Dear list:
I wrote a script that takes a list of ids from an input file and store these
in an array in a pairwise-like manner (if total list is n then the array is
(2 ^n)-n). I need to extract for each pair of ids a certain value from a
huge file that contains the pair of ids and the value (format of the
file: col1 col2 id1 id2 value).
The script works but it is takes too long, specially because the second file
is too big (more than 600 MB).
I would like to increase the speed of the script, but I haven't quite worked
what is the best way to do it.
Any tip?
Thanks in advance,
L. Pardo
ps, I am attaching the script
#!/usr/local/bin/perl
use strict;
use warnings;
my %nuc=();
my @arr=();
open(SN,"file_22.txt") || die "cannot open file: $!\n";
my @a2=(<SN>);
close SN;
chomp(@a2);
for (my $m=0; $m<=$#a2; $m++) {
my @temp0 = split/\s+/,$a2[$m];
$nuc{$temp0[3]} = $temp0[1];
push(@arr,$temp0[3]);
}
print "$#arr\n";
my @couple= ();
open(OUT,">>couple.txt") || die "can not write on it: $!\n";
for (my $i=0; $i<=50; $i++) {
for (my $n=$i; $n<=50; $n++) {
if($nuc{$arr[$i]}>= $nuc{$arr[$n]}- 200000) {
push(@couple,$arr[$i],$arr[$n]);
print OUT"@couple\n";
}
@couple =();
}
}
######SECOND_PART#############
open(LL,"top_22.txt") or die "cannot do it : $!\n";
print `date`;
my @a3 = (<LL>);
print `date`;
open(COUPLE,"couple.txt") or die " can not open file :$!\n";
my @a4 = (<COUPLE>);
open(OUT1,">Not_found.txt");
open(OUT2,">Pairwise.txt");
for (my $y =0; $y <=$#a4; $y= $y+1) {
my @temp1= split/\s+/,$a4[$y];
print "OK $temp1[0],$temp1[1]\n";
for (my $x=0; $x<=$#a3; $x++) {
my @temp2 = split/\s+/,$a3[$x];
if($temp1[0] eq $temp2[3] & $temp1[1] eq $temp2[4] || $temp1[0]
eq $temp2[4] & $temp1[1] eq $temp2[3]) {
print "$temp2[3], $temp2[4],$temp2[5],$temp2[6]\n";
} elsif($x == $#a3) {
print OUT1 "$temp1[0], $temp1[1]\n;"
}
}
}
#system("gzip Not_found.txt");
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