Is there a tool for converting a variable step wig to a fixed step wig?
Thank you in advance for your help
Hi Belhocine,
variableStep and fixedStep are two types of wiggle formats. In variableStep you will have each line with different size (step) whereas in fixedStep each line will be of same width. So there won't be coordinates in fixedStep (Refer: http://genome.ucsc.edu/goldenpath/help/wiggle.html). But if you think your variableStep file is having same step size all over the file then its small awk one liner work only (I can write you the script if this is the case if you could show head of the file). But if the file is really having variable steps then it is difficult to convert, you might have to generate wig file again in fixedStep format.
no my variableStep file have not exactly the same step size all over the file. all regions with zero score are removed. here is an exemple of this file :
track type=wiggle_0 name="test" description="test" visibility=dense color=0,0,255
VariableStep chrom=chr10 start=1254 step=50
1
5
17
12
3
VariableStep chrom=chr10 start=3452 step=50
2
5
9
7
1
Can I ask why you need to convert WIG variable to fixed? It might be that conversion to bedGraph might help.
Hi Mohamed,
Try the following perl script that I wrote a while ago for mouse mm9, I use it all the time. If you want to convert to mm10 then you can change the chr lengths
#!/usr/bin/perl
use strict;
open(INFILE,"@ARGV[0]") or die "could not open @ARGV[0] for reading";
@ARGV[0]=~m/(.*)\./;
my $filename=$1."_fixed.wig";
my $expname=$1;
my @filenames=split(/\//,$expname);
my $size=@filenames;
$expname=@filenames[$size-1];
print "\n\n@ARGV[0]\n\n$filename\n\n";
open(OUTFILE,">$filename") or die "could not open $filename for writing";
my $chr;
my $coordstart=1;
my $wigstart;
my $step;
my $end=0;
while(my $line = )
{
if(($line=~m/chrom/)&&(!($line=~m/#/)))
{
$line=~m/chrom=(chr[0-9_a-zA-Z]*) span=([0-9]*)/;
$chr=$1;
$wigstart=1;
$step=$2;
if($coordstart>1)
{
for(my $i=$coordstart;$i
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools