Difference between revisions of "PSIBlasttrainer.pl"
From Bioinformatikpedia
Line 38: | Line 38: | ||
close STATUS; |
close STATUS; |
||
} |
} |
||
+ | |||
− | |||
print TIME ">\n" |
print TIME ">\n" |
||
for(my $i=1;$i<$maxIt;$i++){ |
for(my $i=1;$i<$maxIt;$i++){ |
Latest revision as of 20:48, 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;