def __init__(self,sample_sheet_file):
"""
Create a new SampleSheetBarcodes instance
Arguments:
sample_sheet_file (str): path of a SampleSheet.csv
file
"""
self._sample_sheet = SampleSheet(sample_sheet_file)
self._sample_lookup = {}
self._barcode_lookup = {}
self._lanes = []
sample_id = self._sample_sheet.sample_id_column
for line in self._sample_sheet.data:
if self._sample_sheet.has_lanes:
lane = line['Lane']
else:
lane = None
if lane not in self._lanes:
self._lanes.append(lane)
self._sample_lookup[lane] = {}
self._barcode_lookup[lane] = {}
sample = line[sample_id]
index_seq = normalise_barcode(samplesheet_index_sequence(line))
self._sample_lookup[lane][index_seq] = sample
self._barcode_lookup[lane][sample] = index_seq
def count_barcode(self,barcode,lane=None,incr=1):
"""
Increment count of a barcode sequence
Arguments:
barcode (str): barcode sequence to count
lane (int): lane that the barcode appears
in (None if unknown)
incr (int): increment the count for the
barcode in the lane by this amount
(defaults to 1)
"""
# Normalise barcode
barcode = normalise_barcode(barcode)
# Store by lane
try:
self._seqs[lane][barcode] += incr
except KeyError:
try:
self._seqs[lane][barcode] = incr
except KeyError:
self._seqs[lane] = { barcode: incr }
# Store overall
try:
self._seqs_all[barcode] += incr
except KeyError:
self._seqs_all[barcode] = incr
def __init__(self,sample_sheet_file):
"""
Create a new SampleSheetBarcodes instance
Arguments:
sample_sheet_file (str): path of a SampleSheet.csv
file
"""
self._sample_sheet = SampleSheet(sample_sheet_file)
self._sample_lookup = {}
self._barcode_lookup = {}
self._lanes = []
sample_id = self._sample_sheet.sample_id_column
for line in self._sample_sheet.data:
if self._sample_sheet.has_lanes:
lane = line['Lane']
else:
lane = None
if lane not in self._lanes:
self._lanes.append(lane)
self._sample_lookup[lane] = {}
self._barcode_lookup[lane] = {}
sample = line[sample_id]
index_seq = normalise_barcode(samplesheet_index_sequence(line))
self._sample_lookup[lane][index_seq] = sample
self._barcode_lookup[lane][sample] = index_seq
def count_barcode(self,barcode,lane=None,incr=1):
"""
Increment count of a barcode sequence
Arguments:
barcode (str): barcode sequence to count
lane (int): lane that the barcode appears
in (None if unknown)
incr (int): increment the count for the
barcode in the lane by this amount
(defaults to 1)
"""
# Normalise barcode
barcode = normalise_barcode(barcode)
# Store by lane
try:
self._seqs[lane][barcode] += incr
except KeyError:
try:
self._seqs[lane][barcode] = incr
except KeyError:
self._seqs[lane] = { barcode: incr }
# Store overall
try:
self._seqs_all[barcode] += incr
except KeyError:
self._seqs_all[barcode] = incr
def barcode_lengths(self, lane=None):
"""
Return lengths of barcode sequences
Returns a list of the barcode sequence lengths.
Arguments:
lane (int): if specified then restricts the
list to barcodes that appear in the named
lane (default is to get lengths from all
barcodes in all lanes)
"""
lengths = set()
for barcode in self.barcodes(lane=lane):
lengths.add(len(normalise_barcode(barcode)))
return sorted(list(lengths))