Hi Monks,

I've written a short script which loops through a file, using some information from a specific line to extract a section of the file using an external program. This section (called $mafBlock) is then used in another external program, and it is the output of this program (called m2.gff) that I am interested in. However, each time the loop proceeds the output file m2.gff is overwritten, so I thought one solution would be to try and open this file within the loop, and then print the lines I require to another output file (m2_most-cons.gff). If I do this I get a syntax error for opening this second filehandle, I've tried a few different ways of writing this but none seem to work. My code is:

use warnings;
use strict;

my $maf = "input.maf";

open (IN1, "input.maf") or die;
open (OUT1, ">m2.maf") or die;
open (OUT2, ">m2_most-cons.gff") or die;

while (my $line1 = <IN1>) {
    chomp $line1;
    if ($line1 =~ /^s\sficAlb2/) {
        my @columns = split(/\t/, $line1);
        my $start = $columns[2] + 1;
        my $end = $columns[2] + $columns[3];
        my $chrom = $columns[1];
        my $mafBlock = qx(maf_parse --start $start --end $end $maf);
        print OUT1 "$mafBlock1\n";
        my $phastCons = qx(phastCons --target-coverage 0.3 --expected-
+length 45 --rho 0.31 --most-conserved m2.gff --seqname $chrom --msa-f
+ormat MAF m2.maf nonconserved-all-4d.mod);
        print "$phastCons\n"
        open (IN2, "m2.gff") or die;
        while (my $line2 = <IN2>) {
            if ($line2 =~ /^fic/) {
                print OUT2 "$line2\n";
            }
        }
    }
    open (OUT1, ">m2.maf") or die;
    close IN2;
}

close IN1;
close OUT1;
close OUT2;

exit;
[download]

Apologies if this is something completely wrong, I'm new to coding and this seemed the most intuitive way to collect the output required.

Many thanks in advance!

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