alignMaker.pl

#!/usr/bin/env perl
use strict;
use warnings;
use feature 'say';
use autodie;

open( my $FILE, '<', $ARGV[0] ) or die;
( my $individual = $ARGV[0] ) =~ s/\.data.prep.txt//g;

open(my $OUT, '>>', "$individual.align.txt") or die;

foreach my $line (<$FILE>) {
    chomp $line;

    next if ( $line =~ /^SAMPLE/ );
    my @parts = split /\t/, $line;

    my $alignLine;
    my ( $file1, $file2, $sm, $id, $lb, $pu, $pl );
    if ( $parts[7] eq 'PAIRED' ) {
        $file1 = $parts[1];
        $file2 = $parts[2];
        $sm    = $parts[0];
        $id    = $parts[11];
        $lb    = $parts[12];
        $pu    = $parts[13];
        $pl    = $parts[8];

        $alignLine = sprintf(
            "Files=%s,%s;Type=PAIRED;RG=\@RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:%s\\tPU:%s",
            $file1, $file2, $id, $sm, $lb, $pl, $pu );
    }
    elsif ( $parts[7] eq 'UNPAIRED' ) {
        $file1 = $parts[1];
        $sm    = $parts[0];
        $id    = $parts[11];
        $lb    = $parts[12];
        $pu    = $parts[13];
        $pl    = $parts[8];

        $alignLine = sprintf(
            "Files=%s;Type=UNPAIRED;RG=\@RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:%s\\tPU:%s",
            $file1, $id, $sm, $lb, $pl, $pu );
    }
    say $OUT $alignLine;
}
close($FILE);
close($OUT);