def check_get_transcript_from_args_add_three_tabix(fmt):
# check endpoints of transcript and CDS
# GTF2 and BED format
bed_ref = REF_FILES["100transcripts_bed"]
cds = {}
tx = {}
for line in open(bed_ref):
items = line.strip("\n").split("\t")
name = items[3]
tx_start = int(items[1])
tx_end = int(items[2])
tx[name] = (tx_start,tx_end)
cds_start = int(items[6])
cds_end = int(items[7])
if cds_start < cds_end:
cds[name] = (cds_start,cds_end)
else:
cds[name] = (None,None)
ref_files = {
"BED" : REF_FILES["100transcripts_bed_tabix"],
"GTF2" : REF_FILES["100transcripts_gtf_tabix"]
}
parser = get_annotation_file_parser()
argstr = "--annotation_format %s --annotation_files %s --tabix" % (fmt,ref_files[fmt])
args = parser.parse_args(shlex.split(argstr))
transcripts = list(get_transcripts_from_args(args))
for my_tx in transcripts:
name = my_tx.get_name()
expected_cds_start, expected_cds_end = cds[name]
found_cds_start = my_tx.cds_genome_start
found_cds_end = my_tx.cds_genome_end
found_tx_start = my_tx.spanning_segment.start
found_tx_end = my_tx.spanning_segment.end
expected_tx_start, expected_tx_end = tx[name]
if found_cds_start is None:
assert_true(found_cds_end is None)
assert_true(expected_cds_start is None,"Unequal CDS start (expected %s, got %s) on transcript %s" % (expected_cds_start,found_cds_start,name))
assert_true(expected_cds_end is None,"Unequal CDS stop (expected %s, got %s) on transcript %s" % (expected_cds_end,found_cds_end,name))
else:
assert_equal(found_cds_start,expected_cds_start,"Unequal CDS start (expected %s, got %s) on transcript %s" % (expected_cds_start,found_cds_start,name))
assert_equal(found_cds_end,expected_cds_end,"Unequal CDS stop (expected %s, got %s) on transcript %s" % (expected_cds_end,found_cds_end,name))
assert_equal(found_tx_start,expected_tx_start,"Unequal transcript start (expected %s, got %s) on transcript %s" % (expected_tx_start,found_tx_start,name))
assert_equal(found_tx_end,expected_tx_end,"Unequal transcript end (expected %s, got %s) on transcript %s" % (expected_tx_end,found_tx_end,name))
assert_equal(len(transcripts),len(cds),"Not all transcripts found in input. Expected %s. Got %s." % (len(cds),len(transcripts)))
def test_get_transcript_from_args_multiple_bigbed_raises_error():
files = " ".join([MINI["bigbed_file"]] * 2)
argstr = "--annotation_format BigBed --annotation_files %s " % (files)
parser = get_annotation_file_parser()
args = parser.parse_args(shlex.split(argstr))
assert_raises(SystemExit,get_transcripts_from_args,args)
"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
in the parser