BedTool.window_maker() fails if genome not provided

[andrewparkermorgan]

Attempting to run BedTool.window_maker() with interval instead of genome input fails as shown below.

Traceback (most recent call last):
  File "./tile_with_probes.py", line 36, in <module>
    kmers = regions.window_maker(w = args.kmer, s = args.step)
  File "/nas02/home/a/p/apm/lib/python2.7/site-packages/pybedtools-0.6.2-py2.7-linux-x86_64.egg/pybedtools/bedtool.py", line 623, in decorated
    result = method(self, *args, **kwargs)
  File "/nas02/home/a/p/apm/lib/python2.7/site-packages/pybedtools-0.6.2-py2.7-linux-x86_64.egg/pybedtools/bedtool.py", line 176, in wrapped
    kwargs = self.check_genome(**kwargs)
  File "/nas02/home/a/p/apm/lib/python2.7/site-packages/pybedtools-0.6.2-py2.7-linux-x86_64.egg/pybedtools/bedtool.py", line 1178, in check_genome
    raise ValueError('No genome specified. Use the "g" or '
ValueError: No genome specified. Use the "g" or "genome" kwargs, or use the .set_chromsizes() method

It looks to me like the contents of the BedTool are not being passed to _wraps() via the implicit argument. If I make the following change at line 1911 in bedtool.py then window_maker() now runs as expected.

## OLD:
# @_wraps(prog='windowMaker', uses_genome=True, genome_none_if=['b'])
## NEW:
@_wraps(prog='windowMaker', implicit='b', uses_genome=True, genome_none_if=['b'])

But I have not checked whether or not this causes the function to break under other input cases.

[daler]

Hmm, looks like this change would breaks existing functionality -- check the output of

nosetests pybedtools/test/test.py:test_window_maker

The way the _wraps decorator is set up, if implicit is specified then it means an interval file is required . . . which is not always the case for bedtools makewindows.

Which version of pybedtools are you running? The latest version uses

@_wraps(prog='windowMaker', uses_genome=True, genome_none_if=['b'],
            other='b', implicit='b')

With the latest version, you should be able to do

kmers = regions.window_maker(regions, w=args.kmer, s=args.step)

It's a little awkward to provide the method with regions itself, but since the bedtools makewindows works with or without a provided interval file, it doesn't fit perfectly with the infrastructure for the other tools.

[leeleavitt]

Would appreciate some updated documentation on this function. Happy to provide with guidance to location to update it.