @args) = @_;
>>   my $self = $class->SUPER::new(@args);
>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>   $self->request_format($self->default_format($format));
>>   return $self;
>> }
>>
>> Cheers
>> Dimitar
>> _______________________________________________
>> 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 at bioperl.org



From dimitark at bii.a-star.edu.sg  Thu Nov 25 00:34:39 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 13:34:39 +0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDDE97.5020406@bioperl.org>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
	<4CEDDE97.5020406@bioperl.org>
Message-ID: <4CEDF56F.3020409@bii.a-star.edu.sg>

I used it like this in the script:

if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


}

i added $retformat to getoptlong as well. but that didnt work well as 
did for GenBank. May be GenBank and GenPept should be made to work in 
the same way. Now they are a bit different. I tried to see why they 
react different but i couldnt understand why.

now my GenPept new method looks like this:
sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
FORMAT)], at args);#dimitar
   $DEFAULTFORMAT=$format if (defined $format);#dimitar
   $self->request_format($self->default_format($format));
   return $self;
}

this way i can get sequences in any format which Eutils is allowing.

On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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
>



On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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 dimitark at bii.a-star.edu.sg  Thu Nov 25 02:05:36 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 15:05:36 +0800
Subject: [Bioperl-l] about NCBI seq reports
Message-ID: <4CEE0AC0.6050104@bii.a-star.edu.sg>

Hi again,
now i can get the sequences in full fasta as NCBI provides them. But can 
I also get and the GenPept reports in some way?
I tried using 'download_query_genbank.pl' but i always get some fasta 
seq but not the GenPept report even though the generated by the script 
request is valid. When i put it in browser i get the report file but the 
script itself returns fasta. I think is limitation of the modules which 
the scripts uses, right? Or am i mistaken.

Cheers
Dimitar


From Marc.Perry at oicr.on.ca  Fri Nov 26 23:53:48 2010
From: Marc.Perry at oicr.on.ca (Marc Perry)
Date: Fri, 26 Nov 2010 23:53:48 -0500
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm; 'sizes' method is broken
Message-ID: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>

Hi,

I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:

=+=+=+=
#!/usr/bin/perl

use strict;
use warnings;
use Bio::SeqIO;
use Bio::Restriction::Analysis;
use Bio::Restriction::Enzyme;
use Bio::Restriction::EnzymeCollection;

my $input = shift or die "No fasta file on command line.";

my $seqio_obj = Bio::SeqIO->new(-file   => $input,
                                                -format => "fasta" );

my $seq = $seqio_obj->next_seq;

my $all_enz = Bio::Restriction::EnzymeCollection->new();

my $h3 = $all_enz->get_enzyme('HindIII');

my $ra = Bio::Restriction::Analysis->new(-seq => $seq);

print join "\n", $ra->sizes($h3), "\n\n";
print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
print join "\n", $ra->sizes($h3, 1, 1), "\n\n";

exit;
=+=+=+=

And here is the output:

48502


48502


48.502

As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:


sub sizes {

    my ($self, $enz, $kb, $sort) = @_;

    $self->throw('no enzyme selected to get fragments for')

        unless $enz;

    $self->cut unless $self->{'_cut'};

    my @frag; my $lastsite=0;

    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG

      $kb ? push (@frag, (int($site-($lastsite))/100)/10)

          : push (@frag, $site-($lastsite));

      $lastsite=$site;

    }

    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)

        : push (@frag, $self->{'_seq'}->length-($lastsite));

    if ($self->{'_seq'}->is_circular) {

       my $first=shift @frag;

       my $last=pop @frag;

       push @frag, ($first+$last);

    }

    $sort ? @frag = sort {$b <=> $a} @frag : 1;



    return @frag;

}


I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:

my $name = $enz->{_seq}->{display_id};
foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {

And now my script yields this output:

23130
2027
2322
9416
564
6682
4361


23130
9416
6682
4361
2322
2027
564


23.13
9.416
6.682
4.361
2.322
2.027
0.564

which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:


You should be able to do these:



  # to see all the fragment sizes,

  print join "\n", @{$re->sizes($enz)}, "\n";

  # to see all the fragment sizes sorted

  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";

  # to see all the fragment sizes in kb sorted

  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";

--Marc

Marc Perry
Scientific Associate

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:       416-673-8593
Toll-free:  1-866-678-6427
Cell:      416-904-8037
www.oicr.on.ca<http://www.oicr.on.ca/>

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all




From cjfields at illinois.edu  Sat Nov 27 00:15:46 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 26 Nov 2010 23:15:46 -0600
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm;
	'sizes' method is broken
In-Reply-To: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
References: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
Message-ID: <66A351B0-D483-490A-90CC-BF7C596D6505@illinois.edu>

Marc,

I've entered this into bugzilla for tracking (the best place for this, BTW).  I can't promise when we'll get to it, but since there is a proposed fix it may be handled fairly soon.  Thanks for pointing this out!

chris

On Nov 26, 2010, at 10:53 PM, Marc Perry wrote:

> Hi,
> 
> I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:
> 
> =+=+=+=
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::SeqIO;
> use Bio::Restriction::Analysis;
> use Bio::Restriction::Enzyme;
> use Bio::Restriction::EnzymeCollection;
> 
> my $input = shift or die "No fasta file on command line.";
> 
> my $seqio_obj = Bio::SeqIO->new(-file   => $input,
>                                                -format => "fasta" );
> 
> my $seq = $seqio_obj->next_seq;
> 
> my $all_enz = Bio::Restriction::EnzymeCollection->new();
> 
> my $h3 = $all_enz->get_enzyme('HindIII');
> 
> my $ra = Bio::Restriction::Analysis->new(-seq => $seq);
> 
> print join "\n", $ra->sizes($h3), "\n\n";
> print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
> print join "\n", $ra->sizes($h3, 1, 1), "\n\n";
> 
> exit;
> =+=+=+=
> 
> And here is the output:
> 
> 48502
> 
> 
> 48502
> 
> 
> 48.502
> 
> As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:
> 
> 
> sub sizes {
> 
>    my ($self, $enz, $kb, $sort) = @_;
> 
>    $self->throw('no enzyme selected to get fragments for')
> 
>        unless $enz;
> 
>    $self->cut unless $self->{'_cut'};
> 
>    my @frag; my $lastsite=0;
> 
>    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG
> 
>      $kb ? push (@frag, (int($site-($lastsite))/100)/10)
> 
>          : push (@frag, $site-($lastsite));
> 
>      $lastsite=$site;
> 
>    }
> 
>    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)
> 
>        : push (@frag, $self->{'_seq'}->length-($lastsite));
> 
>    if ($self->{'_seq'}->is_circular) {
> 
>       my $first=shift @frag;
> 
>       my $last=pop @frag;
> 
>       push @frag, ($first+$last);
> 
>    }
> 
>    $sort ? @frag = sort {$b <=> $a} @frag : 1;
> 
> 
> 
>    return @frag;
> 
> }
> 
> 
> I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:
> 
> my $name = $enz->{_seq}->{display_id};
> foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {
> 
> And now my script yields this output:
> 
> 23130
> 2027
> 2322
> 9416
> 564
> 6682
> 4361
> 
> 
> 23130
> 9416
> 6682
> 4361
> 2322
> 2027
> 564
> 
> 
> 23.13
> 9.416
> 6.682
> 4.361
> 2.322
> 2.027
> 0.564
> 
> which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:
> 
> 
> You should be able to do these:
> 
> 
> 
>  # to see all the fragment sizes,
> 
>  print join "\n", @{$re->sizes($enz)}, "\n";
> 
>  # to see all the fragment sizes sorted
> 
>  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";
> 
>  # to see all the fragment sizes in kb sorted
> 
>  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";
> 
> --Marc
> 
> Marc Perry
> Scientific Associate
> 
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
> 
> Tel:       416-673-8593
> Toll-free:  1-866-678-6427
> Cell:      416-904-8037
> www.oicr.on.ca<http://www.oicr.on.ca/>
> 
> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dimitark at bii.a-star.edu.sg  Mon Nov 29 04:35:26 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 17:35:26 +0800
Subject: [Bioperl-l] genbank
Message-ID: <4CF373DE.4070902@bii.a-star.edu.sg>

Hi again,
it seems that when i download (with 'download_query_genbank.pl') the 
whole proteome from NCBI in fasta format it is first being downloaded 
and from it is being created some kind of SeqFastaSpeedFactory and after 
that from it is being copied to the output file. But i want to download 
and write to output file one by one so i can see the download 
progress(which is working for genbank data).

Its frustrating :)

Any ideas where to look for solution
Cheers
Dimitar




From cjfields at illinois.edu  Mon Nov 29 09:39:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 08:39:16 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF373DE.4070902@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
Message-ID: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>

On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:

> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
> 
> Its frustrating :)
> 
> Any ideas where to look for solution
> Cheers
> Dimitar

You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:

my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
	$out->write_seq($seq);
}

insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.

If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.

chris


From dimitark at bii.a-star.edu.sg  Wed Nov 24 21:20:28 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:20:28 +0800
Subject: [Bioperl-l] question about GenPept.pm
Message-ID: <4CEDC7EC.1000903@bii.a-star.edu.sg>

Hi guys,
i want to get some genomes and proteomes from NCBI in fasta format. I 
found i have to use 'download_query_genbank.pl' for that. It works but 
not as i would like. It uses the modules GenPept and GenBank. They 
retrieve the data in fasta but in different format than i want.

Example:
a) i want the fasta to be like the following:
 >gi|5834889|ref|NP_006959.1|COX3_10021 cytochrome c oxidase subunit III 
[Caenorhabditis elegans]
here sequense...

b) but it comes like this:
 >COX3_10021 cytochrome c oxidase subunit III [Caenorhabditis elegans]
here sequense...

But i need the gi and NP as well. So i dug up a bit and after playing 
with 'download_query_genbank.pl' i managed to make GenBank to give the 
fasta seqs in the format i want.
I made the following changes:
1. added $retformat option for Getopt
2.modified this section:
if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


} else {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenBank->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenBank->new(-verbose => $debug);
     }
}

But i go problem with GenPept. I still cant get the seqs in full fasta 
format as i explained above. Its interesting cos both modules GenPept 
and GenBank are almost identical except that GenBank uses the new method 
of NCBIHelper while GenPept has its own which still uses the 
NCBIHelper's as well.

With my modification i pass the format i want but then somehow it 
reverts to the default set in GenPept which is 'gp' while i need it to 
be 'fasta'.

If i change the defaultformat in GenPept to fasta it works but thats 
just doing the job without adding the needed flexibility.

Any help would be appreciated. I will try to find solution as well.
Cheers

PS: i attache the modified 'download_query_genbank.pl'
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From dimitark at bii.a-star.edu.sg  Mon Nov 29 02:17:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 15:17:50 +0800
Subject: [Bioperl-l] about genpept and genbank
Message-ID: <4CF3539E.8030002@bii.a-star.edu.sg>

hi guys,
i dug up a bit more and found a solution. i think the problem is that in 
'download_query_genbank.pl' there is the 'format' option which only is 
responsible for the format of the output file to which seqs are 
downloaded. While i need 'ret_type' format option according to NCBI 
Eutils. So now i found that i can use GenBank.pm for all DBs in NCBI. I 
restored the GenPept as it was in original but i do not use it, its more 
tricky than GenBank.pm. Now modified 'download_query_genbank.pl' to use 
only GenBank and added one more option 'retformat' which can be set 
according to NCBI 'rettype'. Also added a simple progress bar to follow 
the download. Unfortunately it is working only if im downloading genbank 
data(Bio::SeqIO::genbank) when i download fasta(Bio::SeqIO::fasta) i 
cant use it. Seems that the fasta stream is a big chunk or somewhere the 
flush is set to zero. I dont know yet, still trying to figgure that out.

The modified script is attached.

Cheers
Dimitar


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From lsbrath at gmail.com  Mon Nov 29 16:22:09 2010
From: lsbrath at gmail.com (Mgavi Brathwaite)
Date: Mon, 29 Nov 2010 16:22:09 -0500
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
Message-ID: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>

Hello,

When I run
Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
package but can't figure out what the deal is. Any suggestions.

LomSpace

On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Only if the output appends to that file (I don't recall personally, so it's
> worth a try).
>
> chris
>
> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>
> > Wouldn't using a single filename be the way to go?
> >> my $filename = "blast_ressults.out";
> >>           $factory->save_output($filename);
> > Florent
> >
> >
> > On 09/11/10 19:05, njauxiongjie wrote:
> >> Hi,
> >>
> >> I have used the scripts list in section of "SYNOPSIS" in th webpage
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
> .
> >>
> >> there are two line of the code like below:
> >> my $filename = $result->query_name()."\.out";
> >>           $factory->save_output($filename);
> >> this saved the blast result in separated files by the query name.
> >>
> >> my question is: how can i save the blast results of all querys in one
> file?
> >>
> >>
> >>
> >> _______________________________________________
> >> 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 cjfields at illinois.edu  Mon Nov 29 16:40:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 15:40:08 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
	<AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
Message-ID: <EE86D059-1DAF-478B-9610-0821D6D239E7@illinois.edu>

You haven't installed BioPerl (you need more than Bio::Tools::Run::RemoteBlast).  Please see bioperl.org for installation instructions.

chris

On Nov 29, 2010, at 3:22 PM, Mgavi Brathwaite wrote:

> Hello,
> 
> When I run
> Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
> Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
> package but can't figure out what the deal is. Any suggestions.
> 
> LomSpace
> 
> On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Only if the output appends to that file (I don't recall personally, so it's
>> worth a try).
>> 
>> chris
>> 
>> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>> 
>>> Wouldn't using a single filename be the way to go?
>>>> my $filename = "blast_ressults.out";
>>>>          $factory->save_output($filename);
>>> Florent
>>> 
>>> 
>>> On 09/11/10 19:05, njauxiongjie wrote:
>>>> Hi,
>>>> 
>>>> I have used the scripts list in section of "SYNOPSIS" in th webpage
>> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
>> .
>>>> 
>>>> there are two line of the code like below:
>>>> my $filename = $result->query_name()."\.out";
>>>>          $factory->save_output($filename);
>>>> this saved the blast result in separated files by the query name.
>>>> 
>>>> my question is: how can i save the blast results of all querys in one
>> file?
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jason at bioperl.org  Mon Nov 29 21:19:56 2010
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 29 Nov 2010 18:19:56 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45F4C.7050102@bioperl.org>

Dimitar -

In terms of your question - a GenBank db query previously (ie 4-5 years 
ago when this was written) WOULD NOT return a sequence if a GenPept ID 
was specified so we had to have a separate module for GenBank and 
GenPept db querying since there was a different set of parameters - I 
think that changed so that most of the queries can run through GenBank

I see that must have been improved at NCBI.  For the record if you want 
the full GenPept record with features and annotations you just request a 
different db, in this case 'gb' for genbank instead of the fasta source
As in: http://gist.github.com/721012

But maybe you already figured it out?

-jason
Chris Fields wrote, On 11/29/10 6:39 AM:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org



From dimitark at bii.a-star.edu.sg  Mon Nov 29 21:54:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 10:54:50 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF45F4C.7050102@bioperl.org>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org>
Message-ID: <4CF4677A.5010604@bii.a-star.edu.sg>

On 11/30/2010 10:19 AM, Jason Stajich wrote:
> Dimitar -
>
> In terms of your question - a GenBank db query previously (ie 4-5 
> years ago when this was written) WOULD NOT return a sequence if a 
> GenPept ID was specified so we had to have a separate module for 
> GenBank and GenPept db querying since there was a different set of 
> parameters - I think that changed so that most of the queries can run 
> through GenBank
>
> I see that must have been improved at NCBI.  For the record if you 
> want the full GenPept record with features and annotations you just 
> request a different db, in this case 'gb' for genbank instead of the 
> fasta source
> As in: http://gist.github.com/721012
>
> But maybe you already figured it out?
>
> -jason
> Chris Fields wrote, On 11/29/10 6:39 AM:
>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>
>>> Hi again,
>>> it seems that when i download (with 'download_query_genbank.pl') the 
>>> whole proteome from NCBI in fasta format it is first being 
>>> downloaded and from it is being created some kind of 
>>> SeqFastaSpeedFactory and after that from it is being copied to the 
>>> output file. But i want to download and write to output file one by 
>>> one so i can see the download progress(which is working for genbank 
>>> data).
>>>
>>> Its frustrating :)
>>>
>>> Any ideas where to look for solution
>>> Cheers
>>> Dimitar
>>
>> You can't do this with the default script, but you can use a modified 
>> version and, where you are retrieving a sequence stream, in the last 
>> four lines:
>>
>> my $stream = $dbh->get_Stream_by_query($query);
>> while( my $seq = $stream->next_seq ) {
>>     $out->write_seq($seq);
>> }
>>
>> insert an iterator in the loop that indicates progress.  Realize the 
>> sequence data is processed through Bio::SeqIO, so it won't be exactly 
>> the same as what is retrieved from GenBank, but it should be very close.
>>
>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a 
>> bit more complicated.
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Thank you Jason,
i figured that out yes :)
I know am wandering how to get the GI list so i can download by ID or 
ACC and not by query when i download fasta. I have the simple code:
-------------
my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
                                        -query=>$query_str);

my $count=$query->count;
my @ids=$query->ids; <------- error msg here
------------
but i get an error msg:

MSG: Id list has been truncated even after maxids requested.

How can i get the ID/ACC? Any idea?

