def register_sample_annotations(
argv=None, register_samples=False, coredb=REGISTRY_DATABASE,
out=sys.stdout):
if register_samples:
p = argparse.ArgumentParser(description=SAMPLES_DESC)
else:
p = argparse.ArgumentParser(
description=ANNOTATIONS_DESC, epilog=ANNOTATIONS_EPILOG)
p.add_argument(
"run_accession", type=int,
help="Run accession number")
p.add_argument(
"sample_table", type=argparse.FileType('r'),
help=SAMPLE_TABLE_HELP)
args = p.parse_args(argv)
sample_table = SampleTable.load(args.sample_table)
sample_table.look_up_nextera_barcodes()
sample_table.validate()
registry = SampleRegistry(coredb)
registry.check_run_accession(args.run_accession)
if register_samples:
registry.register_samples(args.run_accession, sample_table)
registry.register_annotations(args.run_accession, sample_table)
def register_sample_annotations(argv=None,
register_samples=False,
db=REGISTRY_DATABASE,
out=sys.stdout):
if register_samples:
p = argparse.ArgumentParser(description=SAMPLES_DESC)
else:
p = argparse.ArgumentParser(description=ANNOTATIONS_DESC,
epilog=ANNOTATIONS_EPILOG)
p.add_argument("run_accession", type=int, help="Run accession number")
p.add_argument("sample_table",
type=argparse.FileType('r'),
help=SAMPLE_TABLE_HELP)
args = p.parse_args(argv)
sample_table = SampleTable.load(args.sample_table)
sample_table.look_up_nextera_barcodes()
sample_table.validate()
registry = SampleRegistry(db)
registry.check_run_accession(args.run_accession)
if register_samples:
registry.register_samples(args.run_accession, sample_table)
registry.register_annotations(args.run_accession, sample_table)
def test_look_up_nextera_barcodes(self):
input_file = io.StringIO(NEXTERA_TSV)
t = SampleTable.load(input_file)
t.look_up_nextera_barcodes()
self.assertEqual(t.recs[1]["BarcodeSequence"], u"ACTCGCTA-TATCCTCT")
self.assertEqual(t.validate(), None)
def test_validate(self):
t = SampleTable(self.recs)
self.assertEqual(t.validate(), None)
def test_parse(self):
input_file = io.StringIO(NORMAL_TSV)
t = SampleTable.load(input_file)
self.assertEqual(t.recs, self.recs)
def test_write(self):
t = SampleTable(self.recs)
output_file = io.StringIO()
t.write(output_file)
self.assertEqual(output_file.getvalue(), NORMAL_TSV)
def temp_sample_file(samples):
f = tempfile.NamedTemporaryFile(mode="wt")
t = SampleTable(samples)
t.write(f)
f.seek(0)
return f
def temp_sample_file(samples):
f = tempfile.NamedTemporaryFile(mode="wt")
t = SampleTable(samples)
t.write(f)
f.seek(0)
return f
def test_look_up_nextera_barcodes(self):
input_file = io.StringIO(NEXTERA_TSV)
t = SampleTable.load(input_file)
t.look_up_nextera_barcodes()
self.assertEqual(t.recs[1]["BarcodeSequence"], u"ACTCGCTA-TATCCTCT")
self.assertEqual(t.validate(), None)
def test_validate_with_duplicated_sample_name(self):
self.recs[1]["SampleID"] = "S1"
t = SampleTable(self.recs)
self.assertRaises(ValueError, t.validate)
def test_validate(self):
t = SampleTable(self.recs)
self.assertEqual(t.validate(), None)
def test_parse(self):
input_file = io.StringIO(NORMAL_TSV)
t = SampleTable.load(input_file)
self.assertEqual(t.recs, self.recs)
def test_write(self):
t = SampleTable(self.recs)
output_file = io.StringIO()
t.write(output_file)
self.assertEqual(output_file.getvalue(), NORMAL_TSV)
