def run(options):
remover = contam_remover.ContamRemover(
options.metadata_tsv,
options.bam_in,
options.counts_out,
options.reads_out_1,
options.reads_out_2,
contam_out_1=options.contam_out_1,
contam_out_2=options.contam_out_2,
no_match_out_1=options.no_match_out_1,
no_match_out_2=options.no_match_out_2,
done_file=options.done_file,
)
remover.run()
def test_run_no_match_not_wanted(self):
"""test run when no_match_are_wanted=False"""
metadata_file = os.path.join(data_dir, "run.metadata.tsv")
samfile = os.path.join(data_dir, "run.sam")
outprefix = "tmp.contam_remover.test_run"
counts_file = outprefix + ".counts.tsv"
reads1 = outprefix + ".wanted_1.fq"
reads2 = outprefix + ".wanted_2.fq"
no_match1 = outprefix + ".no_match_1.fq"
no_match2 = outprefix + ".no_match_2.fq"
contam_1 = outprefix + ".contam_1.fq"
contam_2 = outprefix + ".contam_2.fq"
done_file = outprefix + ".done"
if os.path.exists(done_file):
os.unlink(done_file)
cremover = contam_remover.ContamRemover(
metadata_file,
samfile,
counts_file,
reads1,
reads2,
contam_out_1=contam_1,
contam_out_2=contam_2,
no_match_out_1=no_match1,
no_match_out_2=no_match2,
done_file=done_file,
)
cremover.run()
for read_type in "contam", "no_match", "wanted":
for i in 1, 2:
got_file = outprefix + "." + read_type + "_" + str(i) + ".fq"
self.assertTrue(os.path.exists(got_file))
expected_file = os.path.join(
data_dir,
"run.no_match_not_wanted." + read_type + "_" + str(i) +
".fq",
)
self.assertTrue(
filecmp.cmp(expected_file, got_file, shallow=False))
os.unlink(got_file)
expected_counts_file = os.path.join(data_dir,
"run.expected_counts.tsv")
self.assertTrue(
filecmp.cmp(expected_counts_file, counts_file, shallow=False))
os.unlink(counts_file)
self.assertTrue(os.path.exists(done_file))
os.unlink(done_file)
def test_run_no_match_not_wanted(self):
'''test run when no_match_are_wanted=False'''
metadata_file = os.path.join(data_dir, 'run.metadata.tsv')
samfile = os.path.join(data_dir, 'run.sam')
outprefix = 'tmp.contam_remover.test_run'
counts_file = outprefix + '.counts.tsv'
reads1 = outprefix + '.wanted_1.fq'
reads2 = outprefix + '.wanted_2.fq'
no_match1 = outprefix + '.no_match_1.fq'
no_match2 = outprefix + '.no_match_2.fq'
contam_1 = outprefix + '.contam_1.fq'
contam_2 = outprefix + '.contam_2.fq'
done_file = outprefix + '.done'
if os.path.exists(done_file):
os.unlink(done_file)
cremover = contam_remover.ContamRemover(metadata_file,
samfile,
counts_file,
reads1,
reads2,
contam_out_1=contam_1,
contam_out_2=contam_2,
no_match_out_1=no_match1,
no_match_out_2=no_match2,
done_file=done_file)
cremover.run()
for read_type in 'contam', 'no_match', 'wanted':
for i in 1, 2:
got_file = outprefix + '.' + read_type + '_' + str(i) + '.fq'
self.assertTrue(os.path.exists(got_file))
expected_file = os.path.join(
data_dir, 'run.no_match_not_wanted.' + read_type + '_' +
str(i) + '.fq')
self.assertTrue(
filecmp.cmp(expected_file, got_file, shallow=False))
os.unlink(got_file)
expected_counts_file = os.path.join(data_dir,
'run.expected_counts.tsv')
self.assertTrue(
filecmp.cmp(expected_counts_file, counts_file, shallow=False))
os.unlink(counts_file)
self.assertTrue(os.path.exists(done_file))
os.unlink(done_file)