Thank you
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg



From dimitark at bii.a-star.edu.sg  Mon Nov 29 20:39:07 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:39:07 +0800
Subject: [Bioperl-l] Bioperl-l Digest, Vol 91, Issue 20
In-Reply-To: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
References: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
Message-ID: <4CF455BB.4060608@bii.a-star.edu.sg>

On 11/30/2010 01:00 AM, 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
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> or, via email, send a message with subject or body 'help' to
> 	bioperl-l-request at lists.open-bio.org
>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioperl-l digest..."
>
>
> Today's Topics:
>
>     1.  genbank (Dimitar Kenanov)
>     2. Re:  genbank (Chris Fields)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Nov 2010 17:35:26 +0800
> From: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Subject: [Bioperl-l] genbank
> To: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<4CF373DE.4070902 at bii.a-star.edu.sg>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the
> whole proteome from NCBI in fasta format it is first being downloaded
> and from it is being created some kind of SeqFastaSpeedFactory and after
> that from it is being copied to the output file. But i want to download
> and write to output file one by one so i can see the download
> progress(which is working for genbank data).
>
> Its frustrating :)
>
> Any ideas where to look for solution
> Cheers
> Dimitar
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 29 Nov 2010 08:39:16 -0600
> From: Chris Fields<cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] genbank
> To: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Cc: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<F3C80557-52DE-4D60-9E72-0660031D8F46 at illinois.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>
>
> ------------------------------
>
> _______________________________________________
> 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 91, Issue 20
> *****************************************
>
>    

Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

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From dimitark at bii.a-star.edu.sg  Mon Nov 29 20:50:42 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:50:42 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45872.1060405@bii.a-star.edu.sg>

On 11/29/2010 10:39 PM, Chris Fields wrote:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>    
Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: download_query_genbank.pl
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20101130/f288933b/attachment-0003.pl>

From cjfields at illinois.edu  Mon Nov 29 22:42:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 21:42:14 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4677A.5010604@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
Message-ID: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>

On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:

> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>> Dimitar -
>> 
>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>> 
>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>> As in: http://gist.github.com/721012
>> 
>> But maybe you already figured it out?
>> 
>> -jason
>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>> 
>>>> Hi again,
>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>> 
>>>> Its frustrating :)
>>>> 
>>>> Any ideas where to look for solution
>>>> Cheers
>>>> Dimitar
>>> 
>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>> 
>>> my $stream = $dbh->get_Stream_by_query($query);
>>> while( my $seq = $stream->next_seq ) {
>>>    $out->write_seq($seq);
>>> }
>>> 
>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>> 
>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>> 
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> Thank you Jason,
> i figured that out yes :)
> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
> -------------
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>                                       -query=>$query_str);
> 
> my $count=$query->count;
> my @ids=$query->ids; <------- error msg here
> ------------
> but i get an error msg:
> 
> MSG: Id list has been truncated even after maxids requested.
> 
> How can i get the ID/ACC? Any idea?
> 
> Thank you
> Dimitar

Dimitar, 

You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:

----------------------------------------------
use Bio::DB::Query::GenBank;

my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-maxids => 40000,
                                       -db=>'protein',
                                      -query=>$query_str);

my $count=$query->count;
say "Count: $count";

my @ids=$query->ids;
say scalar(@ids); # equal to $count
----------------------------------------------

Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.

chris






From dimitark at bii.a-star.edu.sg  Tue Nov 30 04:04:30 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 17:04:30 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
Message-ID: <4CF4BE1E.6090100@bii.a-star.edu.sg>

On 11/30/2010 11:42 AM, Chris Fields wrote:
> On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:
>
>    
>> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>>      
>>> Dimitar -
>>>
>>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>>>
>>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>>> As in: http://gist.github.com/721012
>>>
>>> But maybe you already figured it out?
>>>
>>> -jason
>>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>>        
>>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>>>
>>>>          
>>>>> Hi again,
>>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>>>
>>>>> Its frustrating :)
>>>>>
>>>>> Any ideas where to look for solution
>>>>> Cheers
>>>>> Dimitar
>>>>>            
>>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>>>
>>>> my $stream = $dbh->get_Stream_by_query($query);
>>>> while( my $seq = $stream->next_seq ) {
>>>>     $out->write_seq($seq);
>>>> }
>>>>
>>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>>>
>>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>>>
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>          
>>>        
>> Thank you Jason,
>> i figured that out yes :)
>> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
>> -------------
>> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
>> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>>                                        -query=>$query_str);
>>
>> my $count=$query->count;
>> my @ids=$query->ids;<------- error msg here
>> ------------
>> but i get an error msg:
>>
>> MSG: Id list has been truncated even after maxids requested.
>>
>> How can i get the ID/ACC? Any idea?
>>
>> Thank you
>> Dimitar
>>      
> Dimitar,
>
> You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:
>
> ----------------------------------------------
> use Bio::DB::Query::GenBank;
>
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-maxids =>  40000,
>                                         -db=>'protein',
>                                        -query=>$query_str);
>
> my $count=$query->count;
> say "Count: $count";
>
> my @ids=$query->ids;
> say scalar(@ids); # equal to $count
> ----------------------------------------------
>
> Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.
>
> chris
>
>
>
>    
Hi again,
i managed to solve my problem. It may be dirty but it works the way i 
want :)
I reworked the 'download_query_genbank.pl' (attached). Now i can get the 
seqs in full fasta for proteomes and genomes and the genpept report 
files for the proteomes.
For DB handle i only use GenPept now cos it gives me stream which i can 
track with term::progressbar.

For the output i use 2 cases:
-----------------
while( my $seq = $stream->next_seq ) {
     #DIMITAR
     my($gi,$locus,$refnum,$desc,$seqstr);
     if($retformat eq 'fasta'){ <-------------------------| for the 
fasta as i want it
         check_progress($prgs,$seqnum,$count);
         $locus=$seq->display_id;
         $refnum=$seq->accession_number;
         $gi=$seq->primary_id;
         $desc=$seq->desc;
         $desc=~s/\.$//;
         $seqstr=$seq->seq;
         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
     }else{
         check_progress($prgs,$seqnum,$count);
         $out->write_seq($seq); <--------------------------| for the 
genbank reports
     }
     $seqnum++;
     #DIMITAR

#    $out->write_seq($seq);#original

}
------------------

Thank you for your help and time.

Cheers
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

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From jason at bioperl.org  Tue Nov 30 12:06:08 2010
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Nov 2010 09:06:08 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4BE1E.6090100@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
	<4CF4BE1E.6090100@bii.a-star.edu.sg>
Message-ID: <4CF52F00.5000803@bioperl.org>

great - the whole point of the scripts are as examples really, not that 
you need to send patches back to show everything that you modified, but 
that you modify to use modules and code to do whatever special thing you 
want. The hope is that the modules are flexible enough that you can 
write the script to accomplish your goal.

BTW - the one thing you can't recover from the GBK version of the file 
is the source of the accession number -- you have hardcoded in 'ref' but 
it can be 'gb', 'emb', 'sp' etc this field isn't part of the genbank 
record unfortunately -- one can come up with a pattern based on 
knowledge of accession number formats but I don't know that anyone has 
really been that worried about that sort of thing to try and write 
something for it.

>>
> Hi again,
> i managed to solve my problem. It may be dirty but it works the way i 
> want :)
> I reworked the 'download_query_genbank.pl' (attached). Now i can get 
> the seqs in full fasta for proteomes and genomes and the genpept 
> report files for the proteomes.
> For DB handle i only use GenPept now cos it gives me stream which i 
> can track with term::progressbar.
>
> For the output i use 2 cases:
> -----------------
> while( my $seq = $stream->next_seq ) {
>     #DIMITAR
>     my($gi,$locus,$refnum,$desc,$seqstr);
>     if($retformat eq 'fasta'){ <-------------------------| for the 
> fasta as i want it
>         check_progress($prgs,$seqnum,$count);
>         $locus=$seq->display_id;
>         $refnum=$seq->accession_number;
>         $gi=$seq->primary_id;
>         $desc=$seq->desc;
>         $desc=~s/\.$//;
>         $seqstr=$seq->seq;
>         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
>     }else{
>         check_progress($prgs,$seqnum,$count);
>         $out->write_seq($seq); <--------------------------| for the 
> genbank reports
>     }
>     $seqnum++;
>     #DIMITAR
>
> #    $out->write_seq($seq);#original
>
> }
> ------------------
>
> Thank you for your help and time.
>
> Cheers
> Dimitar
>

-- 
Jason Stajich
jason at bioperl.org



From chiragmatkarbioinfo at gmail.com  Mon Nov  1 06:58:55 2010
From: chiragmatkarbioinfo at gmail.com (chirag matkar)
Date: Mon, 1 Nov 2010 13:58:55 +0700
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
Message-ID: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar


From Russell.Smithies at agresearch.co.nz  Wed Nov  3 02:11:36 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Nov 2010 15:11:36 +1300
Subject: [Bioperl-l] how to download PDB files using Bioperl script
In-Reply-To: <AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
References: <AANLkTin6=27avBKXQaRExBpokWqkZ_YnRTeBfLRHN6Mq@mail.gmail.com>
	<01f901cb7203$f66e4040$e34ac0c0$%yin@ucd.ie>
	<AANLkTimtPtBUd9fmcE8qbqbcNnw3-fmRn0yi2dG78prk@mail.gmail.com>
	<AANLkTi=gPcB2-UC8=99DQoTAO-AP2V9rowUJzExTNCPY@mail.gmail.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313A9B7D7C@exchsth.agresearch.co.nz>

Seems a bit like overkill, what's wrong with wget?

wget -i <list_of_urls.txt>

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
Sent: Monday, 1 November 2010 7:59 p.m.
To: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] how to download PDB files using Bioperl script

Use Perl Mechanize Module to fetch pdb data in bulk
Example , Each pdb file is saved in path
http://www.rcsb.org/pdb/files/1HKB.pdb

 use WWW::Mechanize;
    use Storable;

    $url = 'http://www.rcsb.org/pdb/files/1HKB.pdb';
    $m = WWW::Mechanize->new();
    $m->get($url);

    $c = $m->content;
  print $c;



Just create a filehandle to fetch pdb id from text file  and create a new
object for each id and loop it to fetch data



On Wed, Oct 27, 2010 at 11:53 PM, Christopher Bottoms <maizemu at gmail.com>
wrote:
> Ashwani,
>
> Do you need to download the files once or does this need to be automated?
>
> If you just need to do it once, check out
> http://www.rcsb.org/pdb/download/download.do for downloading multiple
> files.
>
> If you need to automate the process, let me know and I'll help you
> figure it out. The easiest way I can think of, which I used to do, is
> downloading them from the ftp site.
>
> Sincerely,
>
> Christopher Bottoms
>
> On Fri, Oct 22, 2010 at 11:12 AM, Jun Yin <jun.yin at ucd.ie> wrote:
>> Hi, Ashwani,
>>
>> I havenot found any module in BioPerl for downloading PDB files, though
>> Bio::Structure::IO::pdb can parse PDB files.
>>
>> However, PDB provides RESTful service
>> (http://www.rcsb.org/pdb/software/rest.do). You can write perl scripts to
>> batch downloading the proteins.
>>
>> Cheers,
>> Jun Yin
>> Ph.D. student in U.C.D.
>>
>> Bioinformatics Laboratory
>> Conway Institute
>> University College Dublin
>>
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of ashwani sharma
>> Sent: Thursday, October 21, 2010 9:39 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] how to download PDB files using Bioperl script
>>
>> Hi All,
>>
>>
>> I have around 150 pdb file names and I need to download them from Protein
>> Data Bank. I wonder if someone could tell me how to do it by using
Bioperl.
>>
>> Thanks in advance.
>>
>> Regards,
>> Ashwani
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> __________ Information from ESET Smart Security, version of virus
signature
>> database 5377 (20100818) __________
>>
>> The message was checked by ESET Smart Security.
>>
>> http://www.eset.com
>>
>>
>>
>> _______________________________________________
>> 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
>



-- 
Regards,
Chirag Matkar
_______________________________________________
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 miguel.pignatelli at uv.es  Wed Nov  3 09:42:49 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 10:42:49 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4C8606FA.3000509@fmi.ch>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch>
Message-ID: <4CD12E99.7080701@uv.es>

Hi all,

I have written a couple of modules that overlap certain functionality 
with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
certain constraints in the environment I had to run it (GRID) made 
impossible to use a bioperl based solution.


The main features of these modules are:

+ No dependencies of non-standard Perl modules
+ NCBI and RDP based taxonomies supported
+ Very fast and low memory footprint -- orders of magnitude faster than 
Bioperl modules (for the tasks they are designed for --).

Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in 
completeness or integration with other tools (e.g. rest of bioperl suit) 
but they are handy for mapping very large datasets (for example blast 
results) with the NCBI or RDP Taxonomy.

The modules are:

Taxonomy::Base -- Finds ancestors, ranks, converts between
                   names, ranks and IDs, etc...

Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file

Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
                   (nodes.dmp and names.dmp)
                   (Similar to Bio::DB::Taxonomy::flatfile)

Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
                             NCBI GIs to Taxids.
                             Uses a binary lookup table.

These modules are being used by several groups now -- mainly working 
with large metagenomics datasets -- and I am considering uploading them 
to CPAN, but I am not clear on where these modules should be placed there.

How do you think I should name these modules? (e.g. where these modules 
should live in CPAN?) Their natural place could be under 
Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
convenient) without being part of Bioperl? Any other suggestions?

Thank you very much in advance,

M;

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


From gabbyteku at gmail.com  Wed Nov  3 11:53:42 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Wed, 3 Nov 2010 13:53:42 +0200
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
Message-ID: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>

I can't get my esearch to work. It's as follows:

my $eut_obj = Bio::DB::EUtilities->new(   -eutil      => 'esearch',
                                                  -email      => '
myemail at gmail.com',
                                                  -term       =>
'$genename[SYMB] AND homo_sapiens[ORGN]',
                                                  -db         => 'geo',
                                                  -usehistory => 'y'
                                              );

When I run this using a gene symbol, it works fine.
But then when I run it as it is with a gene's symbol changed to
$genename(stores the gene's symbol/name), it fails.
How can this be fixed?

Thanks


From miguel.pignatelli at uv.es  Wed Nov  3 13:51:18 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Wed, 03 Nov 2010 14:51:18 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>
Message-ID: <4CD168D6.8030100@uv.es>

Hi all,

I have seen in the Nextgen section of the bioperl wiki 
(http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in 
the wish list. I have some code written for parsing SFF files that I can 
refactor and contribute with it.

Does anyone already took this?

Best regards,

M;



From biopython at maubp.freeserve.co.uk  Wed Nov  3 14:28:56 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Wed, 3 Nov 2010 14:28:56 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <AANLkTikAAz5FP3kiN0U6dtnvpgWAHtLu5DoEBcm_yzVD@mail.gmail.com>

On 2010/11/3 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Hi all,
>
> I have seen in the Nextgen section of the bioperl wiki
> (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the
> wish list. I have some code written for parsing SFF files that I can
> refactor and contribute with it.
>
> Does anyone already took this?
>
> Best regards,
>
> M;

Hi,

This sounds like a good thing for BioPerl.

If you hook this up into Bio::SeqIO then for consistency with
Biopython for the format name note we use "sff" as the full
reads, and "sff-trim" for the reads with the quality trimming
applied. If BioPerl has some built in way to hold a trimmed
sequence (with the head/tail still accessible) then this may
not be a good solution.

Peter


From scott at scottcain.net  Wed Nov  3 14:59:12 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 10:59:12 -0400
Subject: [Bioperl-l] Bio::DB::EUtilities esearch PhraseNotFound error
In-Reply-To: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
References: <AANLkTinuGd+333vugVdJrvch7VDpLuFWfMbxKG0zshrC@mail.gmail.com>
Message-ID: <AANLkTi=VgyrfZPPt+--pVJxfgh9QRsh_OLpsBq79F8z1@mail.gmail.com>

Hi Gabriel,

It looks to me like you've got a few things going wrong.  First, you
are using single quotes for the right hand side of the -term value.
In perl, single quotes are non-interpolating, which means variables
won't be substituted in.  However, if you switch to double quotes,
you'll still have a problem, because this:

  $genename[SYMB]

looks like you are trying to access an element of an array called
genename with a constant called SYMB, which of course you aren't, so
the perl interpreter will die with that.  You can rewrite that section
like this:

  $genename . '[SYMB] AND homo_sapiens[ORGN]'

so that the variable interpolation is moved out of the single quotes.

Scott




On Wed, Nov 3, 2010 at 7:53 AM, gabriel teku <gabbyteku at gmail.com> wrote:
> I can't get my esearch to work. It's as follows:
>
> my $eut_obj = Bio::DB::EUtilities->new( ? -eutil ? ? ?=> 'esearch',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-email ? ? ?=> '
> myemail at gmail.com',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-term ? ? ? =>
> '$genename[SYMB] AND homo_sapiens[ORGN]',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-db ? ? ? ? => 'geo',
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?-usehistory => 'y'
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?);
>
> When I run this using a gene symbol, it works fine.
> But then when I run it as it is with a gene's symbol changed to
> $genename(stores the gene's symbol/name), it fails.
> How can this be fixed?
>
> Thanks
> _______________________________________________
> 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 cseligman at earthlink.net  Wed Nov  3 16:07:05 2010
From: cseligman at earthlink.net (Chet Seligman)
Date: Wed, 3 Nov 2010 09:07:05 -0700
Subject: [Bioperl-l] BioPerl installation was incomplete
Message-ID: <001001cb7b71$294f12c0$7bed3840$@earthlink.net>

My perl is ActiveState 5.10.1

I installed with PPM using the following repositories:

BioPerl-Regular Releases

BioPerl-Release Candidates

Kobes

Bribes

Trouchelle

 

I got the following warnings:

Can't find any package that provides DB_File:: for Bundle-BioPerl-Core

WARNING: Can't find any package that provides IPC::Run for GraphViz

WARNING: Can't find any package that provides Apache:: for SOAP-Lite

 

I do have DB_File installed but do not have:

IPC::Run or,

Apache:: for SOAP-Lite

 

I did try to install SOAP-Lite according to the instructions in the Wiki but
no luck.

In PPM-edit repositories I saw that Kobes, Bribes & Trouchelle all showed
"0"

So how do I get SOAP-Lite, Apache and IPC::Run?

 

Chet Seligman



From cjfields at illinois.edu  Wed Nov  3 17:18:38 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 12:18:38 -0500
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD168D6.8030100@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
Message-ID: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>

Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  

I suggest, though, for long-term maintenance you could be added as a collaborator.  

chris

On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
> 
> Does anyone already took this?
> 
> Best regards,
> 
> M;
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From hanbobio at 126.com  Tue Nov  2 05:29:50 2010
From: hanbobio at 126.com (hanbobio)
Date: Tue, 2 Nov 2010 13:29:50 +0800 (CST)
Subject: [Bioperl-l] bioperl modules
Message-ID: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>

Hi, all.
 I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:

liaoy at linux:~/nd-hn> perl nd-hn.pl

Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.

BEGIN failed--compilation aborted at nd-hn.pl line 26.
 The detail of this script in two ways: the attached file and the following script.
Would you be kindly to test my script and give me some modification or suggestion?
 I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
Thank you very much for your advice.
 
Best regards
Yusheng Liao 2010-11-02
 
# retrive sequence from Genbank
use strict;
use Bio::DB::GenBank;
use Bio::SeqIO;
my $gb = new Bio::DB::GenBank;
open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
my $query = Bio::DB::Query::GenBank->new
    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
   -db      => 'nucleotide');
my $seqio = $gb->get_Stream_by_query($query);
my $i=0;
while( defined (my $seq = $seqio->next_seq )) {
$seqout->write_seq($seq);
$i++;
print ".";
}
print "$i \n";
# run multi sequence alignment
use Bio::Tools::Run::Alignment::Clustalw;
use Bio::SimpleAlign;
use Bio::AlignIO::clustalw;
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $ktuple = 3;
$factory->ktuple($ktuple); 
my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
my $aln = $factory->align($inputfilename);
my $alignout->write_aln(my $aln);

my $line;
my @array=('A','C','G','T','-');
my @arrayX=('a','c','g','t','-');
my @arrayA;
my @arrayB;
my ($i,$j,$k);
my (@a, at b);
my %hash;
open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
while($line=<FILE>){
      chomp;
      if($line=~ /CLUSTAL/){
            next;
      }elsif($line=~ /^[A-Za-z0-9]/){
            @a=split /\s+/,$line;
            if(defined($hash{$a[0]})){
                  push @{$hash{$a[0]}}, $line;
            }else{
                  ${$hash{$a[0]}}[0]=$line;
                  push @b,$a[0];
            }
       }
}
for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
      for(my $l=0;$l<=$#b;$l++){
            print OUT ${$hash{$b[$l]}}[$k];
            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
            @arrayA=split //,$seq;
            for($i=0;$i<=$#arrayA;$i++){
                  if($arrayA[$i] =~ /A/i){
                        $arrayB[0][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /C/i){
                        $arrayB[1][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /G/i){
                        $arrayB[2][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /T/i){
                        $arrayB[3][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\./i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
                  if($arrayA[$i] =~ /\-/i){
                        $arrayB[4][$i]++;
                        $arrayB[5][$i]++;
                  }
            }
       }
       for($j=0;$j<=$#arrayA;$j++){
              my $large=0;my $pos=0;
              for($i=0;$i<=4;$i++){
                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
                    if($arrayB[$i][$j]>$large){
                          $large=$arrayB[$i][$j];
                          $pos=$i;
                    }
              }
                    if($large>0.5){
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]=$array[$pos];
                    }else{
                            $arrayB[5][$j]=$large;
                            $arrayB[6][$j]='N';
                    }
       }
       for($i=0;$i<=5;$i++){
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                    if($arrayB[$i][$j]>0){
                           printf OUT "%.2f\t",$arrayB[$i][$j];
                    }else{
                           print OUT "0\t";
                    }
              }
              print OUT "\n";
        }
              for($j=0;$j<=15;$j++){
                    print OUT " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUT "$arrayB[6][$j]\t";
              }
              print OUT "\n";
              for($j=0;$j<=15;$j++){
                    print OUTA " ";
              }
              for($j=0;$j<=$#arrayA;$j++){
                      print OUTA "$arrayB[6][$j]";
              }
              print OUTA "\n";
        @arrayB=undef;
}
-------------- next part --------------
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From daniel.standage at gmail.com  Wed Nov  3 18:42:07 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 13:42:07 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
Message-ID: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>

Hi

I've got a simple script that is filtering some GFF3 data. The
Bio::Tools::GFF class has methods for reading and writing features and
reading regions (segments), but I cannot find a method for writing regions.
It's not hard to just print out the sequence-region line from the
LocatableSeq object, but then these lines are printed out before the
gff-version line (which is a no-no). Any suggestions about how to handle
this?

