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Id: 53705
Status: new
Priority: 0/
Queue: Bio-SamTools

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Owner: Nobody in particular
Requestors: dan.kortschak [...] adelaide.edu.au
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Subject: $index undefined prior to coverage call
Date: Fri, 15 Jan 2010 09:01:53 +1030
To: bug-Bio-SamTools [...] rt.cpan.org
From: Dan Kortschak <dan.kortschak [...] adelaide.edu.au>
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Hi Lincoln, Preamble: I'm writing a bioperl wrapper for bowtie that makes use of the Bio::DB::Sam module to parse the bowtie output (via Bio::Assembly::IO::sam). There is a weird dependency issue that I don't understand between the bioperl WrapperBase/CommandExts module the bowtie module uses that has cause B:DB:Sam to fail (error below) - this was not the case in my first version that did not use CommandExts nor in a kludge version that modifies the inheritance of CommandExts to be a derived class from WrapperBase rather than MAJ's designed case where it is an extension to WrapperBase. Details: $ uname -a # debian lenny Linux spawn 2.6.26-2-amd64 #1 SMP Wed Aug 19 22:33:18 UTC 2009 x86_64 GNU/Linux $ perl -v This is perl, v5.10.0 built for x86_64-linux-gnu-thread-multi Details for 'Bio::DB::Sam' Author Lincoln D. Stein (lincoln.stein@gmail.com) Description None given Development Stage Unknown Installed File /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm Interface Style Unknown Language Used Unknown Package Bio-SamTools-1.09.tar.gz Public License Unknown Support Level Unknown Version Installed 1.09 Version on CPAN 1.09 Non-working bioperl version: r16693 (bioperl-run) and r16692 (bioperl-live) Working bioperl version: r16689 (bioperl-run) and r16690 (bioperl-live) Test script - requires bowtie to be install. All necessary data files are in the bioperl-run t/ filesystem or the bowtie src package: #!/usr/bin/perl use strict; use warnings; use Bio::Tools::Run::Bowtie; # these will depend on your src location for bioperl-live and bioperl-run my $rdq = '/usr/local/src/bioperl-run/t/data/bowtie/reads/e_coli_1000.fq'; my $refseq = '/usr/local/src/bioperl-run/t/data/bowtie/indexes/e_coli'; my $buildfac = Bio::Tools::Run::Bowtie->new( -command => 'build' ); # located in bowtie src directory my $index = $buildfac->run('/usr/local/src/bowtie-0.11.3/genomes/NC_008253.fna','e_coli'); my $bowtiefac = Bio::Tools::Run::Bowtie->new( -command => 'single', -max_seed_mismatches => 2, -seed_length => 28, -max_qual_mismatch => 70, -sam_format => 0 ); my $align = $bowtiefac->run($rdq,$index); print "$align\n"; open (IN,$align); my $lines =(my @lines)= <IN>; print @lines; print "\n\n$lines\n"; close IN; $bowtiefac = Bio::Tools::Run::Bowtie->new( -command => 'single', -max_seed_mismatches => 2, -seed_length => 28, -max_qual_mismatch => 70 ); $align = $bowtiefac->run($rdq,$index); print $align,"\n"; print "Contigs: ", $align->get_nof_contigs, "\tSinglets: ", $align->get_nof_singlets, "\n"; print "In index: $index\n"; print "Contigs:\n"; for ($align->all_contigs) { print $_->get_consensus_sequence->seq,"\n"; } Returned error: [fai_load] build FASTA index. [bam_index_build] creating index for /tmp/zJZ0YTTQ0F/JcG1TNxxJI.srt.bam [bam_index_load] fail to load BAM index. Can't call method "coverage" on an undefined value at /usr/local/lib/perl/5.10.0/Bio/DB/Sam.pm line 1778. I have looked into offending code and the seems to be the result of $index not be returned with a defined value at 1777 in `Bio::DB::Sam.pm'. I'm afraid even after an hour of following it with the debugger I have no idea why or why it depends on the inheritance of an indirectly calling object. Sorry. It may be an issue with bioperl itself (the Bio::Assembly::IO module most likely, though the files appear to be present after B:A:IO has passed control to B:DB:Sam, so I'm unclear on this). thanks for your time Dan Kortchak
Subject: Re: [rt.cpan.org #53705] AutoReply: $index undefined prior to coverage call
Date: Sat, 16 Jan 2010 11:23:13 +1030
To: bug-Bio-SamTools [...] rt.cpan.org
From: Dan Kortschak <dan.kortschak [...] adelaide.edu.au>
Resolved. Results from tempfile cleaning zealousness in bioperl.


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