[Bioperl-l] bl2seq and disappearing variables

[James Wasmuth]

Hi all,

I've  started to use bl2seq and am having a perplexing problem.  I 
couldn't find this being asked previously so guess it may be a mistake 
in my Perl code, but if any one can see it then I'd be grateful.

This is part of a script where two files are fetched and input into 
bl2seq...

for my $cluster_id (keys %list) {
    print ": $cluster_id : $list{$cluster_id}[0]\n";
    my $file1=$list{$cluster_id}[0];
    my $file2=$list{$cluster_id}[1];
    print "$file1:$file2\n";
    my $input1="$path2files/$file1.pep";
    my $input2="$path2files/$file2.pep";
    print "$input1:$input2\n";
   
    my $factory = Bio::Tools::Run::StandAloneBlast->new('outfile' => 
"$outdir/$cluster_id.out",'program'=>'blastp');
    my $bl2seq_report = $factory->bl2seq($input1, $input2);
}


I get the following error:

------------- EXCEPTION  -------------
MSG:  indiv_seq/Peptide/.pep  not Seq Object or file name!
STACK Bio::Tools::Run::StandAloneBlast::bl2seq 
/usr/local/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/StandAloneBlast.pm:539
STACK toplevel /necator/jamesw/bin/bl2seq_nb.pl:36

--------------------------------------


When I ask to print out $cluster_id nothing is printed.  However if I 
comment out my $bl2seq_report = $factory->bl2seq($input1, $input2); 
 then $cluster_id is found!  I am also able to run bl2seq as a system 
call in the program with the desired results.

I tried reading the files in as seq objects through SeqIO, but again I 
can the error caused through the disappearence of $cluster_id!

Anyone any ideas?

J

 

-- 

Nematode Bioinformatics
Blaxter Nematode Genomics Group
Institute of Cell, Animal and Population Biology
Ashworth Labs
University of Edinburgh
King's Buildings
Edinburgh
EH9 3JT
UK

0131 650 7403

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