[Bioperl-l] issue with closing tempfile and bl2seq

[BHurwitz at twt.com]

Hi,

I am having some trouble using bl2seq within Bioperl.  I have a fairly
large file of sequences that need to be pairwise compared (40K).
Everything runs fine for the first ~500 sequences, but then my program
errors out with the following message:

------------- EXCEPTION  -------------
MSG: Could not open tempfile /tmp/bhurwitz.16882.3051: Too many open files

STACK Bio::Root::IO::tempfile
/usr/lib/perl5/site_perl/5.6.0/Bio/Root/IO.pm:500
STACK Bio::Tools::Run::StandAloneBlast::new
/usr/lib/perl5/site_perl/5.6.0/Bio/Tools/Run/StandAloneBlast.pm:352
STACK main::pairwise ./footprint_checker.pl:117
STACK toplevel ./footprint_checker.pl:82

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

I haven't had a chance to update this machine yet to Bioperl 1.2 yet ( it
is still using Bioperl 1.0 ) so maybe this is why?  Has anyone ever seen
this error?  Is there a way for me to push all of my sequences through and
close these tmp files as I go?  I have tried to pass the sequences into my
subroutine as both a file of 40K and as files of only 1 sequence, but it
seems to error out either way.  I am sure there must be an easy fix??

Thanks,
Bonnie


Here is my subroutine that calls bl2seq

sub pairwise {
   my $infile1 = shift @_;
   my $infile2 = shift @_;
   my $set = shift @_;
   my $query1_in  = Bio::SeqIO->new ( -file   => $infile1,
                                    -format => 'fasta' );
   while (my $q1 = $query1_in->next_seq() ) {
      push(@query1_seqs, $q1);
   }

   my $query2_in  = Bio::SeqIO->new ( -file   => $infile2,
                                    -format => 'fasta' );
   while (my $q2 = $query2_in->next_seq() ) {
      push(@query2_seqs, $q2);
   }

   my $seq_count = @query1_seqs;
   print "seqcount: $seq_count\n";

   my $i;
   for ($i = 0 ; $i < $seq_count; $i++) {
      my $query1 = shift @query1_seqs;
      my $query2 = shift @query2_seqs;
      my $factory = Bio::Tools::Run::StandAloneBlast->new( );
      $factory->e($expectvalue);
      $factory->W($wordsize);
      $factory->F($repeat_mask);
      $factory->r($match_reward);
      $factory->q($mismatch_penalty);
      $factory->p($blprogram);
      $factory->g($gapped);
      my $report = $factory->bl2seq($query1, $query2);
      my $sbjct_name = $report->sbjctName;
      $sbjct_name =~ s/>\s*//;
      while(my $hsp = $report->next_feature) {
         my $pvalue = $hsp->P;
         my $match = $hsp->match;
         my $length = $hsp->length;
         my $q_len;
         if ($set =~ /syn1/) {
            $q_len = $syn1_len{$sbjct_name};
         }
         else {
            $q_len = $syn2_len{$sbjct_name};
         }
         my $frac_iden = $match / $q_len;
         my $s_start = $hsp->hit->start( ); # hit start
         my $s_end = $hsp->hit->end( ); # hit end

         print OUT "$sbjct_name\t$pvalue\t$s_start\t$s_end\t$frac_iden\n";
      }
   }
} #end of sub pairwise