[Bioperl-l] problem parsing FASTA output - bug or my fault?

[Jason Stajich]

Unfortunately there are some changes in the FASTA output in that  
version. The latest version of Bioperl 1.52 can handle it though so  
you'll need to upgrade Bioperl.

-jason
On Apr 26, 2007, at 3:18 AM, Aidan Budd wrote:

> Hi Bioperlers,
>
> I'm trying to parse a FASTA search output file (see attached .out  
> file)
> using Bioperl 1.4. My Bioperl installation has otherwise been working
> fine, however I currently get the following error when running a  
> simple
> script that attempts to access result from this outfile via bioperl.
>
> Is this a problem with the parser?
> Or have I executed FASTA wrongly creating output that isn't covered  
> by the
> parser?
>
> Any suggestions on how to deal with this much appreciated.
>
> Best wishes,
>
> Aidan
>
> Script:
>
> #!/usr/bin/perl -w
> $^W=1;
> use strict;
> use Bio::SearchIO;
>
> my $fasta_report = new Bio::SearchIO ('-format' => 'fasta',
>                                       '-file'   => $ARGV[0]);
>
> my $result = $fasta_report->next_result();
>
> Errors:
>
> Use of uninitialized value in concatenation (.) or string at
> /Users/budd/perl_modules/bioperl_1_4/bioperl-1.4/Bio/Search/HSP/ 
> GenericHSP.pm
> line 231, <GEN3> line 47.
>
> ------------- EXCEPTION  -------------
> MSG: Did not specify a Query End or Query Begin -verbose 0 -algorithm
> FASTP -score 62.4 -hit_frame 0 -hsp_length 180 -hit_seq  -hit_length 0
> -query_length 128 -query_frame 0 -swscore 122 -rank 1 -query_seq
> GTTILQYAQTTDGQQILVPSNQVVVQAASGDVQTYQIRTAPTSTIAPGVVMASS-- 
> PALPTQPAEEAARKREVRLMKNREAARECRRKKKEYVKCLENRVAVLENQ-NKTLIEELKALKD- 
> LYCHKSD
> -homology_seq
> MEMTDFELTSNSQ.NL.IPTNFK.TLP.RKRAKTK..KEQR.IE.ILR..R..HQS.E..RLHLQY..RK 
> CSL...LL.SVNL.K.ADHE.A.T.SHDAFVASLDEYRDFQSTRGASLDTRASSHSSSDTFTPSPLNCTM 
> EPATLSPKSMR
> -hit_name YFL031W -bits 19.4 -query_name CREB1_MONKEY -evalue 1.1  
> (qs='
> STACK Bio::Search::HSP::GenericHSP::new
> /Users/budd/perl_modules/bioperl_1_4/bioperl-1.4/Bio/Search/HSP/ 
> GenericHSP.pm:231
> STACK Bio::Search::HSP::FastaHSP::new
> /Users/budd/perl_modules/bioperl_1_4/bioperl-1.4/Bio/Search/HSP/ 
> FastaHSP.pm:97
> STACK Bio::Factory::ObjectFactory::create_object
> /Users/budd/perl_modules/bioperl_1_4/bioperl-1.4/Bio/Factory/ 
> ObjectFactory.pm:150
> STACK Bio::SearchIO::SearchResultEventBuilder::end_hsp
> /Users/budd/perl_modules/bioperl_1_4/bioperl-1.4/Bio/SearchIO/ 
> SearchResultEventBuilder.pm:275
> STACK Bio::SearchIO::fasta::end_element
> /Users/budd/perl_modules/bioperl_1_4/bioperl-1.4/Bio/SearchIO/ 
> fasta.pm:872
> STACK Bio::SearchIO::fasta::next_result
> /Users/budd/perl_modules/bioperl_1_4/bioperl-1.4/Bio/SearchIO/ 
> fasta.pm:403
> STACK toplevel
> /Users/budd/scripts/test_scripts/test_parsing_fasta_output.pl:22
>
> --------------------------------------
>
> -- 
> ----------------------------------------------------------------------
> Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
> EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
> Meyerhofstr. 1, 69117 Heidelberg, Germany
>
> URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
> <creb_vs_yeast_manual_fasta_changed_infile_formats.out>
> <creb1_human.fasta>
> <yeast_bzips_from_ensembl.fasta>
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--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/