alleledb_bedbowtie2fastq

#!/usr/bin/perl -w

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

=head1 NAME

bowtie2fastq

=head1 SYNOPSIS

 bedbowtie2fastq <bowtie> 
 
   
  Convert bed format that contains bowtie info (output of bowtie2bed) to fastq file 
  
  INPUT (bowtie output) 
  col1: chr
  col2: start(0based)
  col3: end(1based)	
  col4: ID#*o*#sequence#*o*#strand#*o*#score
  
  but it doesnt require the first 3 columns; it requires only the 4th.
  
  OUTPUT
  fastq
  
  Example:
     bedbowtie2fastq file.bed | gzip -c > file.fastq.gz
  
=head1 DESCRIPTION

=cut

#option variables
my $help;

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

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

## input file
my $fn = shift;

## variables
my $fh; 
my %reads2seq;
my %reads2strand;
my %reads2score;

## read in file
open($fh, "<$fn") || die "cannot open the file $fn!";
while (my $l = <$fh>) {
    chomp($l);
   
    my @t = split(/\t/, $l);
        
		
		#my $chr = $t[0];
		#my $sta = $t[1];
		#my $end = $t[2];
		
		my @u = split(/\#\*o\*\#/, $t[3]);
		my $id = $u[0];
		my $seq = $u[1];
		my $strand=$u[2];
		my $score = $u[3];
		
		$reads2seq{$id} = $seq;
		$reads2score{$id} = $score;
}

### print
for my $ID (sort keys %reads2seq)
{
	print "\@$ID\n$reads2seq{$ID}\n+\n$reads2score{$ID}\n";
}



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## subroutines
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