Wig liftover and conversion

[rlh60]

Hi,

I am just wondering if there is a way to liftover wig files? Or alternatively, is it possible to convert wig files to bed so that I could liftover using UCSC and then create a new wig file?

Thanks,
Rebecca

[mgogol]

Sure, you can liftover a bedgraph or a bed file. Galaxy can do this.

[rlh60]

Thanks for that, but I don't have the bed files, only .wig files, so do you know how to first convert from wig back to bed so that I can then use Galaxy?

Thanks,
Rebecca

[mgogol]

If you have variable step wig, I have a perl script that will convert it to bed graph. If you want it, I'll clean it up and post it.

[rlh60]

Yes please, that would be great!

Thank you! :-)

Rebecca

[mgogol]

Okay, this is kind of old code and actually reads in the entire file, which isn't really necessary, but that's how I used to always do things. It also doesn't print out the track line. Right now it just adds one to every variableStep position to get the end, that should probably be changed to be based on span. Hope it helps.

#! /usr/bin/perl
####################
# vstep_to_bedgraph.pl - convert variable step wig to bed-style wig
# By Madelaine Gogol 
# 11/2008 
####################

use strict;

my ($start,$value,$end,$current_chrom,@lines,$filename, $contents, @chunks);
$filename = $ARGV[0];

#read in file
$contents = get_file_data($filename);

#split file at "variableStep lines"
@chunks = split(/\nvariableStep/,$contents);

#for each chromosome
foreach my $chunk (@chunks)
{
	@lines = split('\n',$chunk);
	foreach my $line (@lines)
	{
		#if the line starts with a number
		if($line =~ /^\d/)
		{
			($start,$value) = split(/\s+/,$line);
			$end = $start+1;

			#print out bedgraph format
			print "$current_chrom\t$start\t$end\t$value\n";
		}
		
		#otherwise, the line is a variableStep chrom=chr line
		elsif($line =~ /\schrom=(chr\S+)/)
		{
			$current_chrom = $1; #define current chromosome
		}
	}
}

######################################################    
# subroutine get_file_data
# arguments: filename
# purpose: gets data from file given filename;
# returns file contents
######################################################

sub get_file_data
{
        my($filename) = @_;

        my @filedata = ();

        unless( open(GET_FILE_DATA, $filename))
        {
                print STDERR "Cannot open file \"$filename\": $!\n\n";
                exit;
        }
        @filedata = <GET_FILE_DATA>;
        close GET_FILE_DATA;
        return join('',@filedata);
}

[AndyP]

It's been a long time, but I'll mention anyway I made a program that lifts bigWig files from one assembly to another in one command:

https://github.com/andypohl/bwtool/wiki/lift

Maybe it's useful. bigWig is an easy conversion from wig and is a better format in some ways.