def writeSammpleSheets(sample_list, sheet_path, template_sheet):
samplesheet_name = os.path.basename(sheet_path)
samplesheet_dir = os.path.dirname(os.path.realpath(sheet_path))
count = 0
exit_status = "success"
for key in sample_list:
count += 1
logger.debug(
f"{len(sample_list[key])} samples with idx lengths {key[1]}/{key[2]} for {key[0]} dataset"
)
new_sample_sheet = SampleSheet()
new_sample_sheet.Header = template_sheet.Header
new_sample_sheet.Reads = template_sheet.Reads
new_sample_sheet.Settings = template_sheet.Settings
for sample in sample_list[key]:
new_sample_sheet.add_sample(sample)
new_sample_sheet_file = os.path.join(
samplesheet_dir,
samplesheet_name + ".custom." + str(count) + "." + key[0])
logger.info(f"Creating custom sample sheet: {new_sample_sheet_file}")
try:
with open(new_sample_sheet_file, "w") as ss_writer:
new_sample_sheet.write(ss_writer)
except Exception as error:
logger.error(f"Exception writing new sample sheet: {error}")
exit_status = "failure"
logger.debug(f"Created custom sample sheet: {new_sample_sheet_file}")
return exit_status
def build_samplesheet(df, args):
samplesheet = SampleSheet()
for ix, row in df.iterrows():
s = {
'Sample_ID': row.Sample_ID,
'Sample_Name': row.Sample_Name,
'Sample_Project': row.Sample_Project,
'index': row["index"],
'index2': row.index2
}
if not args.merge_lanes:
s["Lane"] = row.Lane
samplesheet.add_sample(Sample(s))
return samplesheet
class TestUnidentifiedIndexHandler(HandlerTestBase):
def setUp(self):
qc_config = {
'name': 'UnidentifiedIndexHandler',
'significance_threshold': 1,
'white_listed_indexes': ['.*N.*', 'G{8,}']
}
self.unidentifiedIndexHandler = UnidentifiedIndexHandler(qc_config)
conversion_results_key = "ConversionResults"
conversion_results = get_stats_json()["ConversionResults"]
samplesheet_key = "samplesheet"
self.samplesheet = SampleSheet()
sample_1 = Sample(
dict(Lane=1,
Sample_ID='1823A',
Sample_Name='1823A-tissue',
index='AAAA'))
sample_2 = Sample(
dict(Lane=2,
Sample_ID='1823B',
Sample_Name='1823B-tissue',
index='TTTT'))
sample_3 = Sample(
dict(Lane=3,
Sample_ID='1823C',
Sample_Name='1823C-tissue',
index='AAAA',
index2='TTTT'))
sample_4 = Sample(
dict(Lane=4,
Sample_ID='1823D',
Sample_Name='1823D-tissue',
index='GGGG',
index2='CCCC'))
sample_5 = Sample(
dict(Lane=6,
Sample_ID='1823E',
Sample_Name='1823D-tissue',
index='ATCG'))
self.samplesheet.add_sample(sample_1)
self.samplesheet.add_sample(sample_2)
self.samplesheet.add_sample(sample_3)
self.samplesheet.add_sample(sample_4)
self.samplesheet.add_sample(sample_5)
self.unidentifiedIndexHandler.collect(
(conversion_results_key, conversion_results))
self.unidentifiedIndexHandler.collect(
(samplesheet_key, self.samplesheet))
self.samplesheet_searcher = _SamplesheetSearcher(self.samplesheet)
def test_should_be_evaluated(self):
# No
self.assertFalse(
self.unidentifiedIndexHandler.should_be_evaluated(
tag='unknown', count=1, number_of_reads_on_lane=10))
# No
self.assertFalse(
self.unidentifiedIndexHandler.should_be_evaluated(
tag='AAAAAA', count=1, number_of_reads_on_lane=1000))
# Yes
self.assertTrue(
self.unidentifiedIndexHandler.should_be_evaluated(
tag='AAAAAA', count=100, number_of_reads_on_lane=1000))
# Yes
self.assertTrue(
self.unidentifiedIndexHandler.should_be_evaluated(
tag='GGGGGG', count=100, number_of_reads_on_lane=1000))
def test_get_complementary_sequence(self):
res = self.unidentifiedIndexHandler.get_complementary_sequence(
'ATCG+N')
self.assertEqual(res, 'TAGC+N')
def test_validate_configuration(self):
with self.assertRaises(ConfigurationError):
UnidentifiedIndexHandler({
'name': 'UnidentifiedIndexHandler',
'foo': 'bar'
}).validate_configuration()
def test_always_warn_rules(self):
res = next(
self.unidentifiedIndexHandler.always_warn_rule(tag="",
lane=1,
percent_on_lane=1))
self.assertTrue(isinstance(res, QCErrorFatal))
