def test_alignment_parser_input_choices():
# kind of a hack. make sure input choices
# are correct based upon whether or not they
# appear in --help
all_choices = ("bowtie","tagalign","wiggle","BAM","bigwig")
for chosen in itertools.chain.from_iterable(itertools.combinations(all_choices,K) for K in range(len(all_choices))):
tmp_str = " --countfile_format {%s}" % ",".join(list(chosen))
parser = get_alignment_file_parser(input_choices=chosen)
assert_in(tmp_str,parser.format_help())
"annotation_format",
"add_three",
"annotation_files",
"tabix"
}
annotation_file_gff_opts = { "gff_exon_types", "gff_transcript_types"}
annotation_file_parser_disableable = annotation_file_parser_opts - set(["annotation_files"])
ivcollection_file_parser_opts = annotation_file_parser_opts - set(["add_three"])
ivcollection_file_parser_disableable = annotation_file_parser_disableable - set(["add_three"])
mask_file_parser_opts = ivcollection_file_parser_opts
mask_file_parser_disableable = ivcollection_file_parser_disableable
alignment_file_parser = get_alignment_file_parser()
annotation_file_parser = get_annotation_file_parser()
ivcollection_file_parser = get_segmentchain_file_parser()
sequence_file_parser = get_sequence_file_parser()
mask_file_parser = get_mask_file_parser()
def check_prefix(parser_fn,opts):
"""Helper function to test prefix appending to various parsers
Parameters
----------
parser_fn : function
Function that returns a :py:class:`~argparse.ArgumentParser`
opts : list
list of strings of options, without prefixes, included
