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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 CM.CS.parsed(file) .CM(file)\n\n\n";
my $CMCS_parsed = $ARGV[0] or die $usage;
my $CM_file = $ARGV[1] or die $usage;
my %CS;
{
open (my $fh, "$CMCS_parsed") or die $!;
while (<$fh>) {
chomp;
my ($acc, $rest) = split (/\t/, $_, 2);
$CS{$acc} = $rest;
}
close $fh;
}
open (my $fh, $CM_file) or die $!;
while (<$fh>) {
chomp;
if (/^ChimeraMaligner/) {
my ($token, $acc, $flag, $perID, $ranges) = split (/\t/, $_, 5);
$ranges =~ s/\t/ /g;
my $CS_text = $CS{$acc} or die "Error, no CS text for $acc ";
print "$token\t$acc\t$flag\t$perID\t$ranges\t$CS_text\n";
}
}
close $fh;
exit(0);
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