convert_hg19chain_to_hs37d5chain

#!/usr/bin/perl -w

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

=head1 NAME

add_prefix_chr_to_chromosome_names

=head1 SYNOPSIS

 convert_hg19chain_to_hs37d5chain [options]

=head1 DESCRIPTION

 Removes chr prefix of chromosome names for hg19.

=cut

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

#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 $inputChainFile = $ARGV[0];

open(CHAIN, $inputChainFile=~/\.gz$/ ? "gzip -dc $inputChainFile |" : "$inputChainFile");

while(<CHAIN>)
{
    chomp;

    if (/^chain/)
    {
        my @F = split(" ");
        
        $F[2] =~ s/^chr//; 
        $a=join(" ", @F);
        print "$a\n";
    }
    else
    {
        print "$_\n";
    }
}

close(CHAIN);