Script that takes as input a BED file stream and outputs the stream to its corresponding chromosome. Do not use this script in parallel.

split_chr.pl

#!/bin/env perl

use strict;
use warnings;

#hash for filehandles
my %fh = ();

#read from stream
while (<>){
   my ($chr, @rest) = split(/\t/);
   if (exists $fh{$chr}){
      print {$fh{$chr}} "$_";
   } else {
      #open output filehandle for each chromosome
      open(my $fh, ">>", "$chr.bed") || die("Could not open $chr.bed for output: $!\n");
      #store file handle in hash
      $fh{$chr} = $fh;
      print {$fh{$chr}} "$_";
   }
}

#close all filehandles
foreach my $fh (keys %fh){
   close $fh{$fh};
}

exit(0);