[Bioperl-l] New to BioPerl - A little presentation... and a question about GenBank and Bioperl

[Smithies, Russell]

BioPerl-1.6.923.tar.gz installed OK for me and I can run your script on that gbk file from Windows with ActivePerl 5.16.1 and I get no warnings at all.

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Smithies, Russell
Sent: Friday, 7 March 2014 8:03 a.m.
To: Olivier BUHARD; bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] New to BioPerl - A little presentation... and a question about GenBank and Bioperl

Hi,
-w on the shebang line is for displaying warnings, so naturally if you leave it off you won't get warnings.
A slightly better method is to 'use warnings' instead - but be aware it gives you slightly different results Eg.

#!perl 

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

And on Windows systems you can shorten the shebang line to #!perl   as obviously the usual path of #!/usr/bin/perl isn't relevant.

When I run your code on the exact same file I get the required output and no warnings - though admittedly that's on a Linux system.
Is it possible you're running an older version of BioPerl?
I'll update my Windows BioPerl (to CJFIELDS/BioPerl-1.6.923.tar.gz)  install and give it a go.

--Russell



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Olivier BUHARD
Sent: Friday, 7 March 2014 12:06 a.m.
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] New to BioPerl - A little presentation... and a question about GenBank and Bioperl

Hello,


I'm new to BioPerl and would like to ask you for a few advice about the use of Bioperl.

I am a molecular biologist and I frequently use Perl to write scripts to prepare or analyse files I get from various databases, so I'm familiar enough with Perl.
We work in my lab on a particular type of tumorigenic process called MSI, for MicroSatellite Instability. I'll not go through all the story but a hallmark of the associated cancers is that the size of their genomic repeated DNA sequences spread throughout the genome, is altered.
Up to now, we got a list of those sequences from a collaboration who could make that for us. But now the list we have is old and we have to get this information by our own means and naturally I started looking at Bioperl.
And before I go through learning all I need (which I guess, will take some time), I will really appreciate if someone could tell me if I Bioperl can help from start to end.

In summary, I plan to search all the short repetitive sequences (I'm just interested in human genome at the moment) I can find in the Genbank flat file provided by the NCBI FTP site. The idea is to create a BioSQL database (I already installed using a schema for mySQL) that I could query using an appropriate algorithm.
I saw Bioperl is made to read those files with multiple entries. So building the BioSQL database would not be a problem. My first question is about how I will crawl through the genomic sequences to detect short repeat tandem sequences of defined size and patterns (some are mononucleotides repeats, like (A)27, other could be dinucleotides redpeats like (CA)12, etc.). BLAST is not design for such a job... Are there some tools already available in Bioperl to deal with low complexity DNA in general and short tandem repeats in particular, something like repeatmasker or windowmasker but with a different kind of output? I'm interested in retrieving some of the features provided with the genbank format (find repeats in coding or non-coding regions, get their position in the genes or the transcripts with respect to exon position, intron-exon proximity...).

I also have a more direct and "practical" question. I just tried a few sample codes provided in the beginners' toturials on the Bioperl site. I just ran the following on the gbpri1.seq provided on the NCBI FTP but I got some errors and warnings for many (but not all) sequences.

#!/usr/bin/perl -w

use strict;
use Bio::SeqIO;

my $seqio_obj = Bio::SeqIO->new(-file => "<$seq_file", -format => 'genbank' ); while (my $seq_obj = $seqio_obj->next_seq()){
     print $seq_obj->display_id,"\n";
}

This is what I get for AB000095 locus:

Replacement list is longer than search list at C:/Perl/site/lib/Bio/Range.pm lin e 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at
C:/Perl/
site/lib/Bio/Tree/TreeFunctionsI.pm line 94 Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 93, <GE
N0> line 41.
Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Simple.pm
line 115,
<GEN0> line 41.
Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 144, <G
EN0> line 41.
Subroutine length redefined at C:/Perl/site/lib/Bio\Location\Simple.pm
line 190,
  <GEN0> line 41.
Subroutine location_type redefined at
C:/Perl/site/lib/Bio\Location\Simple.pm li ne 281, <GEN0> line 41.
Subroutine to_FTstring redefined at
C:/Perl/site/lib/Bio\Location\Simple.pm line
  328, <GEN0> line 41.
Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location\Simple.pm
line 370,
<GEN0> line 41.
AB000095

But when I remove the shebang option -w... the warnings disappear.
(I use ActivePerl 5.14.2 on a Windows XP computer. I had the idea that shebang was not used under Windows, but it seems tat's wrong here...
Is that due to some problem about my Perl installation, or is it Bio::SeqIO code related?

Thank in advance for any answer.

Kind regards

-- 

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

BUHARD Olivier

"Instabilité de microsatellites et cancer"
Centre de Recherche Saint Antoine
équipe 11/INSERM UMRS 938
Bâtiment Kourilsky,
Hôpital Saint Antoine
34 rue Crozatier
75012 PARIS


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