def test_always_warn_rules_for_white_listed_tag(self):
res = next(
self.unidentifiedIndexHandler.always_warn_rule(tag="NNNNN",
lane=1,
percent_on_lane=1))
self.assertTrue(isinstance(res, QCErrorWarning))
def test_check_swapped_dual_index_yes(self):
res = next(
self.unidentifiedIndexHandler.check_swapped_dual_index(
'TTTT+AAAA', 1, self.samplesheet_searcher))
self.assertTrue(
'It appears that maybe the dual index tag: TTTT+AAAA was swapped. '
'There was a hit for the swapped index: AAAA+TTTT at: Lane: 3, for sample: 1823C-tissue. '
'The tag we found was: AAAA+TTTT' in res.message)
def test_check_swapped_dual_index_no(self):
with self.assertRaises(StopIteration):
next(
self.unidentifiedIndexHandler.check_swapped_dual_index(
'TTGG+AATT', 1, self.samplesheet_searcher))
def test_check_reversed_index_yes(self):
res = next(
self.unidentifiedIndexHandler.check_reversed_index(
'GCTA', 1, self.samplesheet_searcher))
self.assertTrue(
'We found a possible match for the reverse of tag: GCTA, on: Lane: 6, '
'for sample: 1823D-tissue. The tag we found was: ATCG' in
res.message)
def test_check_reversed_index_no(self):
with self.assertRaises(StopIteration):
next(
self.unidentifiedIndexHandler.check_reversed_index(
'GGTT', 1, self.samplesheet_searcher))
def test_check_complement_index_yes(self):
res = next(
self.unidentifiedIndexHandler.check_complement_index(
'TTTT', 1, self.samplesheet_searcher))
self.assertTrue(
'We found a possible match for the complementary of tag: TTTT, on: Lane: 1, for '
'sample: 1823A-tissue. The tag we found was: AAAA' in res.message)
def test_check_complement_index_no(self):
with self.assertRaises(StopIteration):
next(
self.unidentifiedIndexHandler.check_complement_index(
'GGGG', 1, self.samplesheet_searcher))
def test_check_if_index_in_other_lane_hit_yes(self):
res = next(
self.unidentifiedIndexHandler.check_if_index_in_other_lane(
'TTTT', 1, self.samplesheet_searcher))
self.assertTrue(
"We found a possible match for the tag: TTTT, on another lane: Lane: 2, for sample: "
"1823B-tissue. The tag we found was: TTTT" in res.message)
def test_check_if_index_in_other_lane_hit_no(self):
with self.assertRaises(StopIteration):
next(
self.unidentifiedIndexHandler.check_if_index_in_other_lane(
'GGGG', 1, self.samplesheet_searcher))
def test_number_of_reads_per_lane(self):
res = self.unidentifiedIndexHandler.number_of_reads_per_lane()
self.assertDictEqual(res, {1: 162726440, 2: 164470667})
def test_is_significantly_represented(self):
self.assertTrue(
self.unidentifiedIndexHandler.is_significantly_represented(
11, 100))
self.assertFalse(
self.unidentifiedIndexHandler.is_significantly_represented(1, 100))
def test_check_reversed_in_dual_index(self):
res = next(
self.unidentifiedIndexHandler.
check_reverse_complement_in_dual_index('TTTT+TTTT', 1,
self.samplesheet_searcher))
self.assertTrue(
'We found a possible match for the reverse complement of tag: TTTT, on: Lane: 1, for sample: '
'1823A-tissue. The tag we found was: AAAA. This originated from the dual index '
'tag: TTTT+TTTT' in res.message)
def test_check_reverse_complement_in_dual_index(self):
res = next(
self.unidentifiedIndexHandler.
check_reverse_complement_in_dual_index('TTTT+TTTT', 1,
self.samplesheet_searcher))
self.assertTrue(
'We found a possible match for the reverse complement of tag: TTTT, on: Lane: 1,'
' for sample: 1823A-tissue. The tag we found was: AAAA. This originated from the dual '
'index tag: TTTT+TTTT' in res.message)
def test_check_complement_in_dual_index(self):
res = next(
self.unidentifiedIndexHandler.
check_reverse_complement_in_dual_index('TTTT+TTTT', 1,
self.samplesheet_searcher))
self.assertTrue(
'We found a possible match for the reverse complement of tag: TTTT, on: Lane: 1, for sample: '
'1823A-tissue. The tag we found was: AAAA. This originated from the dual '
'index tag: TTTT+TTTT')