[Bioperl-l] more problems with blast

[Chris Fields]

This parsing issue is due to changes in BLAST+, but should be fixed in the latest github code.  Can you run a clean checkout and test this?

chris

On Jun 7, 2010, at 10:22 PM, Dimitar Kenanov wrote:

> hi guys,
> im sorry but i got another problem.
> So in previous email i wrote about psiblast with '-in_pssm' problem, so i just ran psiblast myself with system and all the parameters needed. I got my output file which i gave to SearchIO and hoped i got around the problem but no :) The moment i used 'next_result' i get error:
> ----
> MSG: no data for midline Query       ------------------------------------------------------------
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib64/perl5/site_perl/5.10.0/Bio/Root/Root.pm:368
> STACK: Bio::SearchIO::blast::next_result /usr/lib64/perl5/site_perl/5.10.0/Bio/SearchIO/blast.pm:1829
> ----
> 
> so there are couple of places where the alignments look like the following (i put here only the problem part):
> ---
> Query       ------------------------------------------------------------
> 
> Sbjct  288  HWVNTMALSTDYALRTGAFEPAEASVNPQDLQGSLQELKERALSRYNLVRGQGPERLVSG  347
> ---
> 
> My code for running psiblast:
> ----
> my @args=("$$bl_alg -db $protdb -out $tmpout -num_threads 2 -seg yes -soft_masking TRUE -lcase_masking -num_iterations $$cycles -in_pssm $pssmtmp -out_pssm $pssmtmp -use_sw_tback -word_size 3 -gapopen 11 -gapextend 1 -window_size 40 -threshold 11 -evalue $$eval");
>   system(@args) == 0 or die "system @args failed: $!";
>   my $report=Bio::SearchIO->new(-format => 'blast', -file => $tmpout);
> $blastreport=$report->next_result;
> ----
> 
> Thats not nice :) But how can i go around that stuff so i can get the file parsed?
> 
> Greetings
> Dimitar
> 
> -- 
> Dimitar Kenanov
> Postdoctoral research fellow
> Protein Sequence Analysis Group
> Bioinformatics Institute
> A*STAR, Singapore
> tel: +65 6478 8514
> 
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