def test_bam_filter_by_tax_id(self):
temp_dir = tempfile.gettempdir()
input_dir = util.file.get_test_input_path(self)
taxonomy_dir = os.path.join(util.file.get_test_input_path(),
"TestMetagenomicsSimple", "db", "taxonomy")
filtered_bam = util.file.mkstempfname('.bam')
args = [
os.path.join(input_dir, "input.bam"),
os.path.join(input_dir, "input.kraken-reads.tsv.gz"), filtered_bam,
os.path.join(taxonomy_dir, "nodes.dmp"),
os.path.join(taxonomy_dir, "names.dmp"), "--taxIDs", "186538"
]
args = metagenomics.parser_filter_bam_to_taxa(
argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
expected_bam = os.path.join(input_dir, "expected.bam")
assert_equal_bam_reads(self, filtered_bam, expected_bam)
def test_bam_filter_by_tax_id(self):
temp_dir = tempfile.gettempdir()
input_dir = util.file.get_test_input_path(self)
taxonomy_dir = os.path.join(util.file.get_test_input_path(),"TestMetagenomicsSimple","db","taxonomy")
filtered_bam = util.file.mkstempfname('.bam')
args = [
os.path.join(input_dir,"input.bam"),
os.path.join(input_dir,"input.kraken-reads.tsv.gz"),
filtered_bam,
os.path.join(taxonomy_dir,"nodes.dmp"),
os.path.join(taxonomy_dir,"names.dmp"),
"--taxIDs",
"186538"
]
args = metagenomics.parser_filter_bam_to_taxa(argparse.ArgumentParser()).parse_args(args)
args.func_main(args)
expected_bam = os.path.join(input_dir,"expected.bam")
assert_equal_bam_reads(self, filtered_bam, expected_bam)