def test_3DEC_UmiBarcodeDemuxMethod_matching_barcode(self):
barcode_folder = pkg_resources.resource_filename('singlecellmultiomics','modularDemultiplexer/barcodes/')
barcode_parser = BarcodeParser(barcode_folder)
r1 = FastqRecord(
'@Cluster_s_1_1101_1000',
'ATCACACACTATAGTCATTCAGGAGCAGGTTCTTCAGGTTCCCTGTAGTTGTGTGGTTTTGAGTGAGTTTTTTAAT',
'+',
'AAAAA#EEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEE/EEEEEEEEEEEEEEEEEE'
)
r2 = FastqRecord(
'@Cluster_s_1_1101_1002',
'ACCCCAGATCAACGTTGGACNTCNNCNTTNTNCTCNGCACCNNNNCNNNCTTATNCNNNANNNNNNNNNNTNNGN',
'+',
'6AAAAEEAEE/AEEEEEEEE#EE##<#6E#A#EEE#EAEEA####A###EE6EE#E###E##########E##A#'
)
demux = UmiBarcodeDemuxMethod(umiRead=0,
umiStart=0,
umiLength=3,
barcodeRead=0,
barcodeStart=3,
barcodeLength=8,
barcodeFileParser=barcode_parser,
barcodeFileAlias='maya_384NLA',
indexFileParser=None,
indexFileAlias='illumina_merged_ThruPlex48S_RP',
random_primer_read=None,
random_primer_length=6)
demultiplexed_record = demux.demultiplex([r1,r2])
# The barcode sequence is ACACACTA (first barcode)
self.assertEqual( demultiplexed_record[0].tags['BC'], 'ACACACTA')
self.assertEqual( demultiplexed_record[0].tags['bi'], 1)
def demultiplex(self, records, **kwargs):
if kwargs.get('probe') and records[0].sequence[self.barcodeLength +
self.umiLength] != 'T':
raise NonMultiplexable
# add first 2 bases as ligation tag:
ligation_start = self.barcodeLength + self.umiLength
ligation_end = ligation_start + 2
ligation_sequence = records[0].sequence[ligation_start:ligation_end]
ligation_qualities = records[0].qual[ligation_start:ligation_end]
taggedRecords = UmiBarcodeDemuxMethod.demultiplex(
self, records, **kwargs)
taggedRecords[0].addTagByTag('lh',
ligation_sequence,
isPhred=False,
make_safe=False)
taggedRecords[0].addTagByTag('lq',
ligation_qualities,
isPhred=True,
make_safe=False)
taggedRecords[1].addTagByTag('lh',
ligation_sequence,
isPhred=False,
make_safe=False)
taggedRecords[1].addTagByTag('lq',
ligation_qualities,
isPhred=True,
make_safe=False)
#taggedRecords[0].sequence = taggedRecords[0].sequence[1:]
#taggedRecords[0].qualities = taggedRecords[0].qualities[1:]
return taggedRecords
def demultiplex(self, records, **kwargs):
if kwargs.get('probe') and records[0].sequence[self.barcodeLength + \
self.umiLength: self.barcodeLength + self.umiLength + 4] != 'CATG':
raise NonMultiplexable
taggedRecords = UmiBarcodeDemuxMethod.demultiplex(
self, records, **kwargs)
return taggedRecords
def demultiplex(self, records, **kwargs):
if kwargs.get('probe') and not records[0].sequence[4:].startswith(
'CCTTGAACTTCTGGTTGTAG'):
raise NonMultiplexable
taggedRecords = UmiBarcodeDemuxMethod.demultiplex(
self, records, **kwargs)
return taggedRecords