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#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;
#Method to convert the given hash into WIG format and printing it to a handle. Make sure the handle is either STDOUT or a filehandle
sub convertAndWriteWig {
my $data = shift;
my $handle = shift;
my $span = shift;
if ($span) {
for (my $i=0;$i < scalar(@{$data->{'start'}});$i++) {
if(@{$data->{'coverage'}}[$i] != 0) {
print($handle "variableStep chrom=$data->{'chromosome'} span=",@{$data->{end}}[$i]-@{$data->{start}}[$i],"\n@{$data->{start}}[$i] @{$data->{'coverage'}}[$i]\n");
}
}
}
else {
print($handle qq(variableStep chrom=$data->{'chromosome'}\n));
for (my $i=0;$i < scalar(@{$data->{'start'}});$i++) {
for (my $j= @{$data->{'start'}}[$i]; $j < @{$data->{'end'}}[$i]+1;$j++) {
if(@{$data->{'coverage'}}[$i] != 0) {
print($handle qq($j @{$data->{'coverage'}}[$i]\n));
}
}
}
}
}
sub main {
my $usage = "USAGE:\n\t";
$usage.= "bedgraph2wig.pl --bedgraphfile=<filename> [Output is STDOUT]\n\t";
$usage.= "bedgraph2wig.pl --bedgraphfile=<filename> --outputfile=<filename>\n\n\n";
$usage.= "Parameters:\n";
$usage.= "\t--bedgraphfile: The path to the bedgraphffile\n";
$usage.= "\t--outputfile: The file where the output should be saved. If not supplied, the output is printed to STDOUT\n";
$usage.= "\t--span: Use span notation (see http://genome.ucsc.edu/goldenPath/help/wiggle.html\n";
my $bedgraphfile;
my $outputfile;
my $help;
my $span;
#test if the input is ok
if (scalar(@ARGV)==0) {print "$usage\n"; exit(0);}
my $found;
foreach (@ARGV) {
if ($_ =~ m/--bedgraphfile/) {
$found=1;
}
}
if (!$found) {
print "$usage\n"; exit(0);
}
#fetch params
GetOptions('bedgraphfile=s' => \$bedgraphfile,
'outputfile=s' => \$outputfile,
'help!' => \$help,
'span!' => \$span);
if ($help) { print "$usage\n"; exit(0); }
if (defined($bedgraphfile)) {
open(BEDGRAPH, "<$bedgraphfile") || die "Couldn't open $bedgraphfile\n";
}
else {
die "No begraphfile supplied\n";
}
#Check if we should print to STDOUT or a file. We don't print to a file if it exists.
my $fh=\*STDOUT;
if (defined($outputfile)) {
if (!(-e $outputfile)) {
open $fh, '>>', $outputfile or $fh=\*STDOUT;
}
else {
print(STDERR "Outputfile allready exists, printing to STDOUT\n");
}
}
#initialize the data hash with arrays and strings we need
my %data=('chromosome'=>"",start=>[],end=>[],coverage=>[]);
my $lastchromosome;
#we dont want the first line to be converted, its the track line
my $infostring = <BEDGRAPH>;
chomp($infostring);
$infostring =~ s/.*name=(".*")/$1/i;
print($fh "track type=wiggle_0 name=$infostring \n");
while(<BEDGRAPH>) {
print "$_";
#print($fh "$_\n");
my ($chromosome,$start,$end,$coverage) = split(/\s+/,$_);
# print($fh "$chromosome $start $end $coverage \n");
if (defined($lastchromosome)) {
{
if($chromosome ne $lastchromosome) {
&convertAndWriteWig(\%data,$fh,$span);
}
}
}
$data{'chromosome'} = $chromosome;
push(@{$data{'start'}},$start);
push(@{$data{'end'}},$end);
push(@{$data{'coverage'}},$coverage);
$lastchromosome = $chromosome;
}
}
&main;
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