def test_lane_barcode_valid_case(self):
path = os.path.dirname(os.path.abspath(__file__))
parsed_lane_barcodes = classes.LaneBarcodeParser(
os.path.join(
path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/Demultiplexing/',
'Reports/html/H2WY7CCXX/all/all/all/laneBarcode.html'))
expected_flowcell_data = {
u'Yield (MBases)': u'939,600',
u'Clusters(PF)': u'3,111,257,766',
u'Clusters (Raw)': u'4,966,525,440'
}
expected_sample_data = [{
u'Sample': u'56.64',
u'Lane': u'1',
u'#': u'GAATTCGT',
u'Filtered data': u'P1775_147',
u'Project': u'351,637,396',
u'Raw data': u'D_Moreno_15_01',
u'Clusters': u'106,194',
u'Barcode sequence': u'351,637,396'
}, {
u'Sample': u'43.36',
u'Lane': u'1',
u'#': u'unknown',
u'Filtered data': u'unknown',
u'Project': u'269,178,284',
u'Raw data': u'default',
u'Clusters': u'13,232',
u'Barcode sequence': u'43,813,954'
}]
assert parsed_lane_barcodes.flowcell_data == expected_flowcell_data
assert parsed_lane_barcodes.sample_data == expected_sample_data
def test_lane():
path = os.path.dirname(os.path.abspath(__file__))
k = classes.LaneBarcodeParser(
os.path.join(
path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/Demultiplexing/Reports/html/H2WY7CCXX/all/all/all/laneBarcode.html'
))
assert (k.sample_data is not None)
def test_lane_valid_case(self):
path = os.path.dirname(os.path.abspath(__file__))
parsed_lane = classes.LaneBarcodeParser(os.path.join(
path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/Demultiplexing/',
'Reports/html/H2WY7CCXX/all/all/all/lane.html'))
expected_sample_data = [{u'Yield (Mbases)': u'37.75',
u'Lane': u'1',
u'% One mismatchbarcode': u'63.70',
u'% Perfectbarcode': u'119,426',
u'#': u'95.00',
u'Filtered data': u'100.00',
u'Raw data': u'620,815,680',
u'Clusters': u'88.69',
u'% of thelane': u'395,451,350'}]
self.assertEqual(parsed_lane.sample_data, expected_sample_data)
def write_demuxfile(proc_stats, demux_id):
#Includes windows drive letter support
datafolder = "{}_data".format(proc_stats["Instrument"])
lanebc_path = os.path.join(os.sep, "srv", "mfs", datafolder,
proc_stats["Run ID"], "laneBarcode.html")
try:
laneBC = classes.LaneBarcodeParser(lanebc_path)
except Exception as e:
problem_handler(
"exit", "Unable to fetch laneBarcode.html from {}: {}".format(
lanebc_path, str(e)))
fname = "{}_demuxstats_{}.csv".format(demux_id, proc_stats["Flow Cell ID"])
#Writes less undetermined info than undemultiplex_index.py. May cause problems downstreams
with open(fname, "w") as csvfile:
writer = csv.writer(csvfile)
writer.writerow([
"Project", "Sample ID", "Lane", "# Reads", "Index", "Index name",
"% of >= Q30 Bases (PF)"
])
for entry in laneBC.sample_data:
index_name = ""
if "PF Clusters" in entry:
reads = entry["PF Clusters"]
else:
reads = entry["Clusters"]
if proc_stats["Paired"]:
reads = int(reads.replace(",", "")) * 2
else:
reads = int(reads.replace(",", ""))
try:
writer.writerow([entry["Project"],entry["Sample"],entry["Lane"],reads, \
entry["Barcode sequence"],index_name,entry["% >= Q30bases"]])
except Exception as e:
problem_handler(
"exit",
"Flowcell parser is unable to fetch all necessary fields for demux file: {}"
.format(str(e)))
return laneBC.sample_data