Thanks.

-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From scott at scottcain.net  Wed Nov  3 20:09:45 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:09:45 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
Message-ID: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>

Hi Daniel,

Why do you need the sequence-region line?  It is mostly just
informational.  If you want to define the reference sequence for the
features in the GFF file, I would suggest printing out a full GFF line
for the reference sequence instead anyway.  That way, it can have all
the information that a GFF line can encode, like a source and type, as
well as information in the ninth column.

That said, Bio::Tools::GFF probably does lack that method.  The code
in it is probably a little outdated.

Scott


On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> Hi
>
> I've got a simple script that is filtering some GFF3 data. The
> Bio::Tools::GFF class has methods for reading and writing features and
> reading regions (segments), but I cannot find a method for writing regions.
> It's not hard to just print out the sequence-region line from the
> LocatableSeq object, but then these lines are printed out before the
> gff-version line (which is a no-no). Any suggestions about how to handle
> this?
>
> Thanks.
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
> _______________________________________________
> 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 scott at scottcain.net  Wed Nov  3 20:19:07 2010
From: scott at scottcain.net (Scott Cain)
Date: Wed, 3 Nov 2010 16:19:07 -0400
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
Message-ID: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>

Ah, I see.  Well, you should complain to the authors that
sequence-region isn't a required directive (though if you made that
complaint to me, I'd say "well, it is for this tool" :-)

Of course, you could also use Bio::Graphics or GBrowse to do the
drawing, then I could do more to help. :-)

Scott


On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
<daniel.standage at gmail.com> wrote:
> I'm using a tool called AnnotationSketch (part of the GenomeTools package)
> to create graphics from my GFF3 files. It complains when sequence-region
> lines are not included, even when the reference is printed as a feature.
> That's what got me interested in the problem in the first place.
>
> Thanks for the info, I'll figure something out.
>
> Daniel
>
> On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
>>
>> Hi Daniel,
>>
>> Why do you need the sequence-region line? ?It is mostly just
>> informational. ?If you want to define the reference sequence for the
>> features in the GFF file, I would suggest printing out a full GFF line
>> for the reference sequence instead anyway. ?That way, it can have all
>> the information that a GFF line can encode, like a source and type, as
>> well as information in the ninth column.
>>
>> That said, Bio::Tools::GFF probably does lack that method. ?The code
>> in it is probably a little outdated.
>>
>> Scott
>>
>>
>> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
>> <daniel.standage at gmail.com> wrote:
>> > Hi
>> >
>> > I've got a simple script that is filtering some GFF3 data. The
>> > Bio::Tools::GFF class has methods for reading and writing features and
>> > reading regions (segments), but I cannot find a method for writing
>> > regions.
>> > It's not hard to just print out the sequence-region line from the
>> > LocatableSeq object, but then these lines are printed out before the
>> > gff-version line (which is a no-no). Any suggestions about how to handle
>> > this?
>> >
>> > Thanks.
>> >
>> > --
>> > Daniel S. Standage
>> > Graduate Research Assistant
>> > Bioinformatics and Computational Biology Program
>> > Iowa State University
>> > _______________________________________________
>> > 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
>
>
>
> --
> Daniel S. Standage
> Graduate Research Assistant
> Bioinformatics and Computational Biology Program
> Iowa State University
>
>



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



From daniel.standage at gmail.com  Wed Nov  3 20:14:02 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:14:02 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
Message-ID: <AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>

I'm using a tool called AnnotationSketch (part of the GenomeTools package)
to create graphics from my GFF3 files. It complains when sequence-region
lines are not included, even when the reference is printed as a feature.
That's what got me interested in the problem in the first place.

Thanks for the info, I'll figure something out.

Daniel

On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Daniel,
>
> Why do you need the sequence-region line?  It is mostly just
> informational.  If you want to define the reference sequence for the
> features in the GFF file, I would suggest printing out a full GFF line
> for the reference sequence instead anyway.  That way, it can have all
> the information that a GFF line can encode, like a source and type, as
> well as information in the ninth column.
>
> That said, Bio::Tools::GFF probably does lack that method.  The code
> in it is probably a little outdated.
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > Hi
> >
> > I've got a simple script that is filtering some GFF3 data. The
> > Bio::Tools::GFF class has methods for reading and writing features and
> > reading regions (segments), but I cannot find a method for writing
> regions.
> > It's not hard to just print out the sequence-region line from the
> > LocatableSeq object, but then these lines are printed out before the
> > gff-version line (which is a no-no). Any suggestions about how to handle
> > this?
> >
> > Thanks.
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> > _______________________________________________
> > 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
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From daniel.standage at gmail.com  Wed Nov  3 20:29:29 2010
From: daniel.standage at gmail.com (Daniel Standage)
Date: Wed, 3 Nov 2010 15:29:29 -0500
Subject: [Bioperl-l] Write segments with Bio::Tools::GFF
In-Reply-To: <AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
References: <AANLkTinKk_QucFQRCgJzwDtN0Z8VRSqEkmyTkZmOxawz@mail.gmail.com>
	<AANLkTima354AqtMJ7KR0ZJtqJHvugGo38bYfzSqkZU4k@mail.gmail.com>
	<AANLkTikobG2bsZ+dtxciaOWrGyzobMODzgEYNzx3RGxt@mail.gmail.com>
	<AANLkTi=fR=vQrTu6qO5_aLvkRDt79tm=Djn8tP9Q9NcA@mail.gmail.com>
Message-ID: <AANLkTikv-N-45cgapmZ_yHqHLFtNroBm9KU+ehXn=qad@mail.gmail.com>

Yeah, I guess it's not a show stopper, since it still generates the graphics
fine. The output that clutters the terminal is still annoying, but I can
live with that. Thanks!

Daniel

On Wed, Nov 3, 2010 at 3:19 PM, Scott Cain <scott at scottcain.net> wrote:

> Ah, I see.  Well, you should complain to the authors that
> sequence-region isn't a required directive (though if you made that
> complaint to me, I'd say "well, it is for this tool" :-)
>
> Of course, you could also use Bio::Graphics or GBrowse to do the
> drawing, then I could do more to help. :-)
>
> Scott
>
>
> On Wed, Nov 3, 2010 at 4:14 PM, Daniel Standage
> <daniel.standage at gmail.com> wrote:
> > I'm using a tool called AnnotationSketch (part of the GenomeTools
> package)
> > to create graphics from my GFF3 files. It complains when sequence-region
> > lines are not included, even when the reference is printed as a feature.
> > That's what got me interested in the problem in the first place.
> >
> > Thanks for the info, I'll figure something out.
> >
> > Daniel
> >
> > On Wed, Nov 3, 2010 at 3:09 PM, Scott Cain <scott at scottcain.net> wrote:
> >>
> >> Hi Daniel,
> >>
> >> Why do you need the sequence-region line?  It is mostly just
> >> informational.  If you want to define the reference sequence for the
> >> features in the GFF file, I would suggest printing out a full GFF line
> >> for the reference sequence instead anyway.  That way, it can have all
> >> the information that a GFF line can encode, like a source and type, as
> >> well as information in the ninth column.
> >>
> >> That said, Bio::Tools::GFF probably does lack that method.  The code
> >> in it is probably a little outdated.
> >>
> >> Scott
> >>
> >>
> >> On Wed, Nov 3, 2010 at 2:42 PM, Daniel Standage
> >> <daniel.standage at gmail.com> wrote:
> >> > Hi
> >> >
> >> > I've got a simple script that is filtering some GFF3 data. The
> >> > Bio::Tools::GFF class has methods for reading and writing features and
> >> > reading regions (segments), but I cannot find a method for writing
> >> > regions.
> >> > It's not hard to just print out the sequence-region line from the
> >> > LocatableSeq object, but then these lines are printed out before the
> >> > gff-version line (which is a no-no). Any suggestions about how to
> handle
> >> > this?
> >> >
> >> > Thanks.
> >> >
> >> > --
> >> > Daniel S. Standage
> >> > Graduate Research Assistant
> >> > Bioinformatics and Computational Biology Program
> >> > Iowa State University
> >> > _______________________________________________
> >> > 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
> >
> >
> >
> > --
> > Daniel S. Standage
> > Graduate Research Assistant
> > Bioinformatics and Computational Biology Program
> > Iowa State University
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Daniel S. Standage
Graduate Research Assistant
Bioinformatics and Computational Biology Program
Iowa State University


From cjfields at illinois.edu  Wed Nov  3 21:27:28 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 16:27:28 -0500
Subject: [Bioperl-l] bioperl modules
In-Reply-To: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
References: <6f81b65.7a0e.12c0b100d5b.Coremail.hanbobio@126.com>
Message-ID: <2A3F6A7D-CF80-4C6D-8BE2-EEDA873BCC3D@illinois.edu>

You need to install bioperl-run to get Bio::Tools::Run::Alignment::Clustalw.

chris

On Nov 2, 2010, at 12:29 AM, hanbobio wrote:

> Hi, all.
> I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:
> 
> liaoy at linux:~/nd-hn> perl nd-hn.pl
> 
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.
> 
> BEGIN failed--compilation aborted at nd-hn.pl line 26.
> The detail of this script in two ways: the attached file and the following script.
> Would you be kindly to test my script and give me some modification or suggestion?
> I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
> Thank you very much for your advice.
> 
> Best regards
> Yusheng Liao 2010-11-02
> 
> # retrive sequence from Genbank
> use strict;
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> my $gb = new Bio::DB::GenBank;
> open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
> my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
> my $query = Bio::DB::Query::GenBank->new
>    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
>   -db      => 'nucleotide');
> my $seqio = $gb->get_Stream_by_query($query);
> my $i=0;
> while( defined (my $seq = $seqio->next_seq )) {
> $seqout->write_seq($seq);
> $i++;
> print ".";
> }
> print "$i \n";
> # run multi sequence alignment
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::SimpleAlign;
> use Bio::AlignIO::clustalw;
> my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
> my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> my $ktuple = 3;
> $factory->ktuple($ktuple); 
> my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
> my $aln = $factory->align($inputfilename);
> my $alignout->write_aln(my $aln);
> 
> my $line;
> my @array=('A','C','G','T','-');
> my @arrayX=('a','c','g','t','-');
> my @arrayA;
> my @arrayB;
> my ($i,$j,$k);
> my (@a, at b);
> my %hash;
> open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
> open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
> open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
> while($line=<FILE>){
>      chomp;
>      if($line=~ /CLUSTAL/){
>            next;
>      }elsif($line=~ /^[A-Za-z0-9]/){
>            @a=split /\s+/,$line;
>            if(defined($hash{$a[0]})){
>                  push @{$hash{$a[0]}}, $line;
>            }else{
>                  ${$hash{$a[0]}}[0]=$line;
>                  push @b,$a[0];
>            }
>       }
> }
> for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
>      for(my $l=0;$l<=$#b;$l++){
>            print OUT ${$hash{$b[$l]}}[$k];
>            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
>            @arrayA=split //,$seq;
>            for($i=0;$i<=$#arrayA;$i++){
>                  if($arrayA[$i] =~ /A/i){
>                        $arrayB[0][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /C/i){
>                        $arrayB[1][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /G/i){
>                        $arrayB[2][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /T/i){
>                        $arrayB[3][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\./i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\-/i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>            }
>       }
>       for($j=0;$j<=$#arrayA;$j++){
>              my $large=0;my $pos=0;
>              for($i=0;$i<=4;$i++){
>                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
>                    if($arrayB[$i][$j]>$large){
>                          $large=$arrayB[$i][$j];
>                          $pos=$i;
>                    }
>              }
>                    if($large>0.5){
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]=$array[$pos];
>                    }else{
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]='N';
>                    }
>       }
>       for($i=0;$i<=5;$i++){
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                    if($arrayB[$i][$j]>0){
>                           printf OUT "%.2f\t",$arrayB[$i][$j];
>                    }else{
>                           print OUT "0\t";
>                    }
>              }
>              print OUT "\n";
>        }
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUT "$arrayB[6][$j]\t";
>              }
>              print OUT "\n";
>              for($j=0;$j<=15;$j++){
>                    print OUTA " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUTA "$arrayB[6][$j]";
>              }
>              print OUTA "\n";
>        @arrayB=undef;
> }
> <Moduletest.pl.pl>_______________________________________________
> 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 Nov  4 02:34:30 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 3 Nov 2010 21:34:30 -0500
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD12E99.7080701@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
Message-ID: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>

Miguel,

(Caveat: You should also ask this on the perl module-authors list, just in case: http://lists.perl.org/list/module-authors.html)

Not sure how the other devs feel, but I personally don't think the Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, for example).  It's a fairly generic top-level name.  The only worry I have is if these are too similar to current BioPerl modules; Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN related to BioPerl modules.   

Saying that, tagging them as *::Lite might be fine, as long as the documentation indicated these are not related to BioPerl.  Anyone else want to chime in?  Maybe releasing them as a top-level Taxonomy?  

chris

On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:

> Hi all,
> 
> I have written a couple of modules that overlap certain functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because certain constraints in the environment I had to run it (GRID) made impossible to use a bioperl based solution.
> 
> 
> The main features of these modules are:
> 
> + No dependencies of non-standard Perl modules
> + NCBI and RDP based taxonomies supported
> + Very fast and low memory footprint -- orders of magnitude faster than Bioperl modules (for the tasks they are designed for --).
> 
> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon in completeness or integration with other tools (e.g. rest of bioperl suit) but they are handy for mapping very large datasets (for example blast results) with the NCBI or RDP Taxonomy.
> 
> The modules are:
> 
> Taxonomy::Base -- Finds ancestors, ranks, converts between
>                  names, ranks and IDs, etc...
> 
> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
> 
> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>                  (nodes.dmp and names.dmp)
>                  (Similar to Bio::DB::Taxonomy::flatfile)
> 
> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>                            NCBI GIs to Taxids.
>                            Uses a binary lookup table.
> 
> These modules are being used by several groups now -- mainly working with large metagenomics datasets -- and I am considering uploading them to CPAN, but I am not clear on where these modules should be placed there.
> 
> How do you think I should name these modules? (e.g. where these modules should live in CPAN?) Their natural place could be under Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and convenient) without being part of Bioperl? Any other suggestions?
> 
> Thank you very much in advance,
> 
> M;
> 
> ----------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From David.Messina at sbc.su.se  Thu Nov  4 08:54:33 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 4 Nov 2010 09:54:33 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <4F9F218F-22EC-46B8-8BAB-82BD0956FB76@sbc.su.se>

I agree with Chris. You're welcome to put your code in the Bio:: namespace ? it's not reserved for BioPerl ? but since there are already modules with Taxonomy in their names, it would be likely to cause confusion.

So, if your modules are renamed to be sufficiently distinguishable from existing Taxonomy modules, putting them under Bio:: should be no problem.

Otherwise, I would go whatever the modules list folks recommend.

Dave



From miguel.pignatelli at uv.es  Thu Nov  4 11:13:20 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:13:20 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>
	<4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
Message-ID: <4CD29550.6030005@uv.es>

Thanks Chris,

I will get in touch again when I am able to hook a working module (I 
will check Biopython's Bio.Seq.SffIO)

M;


Chris Fields wrote:
> Sure, you are more than welcome to add this.  Our main source code repository in now on github (so one can fork the code, hack away, and submit pull requests), but we also accept patches.  
> 
> I suggest, though, for long-term maintenance you could be added as a collaborator.  
> 
> chris
> 
> On Nov 3, 2010, at 8:51 AM, Miguel Pignatelli wrote:
> 
>> Hi all,
>>
>> I have seen in the Nextgen section of the bioperl wiki (http://www.bioperl.org/wiki/Nextgen_in_Bioperl) that SFF support is in the wish list. I have some code written for parsing SFF files that I can refactor and contribute with it.
>>
>> Does anyone already took this?
>>
>> Best regards,
>>
>> M;
>>
>> _______________________________________________
>> 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 biopython at maubp.freeserve.co.uk  Thu Nov  4 11:40:13 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Thu, 4 Nov 2010 11:40:13 +0000
Subject: [Bioperl-l] SFF format support
In-Reply-To: <4CD29550.6030005@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk> <4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es> <4CD168D6.8030100@uv.es>
	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>
	<4CD29550.6030005@uv.es>
Message-ID: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>

2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
> Thanks Chris,
>
> I will get in touch again when I am able to hook a working module (I will
> check Biopython's Bio.Seq.SffIO)
>
> M;

Hi Miguel,

In case it helps, the Biopython SFF code is here - this includes embedded
documentation with test examples:

http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

We also have some test SFF files here (see the README file for details):

http://github.com/biopython/biopython/tree/master/Tests/Roche/

Peter


From pignatelli_mig at gva.es  Thu Nov  4 11:49:07 2010
From: pignatelli_mig at gva.es (Miguel Pignatelli)
Date: Thu, 04 Nov 2010 12:49:07 +0100
Subject: [Bioperl-l] SFF format support
In-Reply-To: <AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>	<4CD12E99.7080701@uv.es>	<4CD168D6.8030100@uv.es>	<46FE17F5-32A8-40F8-AAF7-70010B7A0831@illinois.edu>	<4CD29550.6030005@uv.es>
	<AANLkTim4nfcmXLREkis1qLWn_U94XmqYuuVMHsaw5RXg@mail.gmail.com>
Message-ID: <4CD29DB3.9010805@gva.es>

Thanks Peter, I have already took a look at the module. It will 
certainly help a lot. I also have some real SFF files from different 
collaborations that I can use for testing.

Let's roll up the sleeves...

M;


Peter wrote:
> 2010/11/4 Miguel Pignatelli <miguel.pignatelli at uv.es>:
>> Thanks Chris,
>>
>> I will get in touch again when I am able to hook a working module (I will
>> check Biopython's Bio.Seq.SffIO)
>>
>> M;
> 
> Hi Miguel,
> 
> In case it helps, the Biopython SFF code is here - this includes embedded
> documentation with test examples:
> 
> http://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py
> 
> We also have some test SFF files here (see the README file for details):
> 
> http://github.com/biopython/biopython/tree/master/Tests/Roche/
> 
> Peter


From hlapp at drycafe.net  Thu Nov  4 16:12:04 2010
From: hlapp at drycafe.net (Hilmar Lapp)
Date: Thu, 4 Nov 2010 12:12:04 -0400
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>
	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
Message-ID: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>

I agree - Bio:: isn't exclusive to BioPerl, but in choosing module  
name and namespace, as well as in documentation, try to minimize  
potential confusion for users.

