def test_load(self):
expected_records = [dict(lane=1,
tile=2,
cycle=3,
error_rate=0.5,
num_0_errors=4,
num_1_error=5,
num_2_errors=6,
num_3_errors=7,
num_4_errors=8)]
records = list(read_errors(self.sample_stream))
self.assertEqual(expected_records, records)
def test_load(self):
expected_records = [
dict(lane=1,
tile=2,
cycle=3,
error_rate=0.5,
num_0_errors=4,
num_1_error=5,
num_2_errors=6,
num_3_errors=7,
num_4_errors=8)
]
records = list(read_errors(self.sample_stream))
self.assertEqual(expected_records, records)
def summarize_run(args, json):
""" Summarize the run data from the InterOp folder.
Writes some summary files.
:return: a dictionary with summary values.
"""
read_lengths = [json.read_length1,
json.index_length1,
json.index_length2,
json.read_length2]
summary = {}
interop_path = os.path.join(args.data_path,
'input',
'runs',
json.run_id,
'InterOp')
phix_path = os.path.join(interop_path, 'ErrorMetricsOut.bin')
quality_path = os.path.join(args.data_path, 'scratch', 'quality.csv')
bad_cycles_path = os.path.join(args.data_path, 'scratch', 'bad_cycles.csv')
summary_path = build_app_result_path(args.data_path,
json,
json.samples[0],
suffix='_QC')
makedirs(summary_path)
bad_tiles_path = os.path.join(summary_path, 'bad_tiles.csv')
with open(phix_path, 'rb') as phix, open(quality_path, 'w') as quality:
records = error_metrics_parser.read_errors(phix)
error_metrics_parser.write_phix_csv(quality,
records,
read_lengths,
summary)
with open(quality_path, 'rU') as quality, \
open(bad_cycles_path, 'w') as bad_cycles, \
open(bad_tiles_path, 'w') as bad_tiles:
report_bad_cycles(quality, bad_cycles, bad_tiles)
quality_metrics_path = os.path.join(interop_path, 'QMetricsOut.bin')
quality_metrics_parser.summarize_quality(quality_metrics_path,
summary,
read_lengths)
tile_metrics_path = os.path.join(interop_path, 'TileMetricsOut.bin')
summarize_tiles(tile_metrics_path, summary)
return summary
def upload_filter_quality(self, folder_watcher):
read_sizes = parse_read_sizes(folder_watcher.run_folder /
"RunInfo.xml")
read_lengths = [
read_sizes.read1, read_sizes.index1, read_sizes.index2,
read_sizes.read2
]
error_path = folder_watcher.run_folder / "InterOp/ErrorMetricsOut.bin"
quality_csv = StringIO()
with error_path.open('rb') as error_file:
records = error_metrics_parser.read_errors(error_file)
error_metrics_parser.write_phix_csv(quality_csv, records,
read_lengths)
quality_csv_bytes = BytesIO()
quality_csv_bytes.write(quality_csv.getvalue().encode('utf8'))
quality_csv_bytes.seek(0)
folder_watcher.quality_dataset = self.find_or_upload_dataset(
quality_csv_bytes, folder_watcher.run_name + '_quality.csv',
'Error rates for {} run.'.format(folder_watcher.run_name))
def upload_filter_quality(self, folder_watcher):
read_sizes = parse_read_sizes(folder_watcher.run_folder / "RunInfo.xml")
read_lengths = [read_sizes.read1,
read_sizes.index1,
read_sizes.index2,
read_sizes.read2]
error_path = folder_watcher.run_folder / "InterOp/ErrorMetricsOut.bin"
quality_csv = StringIO()
with error_path.open('rb') as error_file:
records = error_metrics_parser.read_errors(error_file)
error_metrics_parser.write_phix_csv(quality_csv,
records,
read_lengths)
quality_csv_bytes = BytesIO()
quality_csv_bytes.write(quality_csv.getvalue().encode('utf8'))
quality_csv_bytes.seek(0)
folder_watcher.quality_dataset = self.find_or_upload_dataset(
quality_csv_bytes,
folder_watcher.run_name + '_quality.csv',
'Error rates for {} run.'.format(folder_watcher.run_name))
def test_new_version(self):
self.sample_data[:2] = [4, 31]
self.sample_data.append(42)
self.sample_data.extend(self.sample_data[2:])
format_string = '<bbHHHfLLLLLbHHHfLLLLLb'
self.sample_stream = BytesIO(pack(format_string, *self.sample_data))
expected_records = [dict(lane=1,
tile=2,
cycle=3,
error_rate=0.5,
num_0_errors=4,
num_1_error=5,
num_2_errors=6,
num_3_errors=7,
num_4_errors=8)] * 2
records = list(read_errors(self.sample_stream))
self.maxDiff = 1000
self.assertEqual(expected_records, records)
def test_new_version(self):
self.sample_data[:2] = [4, 31]
self.sample_data.append(42)
self.sample_data.extend(self.sample_data[2:])
format_string = '<bbHHHfLLLLLbHHHfLLLLLb'
self.sample_stream = StringIO(pack(format_string, *self.sample_data))
expected_records = [
dict(lane=1,
tile=2,
cycle=3,
error_rate=0.5,
num_0_errors=4,
num_1_error=5,
num_2_errors=6,
num_3_errors=7,
num_4_errors=8)
] * 2
records = list(read_errors(self.sample_stream))
self.maxDiff = 1000
self.assertEqual(expected_records, records)
def summarize_run(args, json):
""" Summarize the run data from the InterOp folder.
Writes some summary files.
:return: a dictionary with summary values.
