[Bioperl-l] more problems with blast

[Dimitar Kenanov]

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