	-hilmar
On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:

> Miguel,
>
> (Caveat: You should also ask this on the perl module-authors list,  
> just in case: http://lists.perl.org/list/module-authors.html)
>
> Not sure how the other devs feel, but I personally don't think the  
> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo,  
> for example).  It's a fairly generic top-level name.  The only worry  
> I have is if these are too similar to current BioPerl modules;  
> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN  
> related to BioPerl modules.
>
> Saying that, tagging them as *::Lite might be fine, as long as the  
> documentation indicated these are not related to BioPerl.  Anyone  
> else want to chime in?  Maybe releasing them as a top-level Taxonomy?
>
> chris
>
> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>
>> Hi all,
>>
>> I have written a couple of modules that overlap certain  
>> functionality with Bio::DB::Taxonomy and Bio::Taxon. I had to write  
>> them because certain constraints in the environment I had to run it  
>> (GRID) made impossible to use a bioperl based solution.
>>
>>
>> The main features of these modules are:
>>
>> + No dependencies of non-standard Perl modules
>> + NCBI and RDP based taxonomies supported
>> + Very fast and low memory footprint -- orders of magnitude faster  
>> than Bioperl modules (for the tasks they are designed for --).
>>
>> Of course, they do not compete with Bio::DB::Taxonomy and  
>> Bio::Taxon in completeness or integration with other tools (e.g.  
>> rest of bioperl suit) but they are handy for mapping very large  
>> datasets (for example blast results) with the NCBI or RDP Taxonomy.
>>
>> The modules are:
>>
>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>                 names, ranks and IDs, etc...
>>
>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>
>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>                 (nodes.dmp and names.dmp)
>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>
>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>                           NCBI GIs to Taxids.
>>                           Uses a binary lookup table.
>>
>> These modules are being used by several groups now -- mainly  
>> working with large metagenomics datasets -- and I am considering  
>> uploading them to CPAN, but I am not clear on where these modules  
>> should be placed there.
>>
>> How do you think I should name these modules? (e.g. where these  
>> modules should live in CPAN?) Their natural place could be under  
>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite /  
>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and  
>> convenient) without being part of Bioperl? Any other suggestions?
>>
>> Thank you very much in advance,
>>
>> M;
>>
>> ----------------------------------------------------
>> _______________________________________________
>> 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

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================






From kellert at ohsu.edu  Fri Nov  5 00:45:25 2010
From: kellert at ohsu.edu (Tom Keller)
Date: Thu, 4 Nov 2010 17:45:25 -0700
Subject: [Bioperl-l] parsing PubMed retrievals
Message-ID: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>

Greetings,
I'm getting the following error from the bioplerl 1.6.1 example

$ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.


Any suggestions for getting this to work?

thanks,


Tom
MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
503-494-2442
kellert at ohsu.edu<mailto:kellert at ohsu.edu>
Office: 6588 RJH (CROET/BasicScience)








From cjfields at illinois.edu  Fri Nov  5 04:28:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Thu, 4 Nov 2010 23:28:01 -0500
Subject: [Bioperl-l] parsing PubMed retrievals
In-Reply-To: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <EA90A6B2-7D87-4CC0-B4FB-D8A00FD5C77D@illinois.edu>

It seems that in some cases a webenv/querykey are not returned.  I have committed a fix to github for this which seems to fix the problem from our end.

https://github.com/bioperl/bioperl-live/commit/7c64e8410d291dbd7097b2cd8fc948d95063d153

chris

On Nov 4, 2010, at 7:45 PM, Tom Keller wrote:

> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at /Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> 
> Tom
> MMI DNA Services Core Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert at ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From miguel.pignatelli at uv.es  Fri Nov  5 09:31:46 2010
From: miguel.pignatelli at uv.es (Miguel Pignatelli)
Date: Fri, 05 Nov 2010 10:31:46 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk>	<4C860148.3030000@fmi.ch>	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>	<4C8606FA.3000509@fmi.ch>
	<4CD12E99.7080701@uv.es>	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
Message-ID: <4CD3CF02.9010608@uv.es>

Hi all,

In the perl module-authors list I have been suggested two nice alternatives:

Bio::Lite::Taxonomy::*
BioX::Taxonomy::*

If the devs don't have any objection/preference I will follow the first one.

Regards,

M;


Hilmar Lapp wrote:
> I agree - Bio:: isn't exclusive to BioPerl, but in choosing module name 
> and namespace, as well as in documentation, try to minimize potential 
> confusion for users.
> 
>     -hilmar
> On Nov 3, 2010, at 10:34 PM, Chris Fields wrote:
> 
>> Miguel,
>>
>> (Caveat: You should also ask this on the perl module-authors list, 
>> just in case: http://lists.perl.org/list/module-authors.html)
>>
>> Not sure how the other devs feel, but I personally don't think the 
>> Bio* namespace is reserved only for BioPerl modules (see Bio::Phylo, 
>> for example).  It's a fairly generic top-level name.  The only worry I 
>> have is if these are too similar to current BioPerl modules; 
>> Bio::Taxonomy and Bio::DB::Taxonomy already have namespaces in CPAN 
>> related to BioPerl modules.
>>
>> Saying that, tagging them as *::Lite might be fine, as long as the 
>> documentation indicated these are not related to BioPerl.  Anyone else 
>> want to chime in?  Maybe releasing them as a top-level Taxonomy?
>>
>> chris
>>
>> On Nov 3, 2010, at 4:42 AM, Miguel Pignatelli wrote:
>>
>>> Hi all,
>>>
>>> I have written a couple of modules that overlap certain functionality 
>>> with Bio::DB::Taxonomy and Bio::Taxon. I had to write them because 
>>> certain constraints in the environment I had to run it (GRID) made 
>>> impossible to use a bioperl based solution.
>>>
>>>
>>> The main features of these modules are:
>>>
>>> + No dependencies of non-standard Perl modules
>>> + NCBI and RDP based taxonomies supported
>>> + Very fast and low memory footprint -- orders of magnitude faster 
>>> than Bioperl modules (for the tasks they are designed for --).
>>>
>>> Of course, they do not compete with Bio::DB::Taxonomy and Bio::Taxon 
>>> in completeness or integration with other tools (e.g. rest of bioperl 
>>> suit) but they are handy for mapping very large datasets (for example 
>>> blast results) with the NCBI or RDP Taxonomy.
>>>
>>> The modules are:
>>>
>>> Taxonomy::Base -- Finds ancestors, ranks, converts between
>>>                 names, ranks and IDs, etc...
>>>
>>> Taxonomy::RDP  -- Reads the taxonomic tree from the RDP xml file
>>>
>>> Taxonomy::NCBI -- Reads the taxonomic tree from flat NCBI files
>>>                 (nodes.dmp and names.dmp)
>>>                 (Similar to Bio::DB::Taxonomy::flatfile)
>>>
>>> Taxonomy::NCBI::Gi2taxid -- Converts very fast and efficiently
>>>                           NCBI GIs to Taxids.
>>>                           Uses a binary lookup table.
>>>
>>> These modules are being used by several groups now -- mainly working 
>>> with large metagenomics datasets -- and I am considering uploading 
>>> them to CPAN, but I am not clear on where these modules should be 
>>> placed there.
>>>
>>> How do you think I should name these modules? (e.g. where these 
>>> modules should live in CPAN?) Their natural place could be under 
>>> Bio::DB::Taxonomy, maybe Bio::DB::Taxonomy::Lite / 
>>> Bio::DB::Taxonomy::Lite::NCBI / etc...? Is this possible (and 
>>> convenient) without being part of Bioperl? Any other suggestions?
>>>
>>> Thank you very much in advance,
>>>
>>> M;
>>>
>>> ----------------------------------------------------
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From David.Messina at sbc.su.se  Fri Nov  5 10:36:38 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 11:36:38 +0100
Subject: [Bioperl-l] Another Taxonomy modules to CPAN
In-Reply-To: <4CD3CF02.9010608@uv.es>
References: <005e01caf5be$6d00c9c0$47025d40$@edu.hk>
	<C935BB98-BAAD-4B09-9F3E-EAC25C38E890@sbc.su.se>
	<007401cb4e66$9533ecf0$bf9bc6d0$@edu.hk> <4C860148.3030000@fmi.ch>
	<007501cb4e6d$9b2c3ac0$d184b040$@edu.hk>
	<4C8606FA.3000509@fmi.ch> <4CD12E99.7080701@uv.es>
	<A4D1001D-7CDB-4795-9C1A-DF106ECBEB20@illinois.edu>
	<40104040-BCBF-41D0-86EC-65741F1195A6@drycafe.net>
	<4CD3CF02.9010608@uv.es>
Message-ID: <5E0858F2-3957-46E1-BCD7-0F75FF44DE7D@sbc.su.se>

> Bio::Lite::Taxonomy::*
> BioX::Taxonomy::*

Either works for me.

Thanks for asking, Miguel, and I'm looking forward to checking them out!

Dave


From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 11:33:44 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 12:33:44 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
Message-ID: <4CD3EB98.3050508@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hi folks,

https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser
contains my attempt to get a hmmer parser that is able to detect which
hmmer version output it's given and which parser to call in turn.

I chose to sneak in a Bio::SearchIO::hmmer class into the object
hierarchy that the hmmer2 parser (renamed to Bio::SearchIO::hmmer2) and
the hmmer3 parser subclass from.

I'm not sure if this is the best way to go, though, and I'd like to get
some feedback on the implementation.
The last six patches on
https://github.com/kblin/bioperl-live/commits/hmmer_merged_parser are
the full changeset, the core of the change is in
https://github.com/kblin/bioperl-live/commit/2d4816f1d67880c69948b2ce529fdeb52e0d843f

Thanks in advance for your time,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From David.Messina at sbc.su.se  Fri Nov  5 12:35:32 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 13:35:32 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
Message-ID: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>

I may have missed some recent off-list discussion, but I thought we explicitly talked about *not* merging these since it will complicate future maintenance and Hmmer2 will be obsolete in the near future.


Dave




From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 12:56:23 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 13:56:23 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
Message-ID: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 13:35, Dave Messina wrote:
> I may have missed some recent off-list discussion, but I thought we
> explicitly talked about *not* merging these since it will complicate
> future maintenance and Hmmer2 will be obsolete in the near future.

Yes, that's what I thought until about last week. Then I was bitten by
the fact that Hmmer3 can't do global alignments, so you can't reliably
use Hmmer3 to extract protein domains using the domain's motif. As this
seems to be a common use case, I think we'll end up supporting hmmer2
for quite a while now.

There's currently no plans by the Hmmer authors to add globlal and
glocal (whole profile alignments against parts of the sequence)
alignments to hmmer3. They suggested to keep using hmmer2 for now.

For this reason I decided to try and merge the two parsers to a point
where users don't have to care which version of hmmer their file is.

Cheers,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 14:17:03 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 09:17:03 -0500
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <4CD3FEF7.9010806@biotech.uni-tuebingen.de>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
Message-ID: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>

On Nov 5, 2010, at 7:56 AM, Kai Blin wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
> 
> On 2010-11-05 13:35, Dave Messina wrote:
>> I may have missed some recent off-list discussion, but I thought we
>> explicitly talked about *not* merging these since it will complicate
>> future maintenance and Hmmer2 will be obsolete in the near future.
> 
> Yes, that's what I thought until about last week. Then I was bitten by
> the fact that Hmmer3 can't do global alignments, so you can't reliably
> use Hmmer3 to extract protein domains using the domain's motif. As this
> seems to be a common use case, I think we'll end up supporting hmmer2
> for quite a while now.
> 
> There's currently no plans by the Hmmer authors to add globlal and
> glocal (whole profile alignments against parts of the sequence)
> alignments to hmmer3. They suggested to keep using hmmer2 for now.
> 
> For this reason I decided to try and merge the two parsers to a point
> where users don't have to care which version of hmmer their file is.
> 
> Cheers,
> Kai

Makes sense to me.  We're tackling some Bio::Tree revisions next week, my guess is we can also get this added in.  I'm really keen on getting 1.6.2 out sometime soon, before things get really crazy for me this spring.

Key things to test: can specify the exact hmmer2/3 parser directly?  

   my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

Can one explicitly specify the hmmer parser variant?

   my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file => 'foo')

This will more than likely pop up.  I did something with Bio::SeqIO::fastq to allow specifying sanger/illumina/solexa variants, this would be similar in respect.

chris


From kai.blin at biotech.uni-tuebingen.de  Fri Nov  5 14:53:24 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Fri, 05 Nov 2010 15:53:24 +0100
Subject: [Bioperl-l] Review request: Merged hmmer2/3 parser
In-Reply-To: <283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
References: <4CD3EB98.3050508@biotech.uni-tuebingen.de>
	<D825A8E9-D891-416A-8A58-E52D0591CD93@sbc.su.se>
	<4CD3FEF7.9010806@biotech.uni-tuebingen.de>
	<283FB1D4-559F-4971-A743-CB24254C23DC@illinois.edu>
Message-ID: <4CD41A64.4070104@biotech.uni-tuebingen.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

On 2010-11-05 15:17, Chris Fields wrote:

> Makes sense to me.  We're tackling some Bio::Tree revisions next
> week, my guess is we can also get this added in.  I'm really keen on
> getting 1.6.2 out sometime soon, before things get really crazy for
> me this spring.

I changed my mind about the hmmer parser just in time then, I guess. :)

> Key things to test: can specify the exact hmmer2/3 parser directly?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer3', -file => 'foo')

That's how I started the development. But I just see I changed all tests
over, so I can't prove it. I've added some tests to show this is
equivalent. (907b7d0a2b93d4961f64)

> Can one explicitly specify the hmmer parser variant?
> 
> my $in = Bio::SearchIO->new(-format => 'hmmer', -version => 3, -file
> => 'foo')

I didn't think about this, but that certainly seems reasonable. If
somebody specifies a format explicitly, we can short-circuit the other
detection code. I've added code and a couple of tests to support this.
See c9cd75df492dbef90fff.

Thanks for the input,
Kai

- -- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universit?t T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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From cjfields at illinois.edu  Fri Nov  5 15:06:01 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:06:01 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
Message-ID: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>

All,

I have a local Blat wrapper refactoring that I had to quickly write up for some local work.  Unfortunately, the original Blat wrapper in BioPerl-Run (Bio::Tools::Run::Alignment::Blat) had parameters that weren't compatible with more recent versions of Blat, and which didn't even use most passed parameters, so it was unfortunately pretty much useless in my hands (one couldn't designate whether the query/db was dna, prot, dnax, etc).

Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?  I plan on having it pass the original tests and adding a bit more.

As a small semi-'bonus', along with this I am also writing up additional code for Bio::SearchIO::psl that allows switching parsing logic to cluster distinct regional hits; basically, same query = Result, each Hit = distinct region, each set of blocks = HSP.  This is in response from some users here to making the bp_search2gff.pl script work with PSL a little better.  Should be added in over the next few weeks.

chris


From cjfields at illinois.edu  Fri Nov  5 15:43:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 10:43:13 -0500
Subject: [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utility GEO Database
	name change
References: <A9D8BF3D8A74DF4A925FB541C0F39D2A14C4E64EE2@NIHMLBX15.nih.gov>
Message-ID: <0831372A-B40C-4B62-B423-5BEB7B5D3543@illinois.edu>

FYI, for those GEO users out there.

-c

Begin forwarded message:

> From: <utilities-announce at ncbi.nlm.nih.gov>
> Date: November 5, 2010 10:39:27 AM CDT
> To: NLM/NCBI List utilities-announce <utilities-announce at ncbi.nlm.nih.gov>
> Subject: [Utilities-announce] NCBI E-Utility GEO Database name change
> Reply-To: utilities-announce at ncbi.nlm.nih.gov
> 
> Dear E-Utility Users,
>  
> Recently the name of the GEO Profiles database used within the E-utilities changed from 'geo' to 'geoprofiles'. While the old name (&db=geo) will still function, users are encouraged to change their requests to use the new name (db=geoprofiles). ELink users should be aware that all linknames including 'geo' will no longer function. Instead, these names should include 'geoprofiles' rather than 'geo'. For example, the linkname of links from Gene to GEO Profiles is now &linkname=gene_geoprofiles.
>  
> Thank you.
>  
> 
>  
> _______________________________________________
> Utilities-announce mailing list
> http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce




From David.Messina at sbc.su.se  Fri Nov  5 16:11:41 2010
From: David.Messina at sbc.su.se (Dave Messina)
Date: Fri, 5 Nov 2010 17:11:41 +0100
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
Message-ID: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>

On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:

> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?


Sounds great! Go for it.


Dave




From njauxiongjie at gmail.com  Fri Nov  5 09:12:33 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Fri, 05 Nov 2010 02:12:33 -0700 (PDT)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd3ca81.123f970a.39e2.ffff8e89@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  



From alpita at uvigo.es  Fri Nov  5 15:52:58 2010
From: alpita at uvigo.es (alpita at uvigo.es)
Date: Fri, 05 Nov 2010 16:52:58 +0100
Subject: [Bioperl-l] Primer3
Message-ID: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>

Hi

I am a PhD-student working with EST sequences. I have got an input  
file for Primer3 and the program does not run. I try directly in the  
windows console and with Bioperl. I suppose the problem is with the  
syntax, because I have never used these tools, so I would appreciate  
some help.

How can I invoked my input file in primer 3? If it is easy to run it  
with BioPerl, tell me

Thank you very much


From cjfields at illinois.edu  Fri Nov  5 17:27:13 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 12:27:13 -0500
Subject: [Bioperl-l] Primer3
In-Reply-To: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
References: <20101105165258.88a1uizkeg4k8skg@correoweb.uvigo.es>
Message-ID: <8BBED864-BB9A-4FF7-9B09-2549D927F858@illinois.edu>

This all depends on what version of Primer3 you are using; the Primer3 tools in bioperl-live and bioperl-run do not work with primer3 v2 due to significant changes in the primer3 API.  However, I wrote up a full refactor of these tools, along with tests, here:

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

This includes both the wrapper and the parser (see the test files for examples on how to run them).  They have been renamed because of a change in the module API.  Let me know if they work for you.

chris

On Nov 5, 2010, at 10:52 AM, alpita at uvigo.es wrote:

> Hi
> 
> I am a PhD-student working with EST sequences. I have got an input file for Primer3 and the program does not run. I try directly in the windows console and with Bioperl. I suppose the problem is with the syntax, because I have never used these tools, so I would appreciate some help.
> 
> How can I invoked my input file in primer 3? If it is easy to run it with BioPerl, tell me
> 
> Thank you very much
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From cjfields at illinois.edu  Fri Nov  5 20:57:56 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 5 Nov 2010 15:57:56 -0500
Subject: [Bioperl-l] Blat wrapper rewrite (and a PSL 'bonus')
In-Reply-To: <D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
References: <45EEAF86-33A9-4F5B-9958-85698B2353CF@illinois.edu>
	<D2563947-504A-4215-A5C5-EEE7506DDE14@sbc.su.se>
Message-ID: <374003E7-0F9F-466F-99D9-89F85F22CFF9@illinois.edu>


On Nov 5, 2010, at 11:11 AM, Dave Messina wrote:

> On Nov 5, 2010, at 16:06, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Anyone object to just scrapping the original Blat wrapper in place of this one (which allows all current Blat parameters)?
> 
> 
> Sounds great! Go for it.
> 
> 
> Dave

Okay, now in bioperl-run, master branch.  This passes all prior tests; I added a few more.

chris


From gabbyteku at gmail.com  Fri Nov  5 21:17:55 2010
From: gabbyteku at gmail.com (gabriel teku)
Date: Fri, 5 Nov 2010 23:17:55 +0200
Subject: [Bioperl-l] Bad request from efetch Bio::DB::EUtilities
Message-ID: <AANLkTimT2-K7cA3N1esBQSHb9Q8btUy3572y6L0rv5J=@mail.gmail.com>

Hi
I don't know what the problem is, but the efetch code snippet throws a Bad
request error,

while( my $id = <$in> ){           # $in, file contains list of uids
                chomp $id;

                my $eut_obj = Bio::DB::EUtilities->new(   -eutil      =>
'efetch',
                                                          -email      => '
myemail at gmail.com',
                                                          -db         =>
'geoprofile',
                                                          -id         =>
$id,
                                                      );

                open( my $tmpOut, '>' ,'doc' ) or die "Can't open doc: $!";

                eval{
                        $eut_obj->get_Response(-cb => sub {my ($data) = @_;
print $tmpOut $data );
                };
                .....
}

What is wrong with the request?

