Difference between revisions of "PSIBlasttrainer.pl"
From Bioinformatikpedia
(Created page with " #! /usr/bin/perl use strict; use Getopt::Long; my $input; my $output; my $database; my $maxIt; my $before; my $after; my $result = GetOptions ("i=s" => \$input,"o=s…") |
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} |
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+ | print TIME ">\n" |
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+ | for(my $i=1;$i<$maxIt;$i++){ |
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+ | my $eval = 1/(10**$i); |
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+ | print "iteration: $i\n"; |
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+ | $before = time(); |
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+ | system("time blastpgp -j 1 -d $database -i $input -o $output" . "_integr_" . "$eval -h $eval"); |
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+ | $after = time(); |
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+ | print TIME ($after-$before)."\n"; |
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+ | close STATUS; |
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+ | } |
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+ | |||
close TIME; |
close TIME; |
Latest revision as of 19:48, 6 May 2012
#! /usr/bin/perl use strict; use Getopt::Long; my $input; my $output; my $database; my $maxIt; my $before; my $after; my $result = GetOptions ("i=s" => \$input,"o=s" => \$output,"d=s" => \$database,"j=i" => \$maxIt); open(TIME ,">","time.txt"); print TIME "\# time used for psiblast\n"; #run psiblast each time and save the time; for(my $i =1;$i<=$maxIt;$i++){ print "iteration: $i\n"; $before = time(); open STATUS, "-|","time blastpgp -j $i -d $database -i $input -o $output"."_".$i."_it" or die "can't fork: $!"; while(<STATUS>){ print TIME $_; } $after = time(); print TIME ($after-$before)."\n"; close STATUS; } print TIME ">"; for(my $i=1;$i<$maxIt;$i++){ my $eval = 1/(10**$i); print "iteration: $i\n"; $before = time(); system("time blastpgp -j 1 -d $database -i $input -o $output" . "_eVal_" . "$eval -e $eval"); $after = time(); print TIME ($after-$before)."\n"; close STATUS; } print TIME ">\n" for(my $i=1;$i<$maxIt;$i++){ my $eval = 1/(10**$i); print "iteration: $i\n"; $before = time(); system("time blastpgp -j 1 -d $database -i $input -o $output" . "_integr_" . "$eval -h $eval"); $after = time(); print TIME ($after-$before)."\n"; close STATUS; } close TIME;