Hello, I need help speeding up my perl code and was hoping that someone could give me a few pointers.

My goal of this code is to print out lines from chr1.txt (see below) only when the ID (first column) is shared by chr1.coverage.txt as well.

Hence, I decided to save each unique ID from the "coverage" file as a hash key so that I could then sort through them and print out the corresponding lines from chr1.txt

The problem with this method I currently use is the speed of the program. I am using a nested foreach loop within a while loop, and when there are thousands of unique keys for the "coverage" file the process can take a long time.

Given that my data is well-sorted (there is only 1 chr for each file, in this case chr1, and the numbers are numerically sorted) I know that there should be a faster way to achieve the same results, but I have been struggling to find a working solution. Any help you can provide would be greatly appreciated.

Below is my current perl code

#!/usr/bin/perl -w
# perl.ID.match.pl
use strict; use warnings;

open(KEY, "<chr1.coverage.txt") or die "error reading file";
my %Chr;
my (@Key,@line);
while (my $key = <KEY>) {
    chomp $key;
    @Key=split("\t",$key);
    $Chr{$Key[0]} = undef; 
}


open(FULL, "<chr1.txt") or die "error reading file";
open(OUT, ">chr1.match.txt") or die "error reading file";

while (my $line=<FULL>)
{
    
    chomp $line;
    @line=split("\t",$line);
    foreach my $key (sort keys %Chr) 
    {
    
        if ($line[0] eq $key)
        {
        print OUT "$line\n";
        }
    }
}

close KEY;
close FULL;
close OUT;
exit;

[download]

This is chr1.coverage.txt sample data

chr1:496-588    44    0
chr1:496-588    44    0
chr1:496-588    44    0
chr1:496-588    44    0
chr1:496-588    44    0
chr1:496-588    44    0
chr1:496-588    43    0
chr1:496-588    43    0
chr1:496-588    39    0
chr1:496-588    39    0
chr1:496-588    38    0
chr1:496-588    37    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0.0892857
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0

[download]

This is chr1.txt sample data

chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    43    0
chr1:496-588    43    0
chr1:496-588    39    0
chr1:496-588    39    0
chr1:496-588    38    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    39    0
chr1:496-588    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:648-719    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:720-795    0    0
chr1:126982-127030    0    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0.0892857
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0

[download]

This is the sample output chr1.match.txt

chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    43    0
chr1:496-588    43    0
chr1:496-588    39    0
chr1:496-588    39    0
chr1:496-588    38    0
chr1:496-588    0    0
chr1:496-588    0    0
chr1:496-588    39    0
chr1:496-588    0    0
chr1:126982-127030    0    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0.0892857
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    56    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0
chr1:126982-127030    0    0

[download]

Also note that although the data may look unnecessarily repetitious, it is actually a cropped version of another file with more columns so that each specific line represents a different data point.

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