Thanks in advance


From cselig01 at students.poly.edu  Sat Nov  6 04:07:16 2010
From: cselig01 at students.poly.edu (Chet Seligman)
Date: Sat, 6 Nov 2010 04:07:16 +0000
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
 Graphics in perl 5.8 in windows 7
Message-ID: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>


I'd like to use ppm or cpan.
Does anyone know which repositories to use for the modules in the subject line?

Chet Seligman
 		 	   		  


From Kevin.M.Brown at asu.edu  Mon Nov  8 15:35:56 2010
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Mon, 8 Nov 2010 08:35:56 -0700
Subject: [Bioperl-l] Problem installing Bio::SeqIO, ::SearchIO, ; ;
	Graphics in perl 5.8 in windows 7
In-Reply-To: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
References: <COL116-W40AB3F303BACE6D2970E0A884D0@phx.gbl>
Message-ID: <1A4207F8295607498283FE9E93B775B4072A9051@EX02.asurite.ad.asu.edu>

Follow the directions at:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
To get the main parts of BioPerl installed.

Bio::Graphics is now a separate module
http://search.cpan.org/~lds/Bio-Graphics-2.15/


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Chet Seligman
> Sent: Friday, November 05, 2010 9:07 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Problem installing Bio::SeqIO, 
> ::SearchIO, ; ; Graphics in perl 5.8 in windows 7
> 
> 
> I'd like to use ppm or cpan.
> Does anyone know which repositories to use for the modules in 
> the subject line?
> 
> Chet Seligman
>  		 	   		  
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From dan.bolser at gmail.com  Tue Nov  9 10:41:53 2010
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 9 Nov 2010 10:41:53 +0000
Subject: [Bioperl-l] BP reports "All tests successful.", but some failed ...
Message-ID: <AANLkTing=D4xRTV6Lxzz6z0m=ap7-a7H5jO7eKhev7FK@mail.gmail.com>

I see the following error in the output of ./Build test:

...
t/LocalDB/SeqFeature_BDB.t ................... ok
t/LocalDB/SeqFeature_mysql.t ................. 1/84 DBI
connect('database=test','',...) failed: Can't connect to local MySQL
server through socket '/var/lib/mysql/mysql.sock' (2) at
Bio/DB/SeqFeature/Store/DBI/mysql.pm line 217
sh: -user: command not found
t/LocalDB/SeqFeature_mysql.t ................. ok
...


Related to a bug I filed a while back:
http://bugzilla.open-bio.org/show_bug.cgi?id=2899

IIRC there are a few bugs in Bio::SeqFeature::Store that are hidden
due to this initial failure.


Anyway, the point is that later I see:

All tests successful.
Files=348, Tests=24136, 249 wallclock secs ( 8.99 usr  2.04 sys +
197.16 cusr 26.85 csys = 235.04 CPU)
Result: PASS


How come we get "All tests successful." when there has clearly been an
error in "t/LocalDB/SeqFeature_mysql.t"?



BioPerl version is git bcd3b66f0422493e5f1d7c05220a4e58cced6313


Cheers,
Dan.

# The place to be
irc://irc.freenode.net/#BioPerl

# Sometimes good
irc://irc.perl.org/#gmod


From cjfields at illinois.edu  Tue Nov  9 12:58:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 06:58:40 -0600
Subject: [Bioperl-l] bioperl-primer3
In-Reply-To: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
References: <20101109130552.5pq9y28dwcwkgsww@correoweb.uvigo.es>
Message-ID: <532C3550-5AA1-4A47-9C8D-82899E78B7E5@illinois.edu>

On Nov 9, 2010, at 6:05 AM, alpita at uvigo.es wrote:

> Hi Chris
> 
> As I wrote last day, I have never used bioperl and Primer3. All of this is completely new for me. It seems very interesting but I am in a student exchange, so I have got no-time to deep into it now (I will do this in the future, because I think it is very interesting to my work).
> 
> I want to design some primers, so I have used the tools of Thomas Thiel (MISA and p3_in) to obtain the input file of primer3 software. The next step would be to invoked the primer3 in the windows console (directly with the primer3 software or with bioperl tools) but I always have got problems with error messages. I suppose that I am writting some errors.
> 
> If you can, I would greatly appreciate you to tell me what tool to use and how to write it in the windows console.
> 
> Thank you very much for you effort. I hope to be improving slowly in this task
> Regards

Please make responses to the main bioperl list.  

I rewrote the main set of tools for Primer3, which I believe i pointed out to you previously (unless I'm mistaken):

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

I can't tell you what to use for Windows: I don't develop on that platform.  Any patches are welcome in case you find problems there and fix them.

chris





From njauxiongjie at gmail.com  Tue Nov  9 09:05:04 2010
From: njauxiongjie at gmail.com (njauxiongjie)
Date: Tue, 09 Nov 2010 01:05:04 -0800 (PST)
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
Message-ID: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  



From singh.amarv at epa.gov  Tue Nov  9 18:38:18 2010
From: singh.amarv at epa.gov (Amar Singh)
Date: Tue, 9 Nov 2010 18:38:18 +0000 (UTC)
Subject: [Bioperl-l] parsing PubMed retrievals
References: <36BB76FD-C321-4973-ADA6-80066433C0E6@ohsu.edu>
Message-ID: <loom.20101109T193516-922@post.gmane.org>

Tom Keller <kellert <at> ohsu.edu> writes:

> 
> Greetings,
> I'm getting the following error from the bioplerl 1.6.1 example
> 
> $ perl biblio-eutils-example.pl<http://biblio-eutils-example.pl>
> Can't call method "text" on an undefined value at
/Library/Perl/5.10.0/Bio/DB/Biblio/eutils.pm line 378.
> 
> Any suggestions for getting this to work?
> 
> thanks,
> 
> Tom
> MMI DNA Services Core
Facility<http://www.ohsu.edu/xd/research/research-cores/dna-analysis/>
> 503-494-2442
> kellert at ohsu.edu<mailto:kellert <at> ohsu.edu>
> Office: 6588 RJH (CROET/BasicScience)
> 


Tom,

I am also facing the same problem. This was working a month back and now when I
wanted to test new thing it is giving me the same error. I think this is due to
some changes in the way we access the data. Will keep updated if I find a
solution and same way you too. 

Thanks,

Amar



From Russell.Smithies at agresearch.co.nz  Tue Nov  9 20:08:23 2010
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 10 Nov 2010 09:08:23 +1300
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <18DF7D20DFEC044098A1062202F5FFF3313BCA1138@exchsth.agresearch.co.nz>

Not sure if this will work but have you tried using STDOUT as the filename then piping all the output to a single file?
The other (much simpler) option is just concatenate all the outputs into a single file when it's finished.

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of njauxiongjie
Sent: Tuesday, 9 November 2010 10:05 p.m.
To: bioperl-l
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast

Hi, 

I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.

there are two line of the code like below:
my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
this saved the blast result in separated files by the query name.

my question is: how can i save the blast results of all querys in one file?

  

_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
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taking of any action in reliance upon, this information by persons or
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=======================================================================



From florent.angly at gmail.com  Wed Nov 10 00:54:58 2010
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 10 Nov 2010 10:54:58 +1000
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
Message-ID: <4CD9ED62.50102@gmail.com>

Wouldn't using a single filename be the way to go?
> my $filename = "blast_ressults.out";
>            $factory->save_output($filename);
Florent


On 09/11/10 19:05, njauxiongjie wrote:
> Hi,
>
> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>
> there are two line of the code like below:
> my $filename = $result->query_name()."\.out";
>            $factory->save_output($filename);
> this saved the blast result in separated files by the query name.
>
> my question is: how can i save the blast results of all querys in one file?
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From cjfields at illinois.edu  Wed Nov 10 03:46:00 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Tue, 9 Nov 2010 21:46:00 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <4CD9ED62.50102@gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
Message-ID: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>

Only if the output appends to that file (I don't recall personally, so it's worth a try).

chris

On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:

> Wouldn't using a single filename be the way to go?
>> my $filename = "blast_ressults.out";
>>           $factory->save_output($filename);
> Florent
> 
> 
> On 09/11/10 19:05, njauxiongjie wrote:
>> Hi,
>> 
>> I have used the scripts list in section of "SYNOPSIS" in th webpage http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm.
>> 
>> there are two line of the code like below:
>> my $filename = $result->query_name()."\.out";
>>           $factory->save_output($filename);
>> this saved the blast result in separated files by the query name.
>> 
>> my question is: how can i save the blast results of all querys in one file?
>> 
>> 
>> 
>> _______________________________________________
>> 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 roy.chaudhuri at gmail.com  Wed Nov 10 16:11:27 2010
From: roy.chaudhuri at gmail.com (Roy Chaudhuri)
Date: Wed, 10 Nov 2010 16:11:27 +0000
Subject: [Bioperl-l] Does $tree->remove_Node prune or splice?
In-Reply-To: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
References: <927BEE54-ABC2-428A-AF42-DDEBDEABB878@tamu.edu>
Message-ID: <4CDAC42F.9020708@gmail.com>

Hi Jim,

I don't think you ever got a reply to this. I think you want 
$tree->splice() rather than $tree->remove_Node().

Cheers,
Roy.

On 21/10/2010 18:52, Jim Hu wrote:
> I'm trying to take an unreadable tree from PFAM and prune it down to
> just show the paralogs from E. coli.
>
> When you run remove_Node on an internal node, is it supposed to
> reconnect the ancestors to the descendants?  This seems to be way to
> aggressive in what it's removing.
>
> while( my $tree = $treeio->next_tree ) { for my $node (
> $tree->get_nodes ) { if ($node->id =~ m/_ECOLI/){ #	leave this node
> alone #	print $node->id."\n"; }else{ if ($node->is_Leaf){
> $tree->remove_Node($node); }else{ my $num_children =
> scalar($node->each_Descendent); if ($num_children == 1){ print
> "removing ".$node->id."\n"; $tree->remove_Node($node); } } } }
> $treeio_out->write_tree($tree); }
>
> The idea is that when I've pruned the non-ECOLI leaves, some internal
> nodes will not be branches anymore.  But at the end, all the ECOLI
> nodes are gone, presumably because an ancestor got removed and the
> whole branch was lost.  Is there a way to remove just a node and
> graft the tree back together?  My plan, once I get that working is to
> repeat the traversal until the output stops changing.
>
> Jim
>
>
> ===================================== Jim Hu Associate 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 chandan.kr.singh at gmail.com  Thu Nov 11 11:10:25 2010
From: chandan.kr.singh at gmail.com (CHANDAN SINGH)
Date: Thu, 11 Nov 2010 16:40:25 +0530
Subject: [Bioperl-l] each_gene_symbol() is missing from
	Bio::Phenotype::OMIM::OMIMentry
Message-ID: <AANLkTinSX5oUFNYJFZwos2ODfsXFLj=xntxg43umfxs9@mail.gmail.com>

Hi Christian

The implementation of each_gene_symbol() is missing from
Bio::Phenotype::OMIM::OMIMentry even though the method has been referred in
the module and also in OMIMparser. I'm sure it was just a overlook; in which
case will you be implementing the method in the near future.

Thanks
Chandan


From cjfields at illinois.edu  Sun Nov 14 21:49:52 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Sun, 14 Nov 2010 15:49:52 -0600
Subject: [Bioperl-l] GitHub down
Message-ID: <E008728D-057A-415F-9415-EFD68F5F2B6F@illinois.edu>

Just a note that GitHub (and the main bioperl repo) appear to be down at the moment with a major disruption of service.  If anyone absolutely needs code, we have a synced repo set up here:

http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-db.git
http://repo.or.cz/w/bioperl-run.git
http://repo.or.cz/w/bioperl-network.git

chris


From maj at fortinbras.us  Tue Nov 16 01:08:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Mon, 15 Nov 2010 20:08:25 -0500
Subject: [Bioperl-l] use Bio::Search::Tiling::MapTiling
In-Reply-To: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
References: <72BADBE572A8CA4889991C87507FA1EE22DE278045@NIHMLBX07.nih.gov>
Message-ID: <E703F129EE074EFD9ACA421FED2A87F2@NewLife>

Hi Wei, 
You'll need to install the trunk code to access this method; the "release" is woefully out of date (not that I'm helping much on that these days). Use git to obtain the latests bioperl-live and bioperl-run from https://github.com/bioperl/, or the synchronized repos
http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-run.git
cheers, 
MAJ
----- Original Message ----- 
  From: Shao, Wei (NIH/NCI) [C] 
  To: Mark A Jensen 
  Sent: Monday, November 15, 2010 10:47 AM
  Subject: use Bio::Search::Tiling::MapTiling


Dear Dr. Jensen, I am looking for a bioperl module that can be used to concatenate HSP from a blast into a sequence. I found that your Bio::Search::Tiling::MapTilingcan do exactly that. I used your example script to test it. I got an error message:?Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::MapTiling" at get_hsp.pl line 29, <GEN1> line 2630?.It seems that method ?get_tiled_alns? is not in the bioperl we installed. Is that possible? The script I used is this one:  use Bio::SearchIO;use Bio::Search::Tiling::MapTiling # Note that to get one hit, the user first blasts# the set of contigs against single sequence, the reference sequence.# The result of this BLAST run is in 'contig_tile.bls' $blio = Bio::SearchIO->new( -file => 'contig_tile.bls');$result = $blio->next_result;$hit = $result->next_hit;$tiling = Bio::Search::Tiling::MapTiling->new($hit);@alns = $tiling->get_tiled_alns('query'); # here's the concatenation:$concat_seq_obj = $alns[0]->get_seq_by_id('query'); 

  Best regards,

   

   

  Wei Shao, Ph.D. [Contractor] 
  Bioinformatics Analyst IV

  Advanced Biomedical Computing Center/HIV Drug Resistance Program
  SAIC-Frederick, Inc. 

  National Cancer Institute at Frederick
  P.O. Box B, Frederick, MD 21702
  Phone: 301/846-6021

  Fax:  301/846-6013
  Email:  shaow at mail.nih.gov


  NOTICE:  This communication may contain privileged or other confidential information.  If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information.  Please indicate to the sender that you have received this email in error and delete the copy you received.

   



From dimitark at bii.a-star.edu.sg  Tue Nov 16 02:44:15 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 16 Nov 2010 10:44:15 +0800
Subject: [Bioperl-l] about tblastn and strand
Message-ID: <4CE1EFFF.70304@bii.a-star.edu.sg>

Hi guys,
i have a simple question. How exactly is defined on which strand is 
located a certain HSP in tblastn? I know it is used the strand function 
but i would like to know how is implemented. I ask cos here i made a 
perl script using bioperl but other people want to implement it in Java.

In the output of tblastn there is no strand string only frame+ or 
frame-. Do you just take the + or - to determine on which strand is the HSP?

Thank you for your time and help.

Dimitar


From mmuratet at hudsonalpha.org  Tue Nov 16 21:56:08 2010
From: mmuratet at hudsonalpha.org (Michael Muratet)
Date: Tue, 16 Nov 2010 15:56:08 -0600
Subject: [Bioperl-l] Obtaining Refseq status with eutils
Message-ID: <EEABA734-39A8-44B4-9540-A20FE1BC575E@hudsonalpha.org>

Greetings

I have been trying to get to the Refseq status info that shows up NCBI  
gene webpage. My latest attempt is:

my @accs = qw(SAAV_0049);

my $factory = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -email => 'mmuratet at hudsonalpha.org 
',
                                        -db    => 'gene',
                                        -term  => join(',', at accs));

my @uids = $factory->get_ids;

$factory->reset_parameters(-eutil => 'elink',
                            -dbfrom => 'gene',
                            -db => 'nuccore',
                            -linkname => 'gene_nuccore_refseqgene',
                            -id    => \@uids);

$factory->get_Response(-file => 'temp.txt');

All I get back is the ID number I gave it. Also, $factory->next_DocSum  
returns nothing.

A big part of the problem is that I don't know what field I'm looking  
for. I am also unsure that I am using the elink interface properly.

Does anyone know how to get to the Refseq data for a gene? I am  
looking for evidence of expression of gene models--is there a better  
annotation to use?

Thanks

Mike


Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806







From pcantalupo at gmail.com  Wed Nov 17 17:38:05 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 12:38:05 -0500
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
Message-ID: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>

Hi,

Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm


---
 Bio/SeqIO.pm |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
index fe49822..cf6d3a2 100644
--- a/Bio/SeqIO.pm
+++ b/Bio/SeqIO.pm
@@ -651,6 +651,7 @@ sub _guess_format {
    return 'phd'     if /\.(phd|phred)$/i;
    return 'pir'     if /\.pir$/i;
    return 'pln'     if /\.pln$/i;
+   return 'qual'    if /\.qual$/i;
    return 'raw'     if /\.(txt)$/i;
    return 'scf'     if /\.scf$/i;
    return 'swiss'   if /\.(swiss|sp)$/i;
-- 
1.6.4.2



Paul

Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260


From maj at fortinbras.us  Wed Nov 17 22:59:25 2010
From: maj at fortinbras.us (Mark A. Jensen)
Date: Wed, 17 Nov 2010 22:59:25 +0000
Subject: [Bioperl-l] Fwd: [Bioperl-guts-l] GO annotation
Message-ID: <W347038377283011290034765@webmail27>


redirect to list
-----Original Message-----
From: Christos Noutsos [mailto:cnoutsos at cshl.edu]
Sent: Wednesday, November 17, 2010 05:35 PM
To: bioperl-guts-l at lists.open-bio.org
Subject: [Bioperl-guts-l] GO annotation

Hi all,
I have several clusters of coregulated genes from Arabidopsis and I would like to check  their GO annotation? Is there a module in bioperl which I can use? 
Thank you for your help
Christos


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





From lskatz at gatech.edu  Thu Nov 18 03:20:03 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Wed, 17 Nov 2010 22:20:03 -0500
Subject: [Bioperl-l] Status of assembly modules
Message-ID: <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc@mail.gmail.com>

I have read on the BioPerl site that a 454 ace is not standardized due to
its coordinate system.  How can I convert it to the standard ace file?

