/
bed2junc.pl
executable file
·91 lines (76 loc) · 1.67 KB
/
bed2junc.pl
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#!/usr/bin/env perl
use strict;
use warnings;
use File::Basename;
use Getopt::Long;
use Carp;
my $prog = basename ($0);
my $verbose = 0;
#my $strandaware = 0;
GetOptions (
"v|verbose"=>\$verbose
# "s"=>\$strandaware
);
if (@ARGV != 2)
{
print STDERR "bed format to junctions\n";
print STDERR "Usage: $prog [options] <in.bed> <out> \n";
print STDERR "You can use - to specify STDIN for input or STDOUT for output\n";
exit(1);
}
my ($inputfilename, $outputfilename) = @ARGV;
my ($fin, $fout);
my %junchash;
if ( $inputfilename eq "-")
{
$fin = *STDIN;
}
else
{
open($fin, $inputfilename) or Carp::croak "cannot open file $inputfilename to read!\n";
}
while(my $line = <$fin>)
{
chomp($line);
my @a =split("\t", $line);
my @blockSizes = split(",", $a[10]);
my @blockStarts = split(",", $a[11]);
for (my $i=0; $i<$a[9]-1; $i++)
{
my $start = $a[1] + $blockStarts[$i] + $blockSizes[$i];
my $end = ($a[1] + $blockStarts[$i+1]);
# if( not $strandaware){
# $junchash{join(",", $a[0], $start, $end)}++;
# }
# else
# {
$junchash{join(",", $a[0], $start, $end, $a[5])}++;
# }
}
}
close($fin);
if ( $outputfilename ne "-")
{
open($fout, ">$outputfilename") or Carp::croak "cannot open file $outputfilename to write!\n";
}
else
{
$fout = *STDOUT;
}
foreach my $key (keys %junchash)
{
my @a = split(",", $key);
print $fout $a[0],"\t";
print $fout $a[1], "\t";
print $fout $a[2], "\t";
print $fout "\.\t";
print $fout $junchash {$key},"\t";
# if ( not $strandaware){
# print $fout "+\n";
# }
# else
# {
print $fout $a[3],"\n";
# }
}
close($fout);