"""
read_lengths = [
json.read_length1, json.index_length1, json.index_length2,
json.read_length2
]
summary = {}
interop_path = os.path.join(args.data_path, 'input', 'runs', json.run_id,
'InterOp')
phix_path = os.path.join(interop_path, 'ErrorMetricsOut.bin')
quality_path = os.path.join(args.data_path, 'scratch', 'quality.csv')
bad_cycles_path = os.path.join(args.data_path, 'scratch', 'bad_cycles.csv')
summary_path = build_app_result_path(args.data_path,
json,
json.samples[0],
suffix='_QC')
makedirs(summary_path)
bad_tiles_path = os.path.join(summary_path, 'bad_tiles.csv')
with open(phix_path, 'rb') as phix, open(quality_path, 'w') as quality:
records = error_metrics_parser.read_errors(phix)
error_metrics_parser.write_phix_csv(quality, records, read_lengths,
summary)
with open(quality_path, 'rU') as quality, \
open(bad_cycles_path, 'w') as bad_cycles, \
open(bad_tiles_path, 'w') as bad_tiles:
report_bad_cycles(quality, bad_cycles, bad_tiles)
quality_metrics_path = os.path.join(interop_path, 'QMetricsOut.bin')
quality_metrics_parser.summarize_quality(quality_metrics_path, summary,
read_lengths)
tile_metrics_path = os.path.join(interop_path, 'TileMetricsOut.bin')
summarize_tiles(tile_metrics_path, summary)
return summary
def summarize_run(args, run_json):
""" Summarize the run data from the InterOp folder.
Writes some summary files.
:return: a dictionary with summary values.
"""
read_lengths = [
run_json.read_length1, run_json.index_length1, run_json.index_length2,
run_json.read_length2
]
summary = {}
has_error_metrics = run_json.has_runinfo
if has_error_metrics:
interop_path = os.path.join(args.data_path, 'input', 'runs',
run_json.run_id, 'InterOp')
phix_path = os.path.join(interop_path, 'ErrorMetricsOut.bin')
quality_path = os.path.join(args.data_path, 'scratch', 'quality.csv')
bad_cycles_path = os.path.join(args.data_path, 'scratch',
'bad_cycles.csv')
bad_tiles_path = os.path.join(args.qc_path, 'bad_tiles.csv')
with open(phix_path, 'rb') as phix, open(quality_path, 'w') as quality:
records = error_metrics_parser.read_errors(phix)
error_metrics_parser.write_phix_csv(quality, records, read_lengths,
summary)
with open(quality_path, 'r') as quality, \
open(bad_cycles_path, 'w') as bad_cycles, \
open(bad_tiles_path, 'w') as bad_tiles:
report_bad_cycles(quality, bad_cycles, bad_tiles)
quality_metrics_path = os.path.join(interop_path, 'QMetricsOut.bin')
quality_metrics_parser.summarize_quality(quality_metrics_path, summary,
read_lengths)
tile_metrics_path = os.path.join(interop_path, 'TileMetricsOut.bin')
summarize_tiles(tile_metrics_path, summary)
return summary
def summarize_run(run_info):
""" Summarize the run data from the InterOp folder.
Writes some summary files.
:param RunInfo run_info: details of the run
:return: a dictionary with summary values.
"""
summary = {}
if run_info.read_sizes is not None:
read_lengths = [run_info.read_sizes.read1,
run_info.read_sizes.index1,
run_info.read_sizes.index2,
run_info.read_sizes.read2]
phix_path = os.path.join(run_info.interop_path, 'ErrorMetricsOut.bin')
with open(phix_path, 'rb') as phix, \
open(run_info.quality_csv, 'w') as quality:
records = error_metrics_parser.read_errors(phix)
error_metrics_parser.write_phix_csv(quality,
records,
read_lengths,
summary)
with open(run_info.quality_csv) as quality, \
open(run_info.bad_cycles_csv, 'w') as bad_cycles, \
open(run_info.bad_tiles_csv, 'w') as bad_tiles:
report_bad_cycles(quality, bad_cycles, bad_tiles)
quality_metrics_path = os.path.join(run_info.interop_path,
'QMetricsOut.bin')
quality_metrics_parser.summarize_quality(quality_metrics_path,
summary,
read_lengths)
tile_metrics_path = os.path.join(run_info.interop_path,
'TileMetricsOut.bin')
summarize_tiles(tile_metrics_path, summary)
return summary
def summarize_run(run_info):
""" Summarize the run data from the InterOp folder.
Writes some summary files.
:param RunInfo run_info: details of the run
:return: a dictionary with summary values.
"""
summary = {}
if run_info.read_sizes is not None:
read_lengths = [run_info.read_sizes.read1,
run_info.read_sizes.index1,
run_info.read_sizes.index2,
run_info.read_sizes.read2]
phix_path = os.path.join(run_info.interop_path, 'ErrorMetricsOut.bin')
with open(phix_path, 'rb') as phix, \
open(run_info.quality_csv, 'w') as quality:
records = error_metrics_parser.read_errors(phix)
error_metrics_parser.write_phix_csv(quality,
records,
read_lengths,
summary)
with open(run_info.quality_csv) as quality, \
open(run_info.bad_cycles_csv, 'w') as bad_cycles, \
open(run_info.bad_tiles_csv, 'w') as bad_tiles:
report_bad_cycles(quality, bad_cycles, bad_tiles)
quality_metrics_path = os.path.join(run_info.interop_path,
'QMetricsOut.bin')
quality_metrics_parser.summarize_quality(quality_metrics_path,
summary,
read_lengths)
tile_metrics_path = os.path.join(run_info.interop_path,
'TileMetricsOut.bin')
summarize_tiles(tile_metrics_path, summary)
return summary