When I run this code either by using contig or assembly objects, I get an
error.
Can't call method "get_consensus_sequence" on an undefined value at
Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.

    sub _newblerAceToAce($args){
      my($self,$args)=@_;
      my
$ace454=Bio::Assembly::IO->new(-file=>$$args{ace454Path},-format=>"ace",-variant=>'454');
      my
$ace=Bio::Assembly::IO->new(-file=>">$$args{acePath}",-format=>"ace");
      #while(my $contig=$ace454->next_contig){
      while(my $scaffold=$ace454->next_assembly){
        print Dumper $scaffold;
      }
      return $$args{acePath};
    }


On Fri, Jun 18, 2010 at 5:59 AM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 13
> Date: Fri, 18 Jun 2010 15:39:39 +1000
> From: Florent Angly <florent.angly at gmail.com>
> Subject: [Bioperl-l] Status of assembly modules
> To: Joshua Udall <jaudall at gmail.com>,   bioperl-l List
>        <bioperl-l at lists.open-bio.org>
> Message-ID: <4C1B069B.5020105 at gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Joshua,
>
> Yes, there have been interesting improvements in the assembly BioPerl
> module since v1.6.1. You can find these changes in the development
> version of BioPerl at http://github.com/bioperl/. I'll take this
> opportunity to introduce people who don't follow the commit messages to
> the new features that have been introduced:
>
> First, there is support for more file formats from high-throughput
> platforms, including those generated by de novo assembly and comparative
> assembly tools, such as:
>     * Roche 454 GS Assembler, aka Newbler (the ACE-454 variant)
>     * Maq
>     * Sam
>     * Bowtie
> There is support for running a lot more of these tools in Bioperl-run
> Bio::Tools::Run :
>     * Roche 454 GS Assembler, aka Newbler
>     * Minimo
>     * Maq
>     * Samtools
>     * Bowtie
> In terms of writing assembly file, I added the option to write ACE
> files, which is quite useful because maybe assembly programs recognize
> this format. So now you can read assemblies, modify them as you see fit
> and exporting them to other programs by writing the modified assembly in
> an ACE file.
> The internals of the IO parsers have acquired some granularity as it is
> now possible to read/write assembly files entirely, or one contig at a
> time. This is terrific to reduce memory usage.
>
> That's about it...
>
> Regards,
>
> Florent
>
> PS/ Josh, you filed bug reports related to several of these issues
> (http://bugzilla.open-bio.org/show_bug.cgi?id=2726,
> http://bugzilla.open-bio.org/show_bug.cgi?id=2483). I am closing the
> ones that were not closed yet and thank you for submitting patches.
>
>
> On 18/06/10 14:00, Joshua Udall wrote:
> > Florent -
> >
> > I didn't want to ask a direct question on-list to perhaps avoid
> > confusion.  Were you able to improve/submit a ContigIO to bioperl that
> > works with one entry at a time (instead of slurping the entire ace
> > file)?
> >
> >
>



-- 
Lee Katz
http://leeskatz.com


From rmb32 at cornell.edu  Thu Nov 18 07:03:46 2010
From: rmb32 at cornell.edu (Robert Buels)
Date: Wed, 17 Nov 2010 23:03:46 -0800
Subject: [Bioperl-l] Added '.qual' suffix detection in _guess_format
In-Reply-To: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
References: <AANLkTik=A7NfKfumZK3QEN2yzQ+o1YodarQ7e1FJ7OEk@mail.gmail.com>
Message-ID: <4CE4CFD2.3000901@cornell.edu>

Applied!  Thanks Paul!

Rob

Paul Cantalupo wrote:
> Hi,
> 
> Below is a patch for allowing suffix detection of .qual files in Bio/SeqIO.pm
> 
> 
> ---
>  Bio/SeqIO.pm |    1 +
>  1 files changed, 1 insertions(+), 0 deletions(-)
> 
> diff --git a/Bio/SeqIO.pm b/Bio/SeqIO.pm
> index fe49822..cf6d3a2 100644
> --- a/Bio/SeqIO.pm
> +++ b/Bio/SeqIO.pm
> @@ -651,6 +651,7 @@ sub _guess_format {
>     return 'phd'     if /\.(phd|phred)$/i;
>     return 'pir'     if /\.pir$/i;
>     return 'pln'     if /\.pln$/i;
> +   return 'qual'    if /\.qual$/i;
>     return 'raw'     if /\.(txt)$/i;
>     return 'scf'     if /\.scf$/i;
>     return 'swiss'   if /\.(swiss|sp)$/i;



From pcantalupo at gmail.com  Thu Nov 18 15:15:04 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Thu, 18 Nov 2010 10:15:04 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTikW_cKGovyGyKLZMxAeP1E6Vs8P=KOzAXQsKBxK@mail.gmail.com>

Hi,

I'm resending this to the list (without an attachment) since it got
flagged as having a suspicious header.


I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string":

---
 Bio/Seq/PrimaryQual.pm |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/Bio/Seq/PrimaryQual.pm b/Bio/Seq/PrimaryQual.pm
index 4935639..30383fc 100644
--- a/Bio/Seq/PrimaryQual.pm
+++ b/Bio/Seq/PrimaryQual.pm
@@ -461,7 +461,7 @@ sub qualat {
 sub to_string {
     my ($self,$out,$result) = shift;
     $out = "qual: ".join(',',@{$self->qual()});
-    foreach (qw(display_id accession_number primary_id desc id)) {
+    foreach (qw(display_id accession_number primary_id desc id length)) {
 	$result = $self->$_();
 	if (!$result) { $result = "<unset>"; }
 	$out .= "$_: $result\n";
-- 
1.6.4.2






Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260


From pcantalupo at gmail.com  Wed Nov 17 15:55:52 2010
From: pcantalupo at gmail.com (Paul Cantalupo)
Date: Wed, 17 Nov 2010 10:55:52 -0500
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
Message-ID: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>

Hi,

I simply added "length" to the foreach loop in sub "to_string" of
Bio/Seq/PrimaryQual.pm to match documentation of "to_string"

Paul


Paul Cantalupo
Research Specialist/Systems Programmer
University of Pittsburgh
Pittsburgh, PA 15260
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From twaddlac at gmail.com  Fri Nov 19 20:03:14 2010
From: twaddlac at gmail.com (Alan Twaddle)
Date: Fri, 19 Nov 2010 15:03:14 -0500
Subject: [Bioperl-l] bioperl-ext package installation error
Message-ID: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>

Hello all,

     I am trying to write a simple script to parse an ABI file into usable
data which requires the staden io_lib of which I installed. However, am
receiving an error message when trying to run my script that says the
following:
------------- EXCEPTION: Bio::Root::SystemException -------------
MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
package has been installed successfully!
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
abi.pm:100
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
STACK: AB1_parser.pl:10

I didn't receive any error messages when installing the staden package so
I'm assuming that there's some path specified in some file that is pointing
to the wrong place. I don't know if this is the case but if you have any
suggestions about how to fix this I would greatly appreciate it! Thank you
very much!

-- 

Alan Twaddle, B.S.
MUC class of 2010


From cjfields at illinois.edu  Sat Nov 20 04:33:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:33:14 -0600
Subject: [Bioperl-l] git patch for Bio/Seq/PrimaryQual.pm
In-Reply-To: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
References: <AANLkTim=s9VGGRe7Rm5XVM8Ozhry8qubMPN6=wRSZjy8@mail.gmail.com>
Message-ID: <644615D3-8F59-4E59-B7A1-6BCE6159E9C9@illinois.edu>

Paul, 

Committed this to github master branch.  Thanks for pointing that out.

chris

On Nov 17, 2010, at 9:55 AM, Paul Cantalupo wrote:

> Hi,
> 
> I simply added "length" to the foreach loop in sub "to_string" of
> Bio/Seq/PrimaryQual.pm to match documentation of "to_string"
> 
> Paul
> 
> 
> Paul Cantalupo
> Research Specialist/Systems Programmer
> University of Pittsburgh
> Pittsburgh, PA 15260
> <0001-Added-length-to-foreach-loop-to-match-documentation-.patch>_______________________________________________
> 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  Sat Nov 20 04:50:17 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 19 Nov 2010 22:50:17 -0600
Subject: [Bioperl-l] bioperl-ext package installation error
In-Reply-To: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
References: <AANLkTim8AZc0FR-5hY4zs_JgPQm9QG7f4v3gU=_9TuHV@mail.gmail.com>
Message-ID: <D0C6F261-EFF7-46D3-823D-171BAA240A91@illinois.edu>

Alan, 

You need to install the bioperl-ext module Bio::SeqIO::staden::read, which uses XS bindings to io_lib, but there's a bit of a caveat: we're not really maintaining that code anymore.  Saying that, it does work using io_lib version 1.12.2 (my local version). 

Here's the code, please make sure to note the README (specifically, the version of io_lib you will need and the problems you may run into):

https://github.com/bioperl/bioperl-ext/tree/master/Bio/SeqIO/staden/

chris

On Nov 19, 2010, at 2:03 PM, Alan Twaddle wrote:

> Hello all,
> 
>     I am trying to write a simple script to parse an ABI file into usable
> data which requires the staden io_lib of which I installed. However, am
> receiving an error message when trying to run my script that says the
> following:
> ------------- EXCEPTION: Bio::Root::SystemException -------------
> MSG: Bio::SeqIO::staden::read is not available; make sure the bioperl-ext
> package has been installed successfully!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::SeqIO::abi::_initialize /usr/local/share/perl/5.10.1/Bio/SeqIO/
> abi.pm:100
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:360
> STACK: Bio::SeqIO::new /usr/local/share/perl/5.10.1/Bio/SeqIO.pm:390
> STACK: AB1_parser.pl:10
> 
> I didn't receive any error messages when installing the staden package so
> I'm assuming that there's some path specified in some file that is pointing
> to the wrong place. I don't know if this is the case but if you have any
> suggestions about how to fix this I would greatly appreciate it! Thank you
> very much!
> 
> -- 
> 
> Alan Twaddle, B.S.
> MUC class of 2010
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jordi.durban at gmail.com  Mon Nov 22 20:01:34 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Mon, 22 Nov 2010 21:01:34 +0100
Subject: [Bioperl-l] parse multi xml
Message-ID: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>

Hi all,
I'm a newbie in the list although I've been using bioperl for 2 years.
Now I have a problem with a XML file and I don't know how to parse it.
That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
resulted from  Blast2go software the usage and I suppose the file is the
outcome of multiple blast results concatenation.
Well, I would like to split all 795 different xml chunks in 795 different
files in order to parse them looking for the best hit.
The problem appears using the blastxml parse
(*Bio::SearchIO::blastxml) *because
(and that's a personal opinion) there's another top tag not expected and I
get a error message once the first blast result was parsed.
How can I do that split function?
I hope I was clear
Thanks




-- 
Jordi


From biopython at maubp.freeserve.co.uk  Mon Nov 22 20:23:29 2010
From: biopython at maubp.freeserve.co.uk (Peter)
Date: Mon, 22 Nov 2010 20:23:29 +0000
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
Message-ID: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>

On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
> Hi all,
> I'm a newbie in the list although I've been using bioperl for 2 years.
> Now I have a problem with a XML file and I don't know how to parse it.
> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
> resulted from ?Blast2go software the usage and I suppose the file is the
> outcome of multiple blast results concatenation.

Such a file is NOT a valid XML file (but see below), you can't just
concatenate XML files. I'm pretty sure people have posted scripts
to fix such files on the blast2go mailing list.

> Well, I would like to split all 795 different xml chunks in 795 different
> files in order to parse them looking for the best hit.
> The problem appears using the blastxml parse
> (*Bio::SearchIO::blastxml) *because
> (and that's a personal opinion) there's another top tag not expected
> and I get a error message once the first blast result was parsed.
> How can I do that split function?
> I hope I was clear
> Thanks

Historically the NCBI standalone BLAST used to create these
concatenated XML files when used on multiple queries. It has
since been fixed, but perhaps BioPerl has code still in it to
handle these legacy invalid XML files?

My suggestion (until a BioPerl guru speaks up) would be to
split the file into chunks (in memory) by looking for the string
<?xml version="1.0">, and parsing each chunk individually.
Each chunk should be a valid XML file on its own.

Peter



From lskatz at gatech.edu  Mon Nov 22 20:18:10 2010
From: lskatz at gatech.edu (Lee Katz)
Date: Mon, 22 Nov 2010 15:18:10 -0500
Subject: [Bioperl-l] Re(2): Status of assembly modules
Message-ID: <AANLkTi=JShCLsHDxHK4eeWD3Da=vWmRkGN2rkuLwCjxn@mail.gmail.com>

I figured it out (I haven't tested much though).

To whoever works on Assembly::IO::ace.pm:
I changed a regular expression on line 231 because the contig object was not
initializing properly.  For some reason the 454 ace file had adopted the
reference assembly's ID and therefore there was a GI number followed by a
pipe.  The pipe was not captured with \w+.  I think that the regex will be
safe with \s(\S+)\s.

 if (/^CO\s(\S+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!
#if (/^CO\s(\w+)\s(\d+)\s(\d+)\s(\d+)\s(\w+)/xms) { # New contig starts!

On Thu, Nov 18, 2010 at 12:04 PM, <bioperl-l-request at lists.open-bio.org>wrote:

> Message: 3
> Date: Wed, 17 Nov 2010 22:20:03 -0500
> From: Lee Katz <lskatz at gatech.edu>
> Subject: Re: [Bioperl-l] Status of assembly modules
> To: bioperl-l at lists.open-bio.org
> Message-ID:
>        <AANLkTi=aFAnYrEXj3D4joZeYwxRT971M_ZYR0uFJOrxc at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I have read on the BioPerl site that a 454 ace is not standardized due to
> its coordinate system.  How can I convert it to the standard ace file?
>
> When I run this code either by using contig or assembly objects, I get an
> error.
> Can't call method "get_consensus_sequence" on an undefined value at
> Bio/Assembly/IO/ace.pm line 280, <GEN0> line 93349.
>
>    sub _newblerAceToAce($args){
>      my($self,$args)=@_;
>      my
>
> $ace454=Bio::Assembly::IO->new(-file=>$args{ace454Path},-format=>"ace",-variant=>'454');
>      my
> $ace=Bio::Assembly::IO->new(-file=>">$args{acePath}",-format=>"ace");
>      #while(my $contig=$ace454->next_contig){
>      while(my $scaffold=$ace454->next_assembly){
>        print Dumper $scaffold;
>      }
>      return $args{acePath};
>    }
>



-- 
Lee Katz
http://leeskatz.com


From thomas.sharpton at gmail.com  Mon Nov 22 22:28:52 2010
From: thomas.sharpton at gmail.com (Thomas Sharpton)
Date: Mon, 22 Nov 2010 14:28:52 -0800
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
Message-ID: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>

Hi Evan,

Glad to hear this software is a promising solution to your needs. I  
just tried running the test script under Bio/t/SearchIO/hmmer3.t and  
everything passed. Can you verify that you are using an up-to-date  
version of bioperl-live? You can grab a snapshot from github if you  
haven't already:

https://github.com/bioperl/bioperl-live

Also, I'm cc'ing this to the bioperl list so that others may benefit  
from our discourse (and chime in - Kai Blin, who created the test  
tools, and others have made substantial contributions and improvements  
to the original code and they might have good suggestions).

T



On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:

> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3  
> reports. Everything seems to be working nicely with the test data  
> and my own reports except for getting the $hsp->query_string and  
> $hsp->hit_string. I noticed that these HSP routines were not working  
> with the test script/data (for me anyway) so I thought I would ask  
> before spending days trying to solve this one.
>
> Thanks,
>
> Evan
>
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602



From jordi.durban at gmail.com  Mon Nov 22 23:34:03 2010
From: jordi.durban at gmail.com (Jordi Durban)
Date: Tue, 23 Nov 2010 00:34:03 +0100
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <AANLkTi=RBBL1vC4XRQM=_gf+5CPLiw2+6xdtwzZjFy6a@mail.gmail.com>

Thanks Peter.
That's exactly what I was looking for but so far I've not been able to do
that properly.
Any ideas??


2010/11/22 Peter <biopython at maubp.freeserve.co.uk>

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com>
> wrote:
> > Hi all,
> > I'm a newbie in the list although I've been using bioperl for 2 years.
> > Now I have a problem with a XML file and I don't know how to parse it.
> > That file has 795 xml top tags (thta's is <?xml version="1.0">) because
> they
> > resulted from  Blast2go software the usage and I suppose the file is the
> > outcome of multiple blast results concatenation.
>
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
>
> > Well, I would like to split all 795 different xml chunks in 795 different
> > files in order to parse them looking for the best hit.
> > The problem appears using the blastxml parse
> > (*Bio::SearchIO::blastxml) *because
> > (and that's a personal opinion) there's another top tag not expected
> > and I get a error message once the first blast result was parsed.
> > How can I do that split function?
> > I hope I was clear
> > Thanks
>
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?
>
> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
>
> Peter
>



-- 
Jordi


From cjfields at illinois.edu  Tue Nov 23 00:27:43 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 22 Nov 2010 18:27:43 -0600
Subject: [Bioperl-l] parse multi xml
In-Reply-To: <AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
References: <AANLkTi=1G581Z8A+p7DpMnuH+X-VAhWcdpGVWjM4gf6C@mail.gmail.com>
	<AANLkTimh9-76+T6+cG+F=daS5mT+=AiuM+9P3Dd8oGw6@mail.gmail.com>
Message-ID: <348A592A-D634-4C1C-9F05-DB20FE87F61C@illinois.edu>

On Nov 22, 2010, at 2:23 PM, Peter wrote:

> On Mon, Nov 22, 2010 at 8:01 PM, Jordi Durban <jordi.durban at gmail.com> wrote:
>> Hi all,
>> I'm a newbie in the list although I've been using bioperl for 2 years.
>> Now I have a problem with a XML file and I don't know how to parse it.
>> That file has 795 xml top tags (thta's is <?xml version="1.0">) because they
>> resulted from  Blast2go software the usage and I suppose the file is the
>> outcome of multiple blast results concatenation.
> 
> Such a file is NOT a valid XML file (but see below), you can't just
> concatenate XML files. I'm pretty sure people have posted scripts
> to fix such files on the blast2go mailing list.
> 
>> Well, I would like to split all 795 different xml chunks in 795 different
>> files in order to parse them looking for the best hit.
>> The problem appears using the blastxml parse
>> (*Bio::SearchIO::blastxml) *because
>> (and that's a personal opinion) there's another top tag not expected
>> and I get a error message once the first blast result was parsed.
>> How can I do that split function?
>> I hope I was clear
>> Thanks
> 
> Historically the NCBI standalone BLAST used to create these
> concatenated XML files when used on multiple queries. It has
> since been fixed, but perhaps BioPerl has code still in it to
> handle these legacy invalid XML files?

It does (last I looked).

> My suggestion (until a BioPerl guru speaks up) would be to
> split the file into chunks (in memory) by looking for the string
> <?xml version="1.0">, and parsing each chunk individually.
> Each chunk should be a valid XML file on its own.
> 
> Peter

Or, better yet, push the blast2go folks to create valid XML output or use an updated version of BLAST.  This bug was fixed about 3 years ago.

chris





From statonse at uga.edu  Mon Nov 22 23:41:26 2010
From: statonse at uga.edu (Evan Staton)
Date: Mon, 22 Nov 2010 18:41:26 -0500
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>
	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
Message-ID: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>

Hi Thomas,

Everything works with the latest release of bioperl-live. My bioperl was
1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
did not realize it had been incorporated into the latest distribution). All
the tests passed and all the routines worked before except for the
$hsp->query_string and $hsp->hit_string, but that is resolved now.

Thanks for the quick response, it saved me a lot of time.

Evan

On Mon, Nov 22, 2010 at 5:28 PM, Thomas Sharpton
<thomas.sharpton at gmail.com>wrote:

> Hi Evan,
>
> Glad to hear this software is a promising solution to your needs. I just
> tried running the test script under Bio/t/SearchIO/hmmer3.t and everything
> passed. Can you verify that you are using an up-to-date version of
> bioperl-live? You can grab a snapshot from github if you haven't already:
>
> https://github.com/bioperl/bioperl-live
>
> Also, I'm cc'ing this to the bioperl list so that others may benefit from
> our discourse (and chime in - Kai Blin, who created the test tools, and
> others have made substantial contributions and improvements to the original
> code and they might have good suggestions).
>
> T
>
>
>
> On Nov 22, 2010, at 1:38 PM, Evan Staton wrote:
>
> Hi Thomas,
>
> Thanks for providing the new bioperl methods for parsing hmmer3 reports.
> Everything seems to be working nicely with the test data and my own reports
> except for getting the $hsp->query_string and $hsp->hit_string. I noticed
> that these HSP routines were not working with the test script/data (for me
> anyway) so I thought I would ask before spending days trying to solve this
> one.
>
> Thanks,
>
> Evan
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> S. Evan Staton
> PhD Student - Burke Lab
> University of Georgia
> Department of Genetics
> 3507 Miller Plant Sciences
> Athens, GA 30602
>
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
S. Evan Staton
PhD Student - Burke Lab
University of Georgia
Department of Genetics
3507 Miller Plant Sciences
Athens, GA 30602


From kris.richardson at tufts.edu  Tue Nov 23 17:10:56 2010
From: kris.richardson at tufts.edu (kris richardson)
Date: Tue, 23 Nov 2010 12:10:56 -0500
Subject: [Bioperl-l] GeneMapper
Message-ID: <BA6B80D7-732A-4333-83AD-54AB14BF334D@tufts.edu>

Dear Members,

 I have a list mRNA target positions,  for various mRNAs and  I also have the RefSeq accession NM_#s for their genes  and mRNA (ex; gene: NM_198155 --- mRNA positions: NM_004649: 800-890).   

