[Bioperl-l] more problems with blast

Dimitar Kenanov dimitark at bii.a-star.edu.sg
Mon Jun 7 23:22:04 EDT 2010

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 
STACK: Bio::SearchIO::blast::next_result 

so there are couple of places where the alignments look like the 
following (i put here only the problem part):
Query       ------------------------------------------------------------

Sbjct  288  

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);

Thats not nice :) But how can i go around that stuff so i can get the 
file parsed?


Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
tel: +65 6478 8514

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