How to use pybedtools bedgraph to bigwig using Ensembl genomes

Question

[frymor2]

I would like to know if there is a way to convert bedgraph files into bigwig using the pybedtools package (or any other).

I am running a script to analyze some normalized bedgraph files and would like to One of the steps is this

   for i in range(len(bg_names)):
      bedgraph_to_bigwig(BedTool(bg_names[i]), chrom_sizes, bw_names[i])

but my genome is from Ensembl (so without the chr prefix of the UCSC genome) The bedgraph files look like that:

$head avenorm.bg
1   3138098 3138099 159.292
1   3138282 3138283 159.292
1   3178161 3178162 318.585
1   3178369 3178370 318.585

When running my script I get though this error message,, which makes sense, as my bed file doesn't have chr1 but 1 as chromosome name.

bedgraph_to_bigwig(BedTool(bg_names[i]), chrom_sizes, bw_names[i])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/fs/home/yeroslaviz/miniconda3/envs/py2/lib/python2.7/site-packages/pybedtools/contrib/bigwig.py", line 55, in bedgraph_to_bigwig
    "cmds: %s\nstderr:%s\nstdout:%s" % (" ".join(cmds), stderr, stdout)
ValueError: cmds: bedGraphToBigWig WK38.avenorm.bg /tmp/pybedtools.xAwgug.tmp WK38.avenorm.bw
stderr:1 is not found in chromosome sizes file

Is there any way to run bedGraphToBigWig wiht the ensembl genome, or would it be easier to convert the bed file to _chr1_?

thanks

[ATpoint]

bedGraphToBigWig is a generic tool, all you need is a genome file that lists the chromosome name and then length of the chromosome. You do not need pybedtools here.