I would like to use this info to pull the chromosomal coordinates of NM_198155 corresponding to the resulting transcript positions NM:_004649:800-890.  I am familiarizing myself with bioperl and GeneMapper seems like it can provide this info.  However, the documentation on the module code is sparse, and there are no examples.  I was wondering if anyone has experience with this and could point me in the right direction, or perhaps provide some example code?  

Regards,

Kris







From kai.blin at biotech.uni-tuebingen.de  Wed Nov 24 06:24:22 2010
From: kai.blin at biotech.uni-tuebingen.de (Kai Blin)
Date: Wed, 24 Nov 2010 07:24:22 +0100
Subject: [Bioperl-l] bioperl-hmmer3 question
In-Reply-To: <AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
References: <AANLkTim01fHX5RG62BZO_m-DdeWmfNqh--XXWM=0LJcM@mail.gmail.com>	<085040DC-A2D4-4BD3-8598-AC4D6945FE89@gmail.com>
	<AANLkTinwTmib8v96yqvVkULrhq=nxy4OQQdn-bm8ZmpW@mail.gmail.com>
Message-ID: <4CECAF96.7010706@biotech.uni-tuebingen.de>

On 2010-11-23 00:41, Evan Staton wrote:

Hi Evan,

> Everything works with the latest release of bioperl-live. My bioperl was
> 1.6.1 and I was using bioperl-hmmer3 from github as a separate package (I
> did not realize it had been incorporated into the latest distribution). All
> the tests passed and all the routines worked before except for the
> $hsp->query_string and $hsp->hit_string, but that is resolved now.

I recently fixed this in bioperl-live when I bumped into that feature
missing. I didn't bother to update the bioperl-hmmer3 repository.
Perhaps it should be deleted to avoid the confusion.

Also, in bioperl-live, the Bio::SearchIO::hmmer parser now supports
hmmer2 and hmmer3 parsing, but by all means go for the specific parser
class if you know the version of hmmer result you're loading. :)

On a side note, even though you're probably aware of this... HMMer3 only
does local alignments, so it's not really good for domain extraction. It
is very fast, but if your software uses a profile based search to
extract specific amino acid motifs HMMer3 might let you down.
Just as a caveat that has bitten me recently.

Cheers,
Kai

-- 
Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-University of T?bingen
Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
D-72076 T?bingen                        Fax :   ++49 7071 29-5979
Deutschland
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben


From dimitark at bii.a-star.edu.sg  Thu Nov 25 02:38:52 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:38:52 +0800
Subject: [Bioperl-l] update: genpept module
Message-ID: <4CEDCC3C.9070707@bii.a-star.edu.sg>

Hi guys,
just managed to get GenPept to give me the fasta in the full form. I 
modified GenPept in this way:

sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); 
#DIMITAR
   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
   $self->request_format($self->default_format($format));
   return $self;
}

Cheers
Dimitar


From cjfields at illinois.edu  Thu Nov 25 03:24:40 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Wed, 24 Nov 2010 21:24:40 -0600
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDCC3C.9070707@bii.a-star.edu.sg>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
Message-ID: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>

Dimitar,

Missed your original post, but was it reported as a bug?  

chris

On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:

> Hi guys,
> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
> 
> sub new {
>  my($class, @args) = @_;
>  my $self = $class->SUPER::new(@args);
>  my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>  $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>  $self->request_format($self->default_format($format));
>  return $self;
> }
> 
> Cheers
> Dimitar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jason at bioperl.org  Thu Nov 25 03:57:11 2010
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Nov 2010 19:57:11 -0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
Message-ID: <4CEDDE97.5020406@bioperl.org>

This doesn't seem like the right fix -- you don't want to updated a 
default variable -- why didn't you just use it like this: ?

my $db = new Bio::DB::GenPept->new(-format => 'fasta');



Chris Fields wrote, On 11/24/10 7:24 PM:
> Dimitar,
>
> Missed your original post, but was it reported as a bug?
>
> chris
>
> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>
>> Hi guys,
>> just managed to get GenPept to give me the fasta in the full form. I modified GenPept in this way:
>>
>> sub new {
>>   my($class, @args) = @_;
>>   my $self = $class->SUPER::new(@args);
>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE FORMAT)], at args); #DIMITAR
>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>   $self->request_format($self->default_format($format));
>>   return $self;
>> }
>>
>> Cheers
>> Dimitar
>> _______________________________________________
>> 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 at bioperl.org



From dimitark at bii.a-star.edu.sg  Thu Nov 25 05:34:39 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 13:34:39 +0800
Subject: [Bioperl-l] update: genpept module
In-Reply-To: <4CEDDE97.5020406@bioperl.org>
References: <4CEDCC3C.9070707@bii.a-star.edu.sg>
	<03227AD9-092D-43C4-B0CF-28A7D093B35B@illinois.edu>
	<4CEDDE97.5020406@bioperl.org>
Message-ID: <4CEDF56F.3020409@bii.a-star.edu.sg>

I used it like this in the script:

if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


}

i added $retformat to getoptlong as well. but that didnt work well as 
did for GenBank. May be GenBank and GenPept should be made to work in 
the same way. Now they are a bit different. I tried to see why they 
react different but i couldnt understand why.

now my GenPept new method looks like this:
sub new {
   my($class, @args) = @_;
   my $self = $class->SUPER::new(@args);
   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
FORMAT)], at args);#dimitar
   $DEFAULTFORMAT=$format if (defined $format);#dimitar
   $self->request_format($self->default_format($format));
   return $self;
}

this way i can get sequences in any format which Eutils is allowing.

On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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
>



On 11/25/2010 11:57 AM, Jason Stajich wrote:
> This doesn't seem like the right fix -- you don't want to updated a 
> default variable -- why didn't you just use it like this: ?
>
> my $db = new Bio::DB::GenPept->new(-format => 'fasta');
>
>
>
> Chris Fields wrote, On 11/24/10 7:24 PM:
>> Dimitar,
>>
>> Missed your original post, but was it reported as a bug?
>>
>> chris
>>
>> On Nov 24, 2010, at 8:38 PM, Dimitar Kenanov wrote:
>>
>>> Hi guys,
>>> just managed to get GenPept to give me the fasta in the full form. I 
>>> modified GenPept in this way:
>>>
>>> sub new {
>>>   my($class, @args) = @_;
>>>   my $self = $class->SUPER::new(@args);
>>>   my ($verbose,$format)=$self->_rearrange([qw(VERBOSE 
>>> FORMAT)], at args); #DIMITAR
>>>   $DEFAULTFORMAT='fasta' if (defined $format); #DIMITAR
>>>   $self->request_format($self->default_format($format));
>>>   return $self;
>>> }
>>>
>>> Cheers
>>> Dimitar
>>> _______________________________________________
>>> 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 dimitark at bii.a-star.edu.sg  Thu Nov 25 07:05:36 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 15:05:36 +0800
Subject: [Bioperl-l] about NCBI seq reports
Message-ID: <4CEE0AC0.6050104@bii.a-star.edu.sg>

Hi again,
now i can get the sequences in full fasta as NCBI provides them. But can 
I also get and the GenPept reports in some way?
I tried using 'download_query_genbank.pl' but i always get some fasta 
seq but not the GenPept report even though the generated by the script 
request is valid. When i put it in browser i get the report file but the 
script itself returns fasta. I think is limitation of the modules which 
the scripts uses, right? Or am i mistaken.

Cheers
Dimitar


From Marc.Perry at oicr.on.ca  Sat Nov 27 04:53:48 2010
From: Marc.Perry at oicr.on.ca (Marc Perry)
Date: Fri, 26 Nov 2010 23:53:48 -0500
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm; 'sizes' method is broken
Message-ID: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>

Hi,

I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:

=+=+=+=
#!/usr/bin/perl

use strict;
use warnings;
use Bio::SeqIO;
use Bio::Restriction::Analysis;
use Bio::Restriction::Enzyme;
use Bio::Restriction::EnzymeCollection;

my $input = shift or die "No fasta file on command line.";

my $seqio_obj = Bio::SeqIO->new(-file   => $input,
                                                -format => "fasta" );

my $seq = $seqio_obj->next_seq;

my $all_enz = Bio::Restriction::EnzymeCollection->new();

my $h3 = $all_enz->get_enzyme('HindIII');

my $ra = Bio::Restriction::Analysis->new(-seq => $seq);

print join "\n", $ra->sizes($h3), "\n\n";
print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
print join "\n", $ra->sizes($h3, 1, 1), "\n\n";

exit;
=+=+=+=

And here is the output:

48502


48502


48.502

As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:


sub sizes {

    my ($self, $enz, $kb, $sort) = @_;

    $self->throw('no enzyme selected to get fragments for')

        unless $enz;

    $self->cut unless $self->{'_cut'};

    my @frag; my $lastsite=0;

    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG

      $kb ? push (@frag, (int($site-($lastsite))/100)/10)

          : push (@frag, $site-($lastsite));

      $lastsite=$site;

    }

    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)

        : push (@frag, $self->{'_seq'}->length-($lastsite));

    if ($self->{'_seq'}->is_circular) {

       my $first=shift @frag;

       my $last=pop @frag;

       push @frag, ($first+$last);

    }

    $sort ? @frag = sort {$b <=> $a} @frag : 1;



    return @frag;

}


I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:

my $name = $enz->{_seq}->{display_id};
foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {

And now my script yields this output:

23130
2027
2322
9416
564
6682
4361


23130
9416
6682
4361
2322
2027
564


23.13
9.416
6.682
4.361
2.322
2.027
0.564

which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:


You should be able to do these:



  # to see all the fragment sizes,

  print join "\n", @{$re->sizes($enz)}, "\n";

  # to see all the fragment sizes sorted

  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";

  # to see all the fragment sizes in kb sorted

  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";

--Marc

Marc Perry
Scientific Associate

Ontario Institute for Cancer Research
MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Tel:       416-673-8593
Toll-free:  1-866-678-6427
Cell:      416-904-8037
www.oicr.on.ca<http://www.oicr.on.ca/>

This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all




From cjfields at illinois.edu  Sat Nov 27 05:15:46 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Fri, 26 Nov 2010 23:15:46 -0600
Subject: [Bioperl-l] Bio::Restriction::Analysis.pm;
	'sizes' method is broken
In-Reply-To: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
References: <A4389E6D91BF264292311AE9DDC0735B5D720151E9@EXCHANGE01.ad.oicr.on.ca>
Message-ID: <66A351B0-D483-490A-90CC-BF7C596D6505@illinois.edu>

Marc,

I've entered this into bugzilla for tracking (the best place for this, BTW).  I can't promise when we'll get to it, but since there is a proposed fix it may be handled fairly soon.  Thanks for pointing this out!

chris

On Nov 26, 2010, at 10:53 PM, Marc Perry wrote:

> Hi,
> 
> I was following along in the Bioperl tutorial, and in the POD for this module and I discovered that the 'sizes' method was not working as advertised (in my hands).  For the input file I was using the complete genome of bacteriophage lambda as a plain vanilla fasta file.  Here is the script I used:
> 
> =+=+=+=
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> use Bio::SeqIO;
> use Bio::Restriction::Analysis;
> use Bio::Restriction::Enzyme;
> use Bio::Restriction::EnzymeCollection;
> 
> my $input = shift or die "No fasta file on command line.";
> 
> my $seqio_obj = Bio::SeqIO->new(-file   => $input,
>                                                -format => "fasta" );
> 
> my $seq = $seqio_obj->next_seq;
> 
> my $all_enz = Bio::Restriction::EnzymeCollection->new();
> 
> my $h3 = $all_enz->get_enzyme('HindIII');
> 
> my $ra = Bio::Restriction::Analysis->new(-seq => $seq);
> 
> print join "\n", $ra->sizes($h3), "\n\n";
> print join "\n", $ra->sizes($h3, 0, 1), "\n\n";
> print join "\n", $ra->sizes($h3, 1, 1), "\n\n";
> 
> exit;
> =+=+=+=
> 
> And here is the output:
> 
> 48502
> 
> 
> 48502
> 
> 
> 48.502
> 
> As I recall, there are six HindIII sites in lambda, which should yield 7 fragments from a linear genome.  Here is the subroutine code from github:
> 
> 
> sub sizes {
> 
>    my ($self, $enz, $kb, $sort) = @_;
> 
>    $self->throw('no enzyme selected to get fragments for')
> 
>        unless $enz;
> 
>    $self->cut unless $self->{'_cut'};
> 
>    my @frag; my $lastsite=0;
> 
>    foreach my $site (@{$self->{'_cut_positions'}->{$enz}}) { # BUG
> 
>      $kb ? push (@frag, (int($site-($lastsite))/100)/10)
> 
>          : push (@frag, $site-($lastsite));
> 
>      $lastsite=$site;
> 
>    }
> 
>    $kb ? push (@frag, (int($self->{'_seq'}->length-($lastsite))/100)/10)
> 
>        : push (@frag, $self->{'_seq'}->length-($lastsite));
> 
>    if ($self->{'_seq'}->is_circular) {
> 
>       my $first=shift @frag;
> 
>       my $last=pop @frag;
> 
>       push @frag, ($first+$last);
> 
>    }
> 
>    $sort ? @frag = sort {$b <=> $a} @frag : 1;
> 
> 
> 
>    return @frag;
> 
> }
> 
> 
> I eventually tracked the bug down to the indicated line.  As written, we are feeding in the enzyme object as a hash key instead of the enzyme's name, and everybody is unhappy.  Here is the solution that I hacked out:
> 
> my $name = $enz->{_seq}->{display_id};
> foreach my $site (@{$self->{'_cut_positions'}->{$name}}) {
> 
> And now my script yields this output:
> 
> 23130
> 2027
> 2322
> 9416
> 564
> 6682
> 4361
> 
> 
> 23130
> 9416
> 6682
> 4361
> 2322
> 2027
> 564
> 
> 
> 23.13
> 9.416
> 6.682
> 4.361
> 2.322
> 2.027
> 0.564
> 
> which makes me happier.  Oh, the example shown in the POD is also incorrect; using it like this throws an exception:
> 
> 
> You should be able to do these:
> 
> 
> 
>  # to see all the fragment sizes,
> 
>  print join "\n", @{$re->sizes($enz)}, "\n";
> 
>  # to see all the fragment sizes sorted
> 
>  print join "\n", @{$re->sizes($enz, 0, 1)}, "\n";
> 
>  # to see all the fragment sizes in kb sorted
> 
>  print join "\n", @{$re->sizes($enz, 1, 1)}, "\n";
> 
> --Marc
> 
> Marc Perry
> Scientific Associate
> 
> Ontario Institute for Cancer Research
> MaRS Centre, South Tower
> 101 College Street, Suite 800
> Toronto, Ontario, Canada M5G 0A3
> 
> Tel:       416-673-8593
> Toll-free:  1-866-678-6427
> Cell:      416-904-8037
> www.oicr.on.ca<http://www.oicr.on.ca/>
> 
> This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From dimitark at bii.a-star.edu.sg  Mon Nov 29 09:35:26 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 17:35:26 +0800
Subject: [Bioperl-l] genbank
Message-ID: <4CF373DE.4070902@bii.a-star.edu.sg>

Hi again,
it seems that when i download (with 'download_query_genbank.pl') the 
whole proteome from NCBI in fasta format it is first being downloaded 
and from it is being created some kind of SeqFastaSpeedFactory and after 
that from it is being copied to the output file. But i want to download 
and write to output file one by one so i can see the download 
progress(which is working for genbank data).

Its frustrating :)

Any ideas where to look for solution
Cheers
Dimitar




From cjfields at illinois.edu  Mon Nov 29 14:39:16 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 08:39:16 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF373DE.4070902@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
Message-ID: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>

On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:

> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
> 
> Its frustrating :)
> 
> Any ideas where to look for solution
> Cheers
> Dimitar

You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:

my $stream = $dbh->get_Stream_by_query($query);
while( my $seq = $stream->next_seq ) {
	$out->write_seq($seq);
}

insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.

If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.

chris


From dimitark at bii.a-star.edu.sg  Thu Nov 25 02:20:28 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Thu, 25 Nov 2010 10:20:28 +0800
Subject: [Bioperl-l] question about GenPept.pm
Message-ID: <4CEDC7EC.1000903@bii.a-star.edu.sg>

Hi guys,
i want to get some genomes and proteomes from NCBI in fasta format. I 
found i have to use 'download_query_genbank.pl' for that. It works but 
not as i would like. It uses the modules GenPept and GenBank. They 
retrieve the data in fasta but in different format than i want.

Example:
a) i want the fasta to be like the following:
 >gi|5834889|ref|NP_006959.1|COX3_10021 cytochrome c oxidase subunit III 
[Caenorhabditis elegans]
here sequense...

b) but it comes like this:
 >COX3_10021 cytochrome c oxidase subunit III [Caenorhabditis elegans]
here sequense...

But i need the gi and NP as well. So i dug up a bit and after playing 
with 'download_query_genbank.pl' i managed to make GenBank to give the 
fasta seqs in the format i want.
I made the following changes:
1. added $retformat option for Getopt
2.modified this section:
if( $options{'-db'} eq 'protein' ) {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenPept->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenPept->new(-verbose => $debug);
     }


} else {
     ### DIMITAR ###
     if( $retformat eq 'fasta'){
     $dbh = Bio::DB::GenBank->new(-verbose => $debug,
                             -format => 'Fasta');
     ### END DIMITAR ###
     }else{
     $dbh = Bio::DB::GenBank->new(-verbose => $debug);
     }
}

But i go problem with GenPept. I still cant get the seqs in full fasta 
format as i explained above. Its interesting cos both modules GenPept 
and GenBank are almost identical except that GenBank uses the new method 
of NCBIHelper while GenPept has its own which still uses the 
NCBIHelper's as well.

With my modification i pass the format i want but then somehow it 
reverts to the default set in GenPept which is 'gp' while i need it to 
be 'fasta'.

If i change the defaultformat in GenPept to fasta it works but thats 
just doing the job without adding the needed flexibility.

Any help would be appreciated. I will try to find solution as well.
Cheers

PS: i attache the modified 'download_query_genbank.pl'
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From dimitark at bii.a-star.edu.sg  Mon Nov 29 07:17:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Mon, 29 Nov 2010 15:17:50 +0800
Subject: [Bioperl-l] about genpept and genbank
Message-ID: <4CF3539E.8030002@bii.a-star.edu.sg>

hi guys,
i dug up a bit more and found a solution. i think the problem is that in 
'download_query_genbank.pl' there is the 'format' option which only is 
responsible for the format of the output file to which seqs are 
downloaded. While i need 'ret_type' format option according to NCBI 
Eutils. So now i found that i can use GenBank.pm for all DBs in NCBI. I 
restored the GenPept as it was in original but i do not use it, its more 
tricky than GenBank.pm. Now modified 'download_query_genbank.pl' to use 
only GenBank and added one more option 'retformat' which can be set 
according to NCBI 'rettype'. Also added a simple progress bar to follow 
the download. Unfortunately it is working only if im downloading genbank 
data(Bio::SeqIO::genbank) when i download fasta(Bio::SeqIO::fasta) i 
cant use it. Seems that the fasta stream is a big chunk or somewhere the 
flush is set to zero. I dont know yet, still trying to figgure that out.

The modified script is attached.

Cheers
Dimitar


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From lsbrath at gmail.com  Mon Nov 29 21:22:09 2010
From: lsbrath at gmail.com (Mgavi Brathwaite)
Date: Mon, 29 Nov 2010 16:22:09 -0500
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
Message-ID: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>

Hello,

When I run
Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
package but can't figure out what the deal is. Any suggestions.

LomSpace

On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:

> Only if the output appends to that file (I don't recall personally, so it's
> worth a try).
>
> chris
>
> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>
> > Wouldn't using a single filename be the way to go?
> >> my $filename = "blast_ressults.out";
> >>           $factory->save_output($filename);
> > Florent
> >
> >
> > On 09/11/10 19:05, njauxiongjie wrote:
> >> Hi,
> >>
> >> I have used the scripts list in section of "SYNOPSIS" in th webpage
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
> .
> >>
> >> there are two line of the code like below:
> >> my $filename = $result->query_name()."\.out";
> >>           $factory->save_output($filename);
> >> this saved the blast result in separated files by the query name.
> >>
> >> my question is: how can i save the blast results of all querys in one
> file?
> >>
> >>
> >>
> >> _______________________________________________
> >> 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 cjfields at illinois.edu  Mon Nov 29 21:40:08 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 15:40:08 -0600
Subject: [Bioperl-l] question about Bio::Tools::Run::RemoteBlast
In-Reply-To: <AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
References: <4cd90ec0.0c44970a.506d.2a81@mx.google.com>
	<4CD9ED62.50102@gmail.com>
	<14F0D22D-6AEC-4453-B089-8BDF9E9A481E@illinois.edu>
	<AANLkTim_jTxkAo9m82tBDKCP3X3jJve6zN3oCiAhhGzq@mail.gmail.com>
Message-ID: <EE86D059-1DAF-478B-9610-0821D6D239E7@illinois.edu>

You haven't installed BioPerl (you need more than Bio::Tools::Run::RemoteBlast).  Please see bioperl.org for installation instructions.

chris

On Nov 29, 2010, at 3:22 PM, Mgavi Brathwaite wrote:

> Hello,
> 
> When I run
> Bio::Tools::Run::RemoteBlast I get an error when I enter the line use
> Bio::SeqIO that says *can't locate Bio/SeqIO.pm in @INC*. I downloaded the
> package but can't figure out what the deal is. Any suggestions.
> 
> LomSpace
> 
> On Tue, Nov 9, 2010 at 10:46 PM, Chris Fields <cjfields at illinois.edu> wrote:
> 
>> Only if the output appends to that file (I don't recall personally, so it's
>> worth a try).
>> 
>> chris
>> 
>> On Nov 9, 2010, at 6:54 PM, Florent Angly wrote:
>> 
>>> Wouldn't using a single filename be the way to go?
>>>> my $filename = "blast_ressults.out";
>>>>          $factory->save_output($filename);
>>> Florent
>>> 
>>> 
>>> On 09/11/10 19:05, njauxiongjie wrote:
>>>> Hi,
>>>> 
>>>> I have used the scripts list in section of "SYNOPSIS" in th webpage
>> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.1/Bio/Tools/Run/RemoteBlast.pm>
>> .
>>>> 
>>>> there are two line of the code like below:
>>>> my $filename = $result->query_name()."\.out";
>>>>          $factory->save_output($filename);
>>>> this saved the blast result in separated files by the query name.
>>>> 
>>>> my question is: how can i save the blast results of all querys in one
>> file?
>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




From jason at bioperl.org  Tue Nov 30 02:19:56 2010
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 29 Nov 2010 18:19:56 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45F4C.7050102@bioperl.org>

Dimitar -

In terms of your question - a GenBank db query previously (ie 4-5 years 
ago when this was written) WOULD NOT return a sequence if a GenPept ID 
was specified so we had to have a separate module for GenBank and 
GenPept db querying since there was a different set of parameters - I 
think that changed so that most of the queries can run through GenBank

I see that must have been improved at NCBI.  For the record if you want 
the full GenPept record with features and annotations you just request a 
different db, in this case 'gb' for genbank instead of the fasta source
As in: http://gist.github.com/721012

But maybe you already figured it out?

-jason
Chris Fields wrote, On 11/29/10 6:39 AM:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Jason Stajich
jason at bioperl.org



From dimitark at bii.a-star.edu.sg  Tue Nov 30 02:54:50 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 10:54:50 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF45F4C.7050102@bioperl.org>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org>
Message-ID: <4CF4677A.5010604@bii.a-star.edu.sg>

On 11/30/2010 10:19 AM, Jason Stajich wrote:
> Dimitar -
>
> In terms of your question - a GenBank db query previously (ie 4-5 
> years ago when this was written) WOULD NOT return a sequence if a 
> GenPept ID was specified so we had to have a separate module for 
> GenBank and GenPept db querying since there was a different set of 
> parameters - I think that changed so that most of the queries can run 
> through GenBank
>
> I see that must have been improved at NCBI.  For the record if you 
> want the full GenPept record with features and annotations you just 
> request a different db, in this case 'gb' for genbank instead of the 
> fasta source
> As in: http://gist.github.com/721012
>
> But maybe you already figured it out?
>
> -jason
> Chris Fields wrote, On 11/29/10 6:39 AM:
>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>
>>> Hi again,
>>> it seems that when i download (with 'download_query_genbank.pl') the 
>>> whole proteome from NCBI in fasta format it is first being 
>>> downloaded and from it is being created some kind of 
>>> SeqFastaSpeedFactory and after that from it is being copied to the 
>>> output file. But i want to download and write to output file one by 
>>> one so i can see the download progress(which is working for genbank 
>>> data).
>>>
>>> Its frustrating :)
>>>
>>> Any ideas where to look for solution
>>> Cheers
>>> Dimitar
>>
>> You can't do this with the default script, but you can use a modified 
>> version and, where you are retrieving a sequence stream, in the last 
>> four lines:
>>
>> my $stream = $dbh->get_Stream_by_query($query);
>> while( my $seq = $stream->next_seq ) {
>>     $out->write_seq($seq);
>> }
>>
>> insert an iterator in the loop that indicates progress.  Realize the 
>> sequence data is processed through Bio::SeqIO, so it won't be exactly 
>> the same as what is retrieved from GenBank, but it should be very close.
>>
>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a 
>> bit more complicated.
>>
>> chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

Thank you Jason,
i figured that out yes :)
I know am wandering how to get the GI list so i can download by ID or 
ACC and not by query when i download fasta. I have the simple code:
-------------
my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
                                        -query=>$query_str);

my $count=$query->count;
my @ids=$query->ids; <------- error msg here
------------
but i get an error msg:

MSG: Id list has been truncated even after maxids requested.

How can i get the ID/ACC? Any idea?

Thank you
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg



From dimitark at bii.a-star.edu.sg  Tue Nov 30 01:39:07 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:39:07 +0800
Subject: [Bioperl-l] Bioperl-l Digest, Vol 91, Issue 20
In-Reply-To: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
References: <mailman.5.1291050004.17309.bioperl-l@lists.open-bio.org>
Message-ID: <4CF455BB.4060608@bii.a-star.edu.sg>

On 11/30/2010 01:00 AM, 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
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> or, via email, send a message with subject or body 'help' to
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> than "Re: Contents of Bioperl-l digest..."
>
>
> Today's Topics:
>
>     1.  genbank (Dimitar Kenanov)
>     2. Re:  genbank (Chris Fields)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Nov 2010 17:35:26 +0800
> From: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Subject: [Bioperl-l] genbank
> To: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<4CF373DE.4070902 at bii.a-star.edu.sg>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi again,
> it seems that when i download (with 'download_query_genbank.pl') the
> whole proteome from NCBI in fasta format it is first being downloaded
> and from it is being created some kind of SeqFastaSpeedFactory and after
> that from it is being copied to the output file. But i want to download
> and write to output file one by one so i can see the download
> progress(which is working for genbank data).
>
> Its frustrating :)
>
> Any ideas where to look for solution
> Cheers
> Dimitar
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 29 Nov 2010 08:39:16 -0600
> From: Chris Fields<cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] genbank
> To: Dimitar Kenanov<dimitark at bii.a-star.edu.sg>
> Cc: "'bioperl-l at bioperl.org'"<bioperl-l at bioperl.org>
> Message-ID:<F3C80557-52DE-4D60-9E72-0660031D8F46 at illinois.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>
>
> ------------------------------
>
> _______________________________________________
> 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 91, Issue 20
> *****************************************
>
>    

Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

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From dimitark at bii.a-star.edu.sg  Tue Nov 30 01:50:42 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 09:50:42 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
Message-ID: <4CF45872.1060405@bii.a-star.edu.sg>

On 11/29/2010 10:39 PM, Chris Fields wrote:
> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>
>    
>> Hi again,
>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>
>> Its frustrating :)
>>
>> Any ideas where to look for solution
>> Cheers
>> Dimitar
>>      
> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>
> my $stream = $dbh->get_Stream_by_query($query);
> while( my $seq = $stream->next_seq ) {
> 	$out->write_seq($seq);
> }
>
> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>
> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>
> chris
>    
Hi,
thank you for the info.
I already have inserted a progress bar(Term::ProgressBar) in the last 
four lines. The problem is that i see the progress at the end. I see 
directly 100%done. See the attached script.
What i was reading in the modules underlying the script the way the 
stream is constructed it should be able to be read from while is being 
downloaded. But when i get fasta seqs with NCBI rettype=fasta it is not 
possible.

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

-------------- next part --------------
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From cjfields at illinois.edu  Tue Nov 30 03:42:14 2010
From: cjfields at illinois.edu (Chris Fields)
Date: Mon, 29 Nov 2010 21:42:14 -0600
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4677A.5010604@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
Message-ID: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>

On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:

> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>> Dimitar -
>> 
>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>> 
>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>> As in: http://gist.github.com/721012
>> 
>> But maybe you already figured it out?
>> 
>> -jason
>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>> 
>>>> Hi again,
>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>> 
>>>> Its frustrating :)
>>>> 
>>>> Any ideas where to look for solution
>>>> Cheers
>>>> Dimitar
>>> 
>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>> 
>>> my $stream = $dbh->get_Stream_by_query($query);
>>> while( my $seq = $stream->next_seq ) {
>>>    $out->write_seq($seq);
>>> }
>>> 
>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>> 
>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>> 
>>> chris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> Thank you Jason,
> i figured that out yes :)
> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
> -------------
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>                                       -query=>$query_str);
> 
> my $count=$query->count;
> my @ids=$query->ids; <------- error msg here
> ------------
> but i get an error msg:
> 
> MSG: Id list has been truncated even after maxids requested.
> 
> How can i get the ID/ACC? Any idea?
> 
> Thank you
> Dimitar

Dimitar, 

You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:

----------------------------------------------
use Bio::DB::Query::GenBank;

my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
my $query=Bio::DB::Query::GenBank->new(-maxids => 40000,
                                       -db=>'protein',
                                      -query=>$query_str);

my $count=$query->count;
say "Count: $count";

my @ids=$query->ids;
say scalar(@ids); # equal to $count
----------------------------------------------

Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.

chris






From dimitark at bii.a-star.edu.sg  Tue Nov 30 09:04:30 2010
From: dimitark at bii.a-star.edu.sg (Dimitar Kenanov)
Date: Tue, 30 Nov 2010 17:04:30 +0800
Subject: [Bioperl-l] genbank
In-Reply-To: <696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
Message-ID: <4CF4BE1E.6090100@bii.a-star.edu.sg>

On 11/30/2010 11:42 AM, Chris Fields wrote:
> On Nov 29, 2010, at 8:54 PM, Dimitar Kenanov wrote:
>
>    
>> On 11/30/2010 10:19 AM, Jason Stajich wrote:
>>      
>>> Dimitar -
>>>
>>> In terms of your question - a GenBank db query previously (ie 4-5 years ago when this was written) WOULD NOT return a sequence if a GenPept ID was specified so we had to have a separate module for GenBank and GenPept db querying since there was a different set of parameters - I think that changed so that most of the queries can run through GenBank
>>>
>>> I see that must have been improved at NCBI.  For the record if you want the full GenPept record with features and annotations you just request a different db, in this case 'gb' for genbank instead of the fasta source
>>> As in: http://gist.github.com/721012
>>>
>>> But maybe you already figured it out?
>>>
>>> -jason
>>> Chris Fields wrote, On 11/29/10 6:39 AM:
>>>        
>>>> On Nov 29, 2010, at 3:35 AM, Dimitar Kenanov wrote:
>>>>
>>>>          
>>>>> Hi again,
>>>>> it seems that when i download (with 'download_query_genbank.pl') the whole proteome from NCBI in fasta format it is first being downloaded and from it is being created some kind of SeqFastaSpeedFactory and after that from it is being copied to the output file. But i want to download and write to output file one by one so i can see the download progress(which is working for genbank data).
>>>>>
>>>>> Its frustrating :)
>>>>>
>>>>> Any ideas where to look for solution
>>>>> Cheers
>>>>> Dimitar
>>>>>            
>>>> You can't do this with the default script, but you can use a modified version and, where you are retrieving a sequence stream, in the last four lines:
>>>>
>>>> my $stream = $dbh->get_Stream_by_query($query);
>>>> while( my $seq = $stream->next_seq ) {
>>>>     $out->write_seq($seq);
>>>> }
>>>>
>>>> insert an iterator in the loop that indicates progress.  Realize the sequence data is processed through Bio::SeqIO, so it won't be exactly the same as what is retrieved from GenBank, but it should be very close.
>>>>
>>>> If you want raw sequence, you can use Bio::DB::EUtilities, but it's a bit more complicated.
>>>>
>>>> chris
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>          
>>>        
>> Thank you Jason,
>> i figured that out yes :)
>> I know am wandering how to get the GI list so i can download by ID or ACC and not by query when i download fasta. I have the simple code:
>> -------------
>> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
>> my $query=Bio::DB::Query::GenBank->new(-db=>'protein',
>>                                        -query=>$query_str);
>>
>> my $count=$query->count;
>> my @ids=$query->ids;<------- error msg here
>> ------------
>> but i get an error msg:
>>
>> MSG: Id list has been truncated even after maxids requested.
>>
>> How can i get the ID/ACC? Any idea?
>>
>> Thank you
>> Dimitar
>>      
> Dimitar,
>
> You are retrieving a huge number of IDs; if you print out $count above, the total is 23906.  Set -maxids to raise the returned default maximum number of IDs higher:
>
> ----------------------------------------------
> use Bio::DB::Query::GenBank;
>
> my $query_str='Caenorhabditis elegans[organism] AND refseq[filter]';
> my $query=Bio::DB::Query::GenBank->new(-maxids =>  40000,
>                                         -db=>'protein',
>                                        -query=>$query_str);
>
> my $count=$query->count;
> say "Count: $count";
>
> my @ids=$query->ids;
> say scalar(@ids); # equal to $count
> ----------------------------------------------
>
> Realize, though, you must submit these in batches of ~300 if retrieving sequences (IIRC, Bio::DB::GenBank only uses GET instead of POST, so there is a URL length limit).  Bio::DB::EUtilities can retrieve more, about ~3000 or so in a batch, when using POST.
>
> chris
>
>
>
>    
Hi again,
i managed to solve my problem. It may be dirty but it works the way i 
want :)
I reworked the 'download_query_genbank.pl' (attached). Now i can get the 
seqs in full fasta for proteomes and genomes and the genpept report 
files for the proteomes.
For DB handle i only use GenPept now cos it gives me stream which i can 
track with term::progressbar.

For the output i use 2 cases:
-----------------
while( my $seq = $stream->next_seq ) {
     #DIMITAR
     my($gi,$locus,$refnum,$desc,$seqstr);
     if($retformat eq 'fasta'){ <-------------------------| for the 
fasta as i want it
         check_progress($prgs,$seqnum,$count);
         $locus=$seq->display_id;
         $refnum=$seq->accession_number;
         $gi=$seq->primary_id;
         $desc=$seq->desc;
         $desc=~s/\.$//;
         $seqstr=$seq->seq;
         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
     }else{
         check_progress($prgs,$seqnum,$count);
         $out->write_seq($seq); <--------------------------| for the 
genbank reports
     }
     $seqnum++;
     #DIMITAR

#    $out->write_seq($seq);#original

}
------------------

Thank you for your help and time.

Cheers
Dimitar

-- 
Dimitar Kenanov
Post doctoral fellow
Bioinformatics Institute
A*STAR Singapore
tel: +65 6478 8514
email: dimitark at bii.a-star.edu.sg

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From jason at bioperl.org  Tue Nov 30 17:06:08 2010
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Nov 2010 09:06:08 -0800
Subject: [Bioperl-l] genbank
In-Reply-To: <4CF4BE1E.6090100@bii.a-star.edu.sg>
References: <4CF373DE.4070902@bii.a-star.edu.sg>
	<F3C80557-52DE-4D60-9E72-0660031D8F46@illinois.edu>
	<4CF45F4C.7050102@bioperl.org> <4CF4677A.5010604@bii.a-star.edu.sg>
	<696A04DF-8735-4630-B233-E0189B252CF9@illinois.edu>
	<4CF4BE1E.6090100@bii.a-star.edu.sg>
Message-ID: <4CF52F00.5000803@bioperl.org>

great - the whole point of the scripts are as examples really, not that 
you need to send patches back to show everything that you modified, but 
that you modify to use modules and code to do whatever special thing you 
want. The hope is that the modules are flexible enough that you can 
write the script to accomplish your goal.

BTW - the one thing you can't recover from the GBK version of the file 
is the source of the accession number -- you have hardcoded in 'ref' but 
it can be 'gb', 'emb', 'sp' etc this field isn't part of the genbank 
record unfortunately -- one can come up with a pattern based on 
knowledge of accession number formats but I don't know that anyone has 
really been that worried about that sort of thing to try and write 
something for it.

>>
> Hi again,
> i managed to solve my problem. It may be dirty but it works the way i 
> want :)
> I reworked the 'download_query_genbank.pl' (attached). Now i can get 
> the seqs in full fasta for proteomes and genomes and the genpept 
> report files for the proteomes.
> For DB handle i only use GenPept now cos it gives me stream which i 
> can track with term::progressbar.
>
> For the output i use 2 cases:
> -----------------
> while( my $seq = $stream->next_seq ) {
>     #DIMITAR
>     my($gi,$locus,$refnum,$desc,$seqstr);
>     if($retformat eq 'fasta'){ <-------------------------| for the 
> fasta as i want it
>         check_progress($prgs,$seqnum,$count);
>         $locus=$seq->display_id;
>         $refnum=$seq->accession_number;
>         $gi=$seq->primary_id;
>         $desc=$seq->desc;
>         $desc=~s/\.$//;
>         $seqstr=$seq->seq;
>         print $fhout ">gi\|$gi\|ref\|$refnum\|$locus $desc\n$seqstr\n";
>     }else{
>         check_progress($prgs,$seqnum,$count);
>         $out->write_seq($seq); <--------------------------| for the 
> genbank reports
>     }
>     $seqnum++;
>     #DIMITAR
>
> #    $out->write_seq($seq);#original
>
> }
> ------------------
>
> Thank you for your help and time.
>
> Cheers
> Dimitar
>

-- 
Jason Stajich
jason at bioperl.org