[Bioperl-l] reducing time

KHOUEIRY pierre khoueiry at ibsm.cnrs-mrs.fr
Tue Jan 27 08:12:37 EST 2004

Hi all,
In my script, I make a treatment on a big number of fasta files *(same 
size)*. The problem is (with my exstimations) the total time will be at 
about 26 hours . In fact it tooks 951 seconds for 10 files.
Is there any way to reduce time waist... Or is there a probleme in my 
code. I add that the script goes faster for the first 20 or 30 files 
then it slow down but still fix (tested on a big number of files without 
samll loop on sequences). The output file still empty at the begining 
till a number of files is being studied and then it stills like that 
until another series of files is treated. I think it's a buffer problem...!

_Her's a bit of the code i use:_

while(my $file = readdir DH)
   next if ($file =~ /^\./);
   my $stream = Bio::SeqIO->new(-file => 
"</home/Perl/proteome/Output/$file", -format => 'fasta');

   while(my $one_seq = $stream->next_seq())
     $heatcount = 0;
     $nbhotspot = 0;
     $aacount = 0;
     $maxaacount = 0;
     $nbaamotif = 0;
     $aanb= 0;
     my $seq = $one_seq->seq();
              /a for loop over each sequence goes here (a heavy one)/
    $HSPercernt = $nbhotprot/$nbprot;
   print "$file\t\t\t"."$nbhotprot\t".substr(($HSPercernt*100),0,4)."\n";
   print OUT 
   $nbprotanalysed ++;
   $HSPercernt = 0;
   $nbhotprot = 0;
   my $endtime = time();
   my $totaltime = $endtime-$inittime;
   print "the procedure took ---->", $totaltime,"seconds\n";
  }#End of reading directory while loop

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