PSIBlasttrainer.pl

#! /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;