clean_lobstr_trf_bed

#!/usr/bin/perl -w

use warnings;
use strict;
use POSIX;
use Getopt::Long;
use File::Path;
use File::Basename;
use Pod::Usage;

=head1 NAME

clean_lobstr_bed

=head1 SYNOPSIS

 clean_lobstr_bed [options]

=head1 DESCRIPTION

 Cleans lobstr trf BED file.

=cut

#option variables
my $help;
my $verbose;
my $debug;
my $refFASTAFile;

#initialize options
Getopt::Long::Configure ('bundling');

if(!GetOptions('h'=>\$help, 'v'=>\$verbose, 'd'=>\$debug) ||
   scalar(@ARGV)!=1)
{
    if ($help)
    {
        pod2usage(-verbose => 2);
    }
    else
    {
        pod2usage(1);
    }
}

my $lobstrTrfBEDFile = $ARGV[0];

open(BED, "$lobstrTrfBEDFile") || die "Cannot open  $lobstrTrfBEDFile";

#note that lobSTR BED file interval is not 0 based half open but instead is 1 based closed

#chr1   10001   10468   6   77.2    6   10001   10468   789 33  51  0   15  1.43    TAACCC  .
#chr1   54713   54817   4   25.8    4   54713   54817   149 0   26  0   72  0.91    TTTC    .
#chr1   66161   66630   2   262.0   2   66161   66630   339 49  0   0   49  1.08    TA  66205,66632,5,202;
#chr1   83792   84041   4   64.8    4   83792   84041   335 72  0   28  0   0.86    AAAG    .
#chr1   99000   99042   4   10.8    4   99000   99042   86  23  0   0   76  0.78    TTTA    .
#chr1   99047   99116   1   70.0    1   99047   99116   68  0   11  0   88  0.51    T   .

#chr1   : chromosome
#10001  : start position
#10468  : end position
#6      : period size
#77.2   : copy number
#789    : purity score
#33     : %tage A
#51     : %tage C
#0      : %tage G
#15     : %tage T
#1.43   :
#TAACCC : STR repeat unit
#.

#CCCAGCCCACCCATCCCATCCCCGCCCACCCATCCCATCCC   <STR>   .   PASS    RU=CCCAT;RL=43;REF=8.6;PSCORE=41;COMP=17,4,9,68;ENTROPY=1.35

while(<BED>)
{
    s/\r?\n?$//;

    my ($chrom, $start, $end, $periodSize, $refCopyNo,
        $dummy1, $dummy2, $dummy3,
        $purityScore, $A, $C, $G, $T, $entropy, $repeatUnit, $overlap) = split("\t");

    $chrom =~ s/chr//;
    --$start;

    print "$chrom\t$start\t$end\n";
}

close(BED);