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Hi, This is my first day working with perl, so I really dont know anything. It took me whole day to come up with some code, but still it doesn't work :( I have two text files which are tab delimited like this:
file 1 (test) chr1 30 chr2 20 chr2 50 chr3 80 file 2 (reference) chr1 40 chr1 50 chr2 60 chr2 80 chr3 100
I want to compare file1 which is the testfile agains file2 which is the reference file. When column 1 of both files is the same, I want to get the difference between the two files for column 2, and it must return the smallest value for that particular chr. So the output should look like this:
output chr1 10 chr2 40 chr2 10 chr3 20
My code looks like this now:
#!/usr/bin/env perl use strict; use warnings; my ( @cols, $p1, $p2, $p3, $p4, @sec, @cols2 ); @ARGV or die "No input file specified"; open my $first , '<',$ARGV[0] or die "Unable to open input file: $!"; open my $second,'<', $ARGV[1] or die "Unable to open input file: $!"; print scalar <$first>; <$second>; #...throw away first line... while (<$first>) { @cols = split /\s+/; $p1 = $cols[0]; $p2 = $cols[1]; #print $p1; while (<$second>) { @cols2 = split /\s+/; $p3 = $cols2[0]; $p4 = $cols2[1]; if ($p3 eq $p1) { print "yes"; } } }
But this doesn't work.. Could somebody please help me? Thanks!

In reply to compare text files by linseyr

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