in reply to Faulty Control Structures?

Seems to me your main block should look more like:

#!/usr/bin/perl -w use strict; my @main = &open_file_main (); my @annot = &open_file_annot (); open OUTPUT, '>', 'output.txt' or die "Cannot open $!"; # loop through the main data file foreach my $md (@main) { chomp $md; my ($main_chrom, $winl, $winr) = split (/\s{2,}/, $md); foreach my $ad (@annot) { my ($an_chrom, undef, undef, $prol, $pror, undef, undef, undef +, $mess) = split (/\s{2,}/, $ad); next unless $main_chrom eq $an_chrom; my (undef, undef, $name) = split (/\;/, $mess); next if $winr < $prol or $winl > $pror; print OUTPUT "$name\t $md\n"; #last; } } exit;

Note that there is no need for a sub to open the output file! If you need to do complicated stuff in the context of opening the output file, return the file handle from the sub - do not use a 'global' variable that is set as a side effect!

Perl is environmentally friendly - it saves trees