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 __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'maya_mspj1'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=3,
barcodeRead=0,
barcodeStart=3,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'MSPJIC8U3'
self.longName = 'MSPJI, CB: 8bp UMI: 3bp'
self.autoDetectable = True
self.description = 'MSPJI barcoded fragments. 3bp umi followed by 8bp cell barcode.'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'scartrace'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=0,
barcodeRead=0,
barcodeStart=0,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'SCARC8R1'
self.longName = 'Scartrace, CB: 8bp'
self.description = '384 well format. Scar amplicon demultiplexing, cell barcode in read 1'
self.autoDetectable = True
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 __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'lennart96NLA'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=3,
barcodeRead=0,
barcodeStart=3,
barcodeLength=8,
random_primer_read=None,
random_primer_length=None,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'NLAIII96C8U3SE'
self.longName = 'NLAIII, 96 well CB: 8bp UMI: 3bp RP:6bp, single ended'
self.autoDetectable = True
self.description = '96 well format. 3bp umi followed by 8bp barcode. Single end: R2 is missing'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'lennart96NLA'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=3,
random_primer_read=1,
random_primer_length=6,
barcodeRead=0,
barcodeStart=3,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'NLAIII96C8U3'
self.longName = 'NLAIII, 96well CB: 8bp UMI: 3bp RP: 6bp'
self.autoDetectable = True
self.description = '96 well format. 3bp umi followed by 8bp barcode. R2 starts with a 6bp random primer'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'celseq1'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=8,
umiLength=4,
barcodeRead=0,
barcodeStart=0,
barcodeLength=8,
random_primer_read=1,
random_primer_length=6,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'CS1C8U4'
self.longName = 'CELSeq 1, CB: 8bp, UMI: 4bp'
self.autoDetectable = True
self.description = 'R1 starts with a 8bp cell barcode followed by a 4bp UMI. R2 ends with a 6bp random primer'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'celseq2'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=1,
umiStart=0,
umiLength=8,
barcodeRead=1,
barcodeStart=8,
barcodeLength=8,
random_primer_read=0,
random_primer_length=6,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'CS2C8U8S'
self.longName = 'CELSeq 2, CB: 8bp, UMI: 8bp'
self.autoDetectable = True
self.description = 'R2 starts with a longer 8bp UMI followed by a 8bp cell barcode. R1 ends with a 6bp primer'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'celseq2'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=6,
barcodeRead=0,
barcodeStart=6,
barcodeLength=8,
random_primer_read=None,
random_primer_length=None,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'CS2C8U6NH'
self.longName = 'CELSeq 2, CB: 8bp, UMI: 6bp, NO random primer'
self.autoDetectable = False
self.description = 'R1 starts with a 6bp UMI followed by a 8bp cell barcode. R2 has no random primer. Use this demultiplexing method for VASA'
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'celseq2_noNla'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=8,
barcodeRead=0,
barcodeStart=8,
barcodeLength=8,
random_primer_read=1,
random_primer_length=6,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'CS2C8U8NNLA'
self.longName = 'CELSeq 2, CB: 8bp, UMI: 8bp, NLAIII free'
self.autoDetectable = True
self.description = 'CEL-Seq2 without NLAIII digestable barcodes '
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
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'scartrace'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=0,
barcodeRead=1,
barcodeStart=0,
barcodeLength=8,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
random_primer_end=False,
random_primer_read=0,
random_primer_length=4,
**kwargs)
self.shortName = 'SCARC8R2R4'
self.longName = 'Scartrace, CB: 8bp, with 4bp random sequence in read 1'
self.description = '384 well format. Scar amplicon demultiplexing, cell barcode in read , 4bp random sequence in R1'
self.autoDetectable = True
def __init__(self, barcodeFileParser, **kwargs):
self.barcodeFileAlias = 'maya_384NLA'
UmiBarcodeDemuxMethod.__init__(self,
umiRead=0,
umiStart=0,
umiLength=3,
barcodeRead=0,
barcodeStart=3,
barcodeLength=8,
random_primer_read=1,
random_primer_length=6,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.shortName = 'scCHIC384C8U3'
self.longName = 'Single cell CHIC, 384well CB: 8bp UMI: 3bp, RP: 6BP'
self.autoDetectable = True
self.description = '384 well format. 3bp umi followed by 8bp barcode and a single A. R2 ends with a 6bp random primer'
self.sequenceCapture[0] = slice(self.barcodeLength + self.umiLength +
1, None) # dont capture the first base
def __init__(self,
umiRead=0, umiStart=0, umiLength=8, # default settings UMI
barcodeRead=0, barcodeStart=8, barcodeLength=8, # default settings Barcode
enzymeRead=0, enzymeStart=16, enzymeLength=3, # default settings Enzyme ID
ispcrRead=0, ispcrStart=19, ispcrLength=15, # default settings ISPCR
ispcrSeq="CAGTGGTATCAGAGT",
barcodeFileParser=None, # compatible, no need to change
barcodeFileAlias=None, # passed from lower-level Classes, e.g. "reBS_nla384w"
indexFileParser=None, # compatible, no need to change
**kwargs): # additional arguments
self.description = 'base class for restriction bisulfite'
self.barcodeFileAlias = barcodeFileAlias # description , e.g. "maya_384NLA"
self.barcodeFileParser = barcodeFileParser # Namespace for barcode file parse
UmiBarcodeDemuxMethod.__init__(
self,
umiRead=umiRead,
umiStart=umiStart,
umiLength=umiLength,
barcodeRead=barcodeRead,
barcodeStart=barcodeStart,
barcodeLength=barcodeLength,
barcodeFileAlias=self.barcodeFileAlias,
barcodeFileParser=barcodeFileParser,
**kwargs)
self.barcodeSummary = self.barcodeFileAlias
self.umiRead = umiRead # 0:Read 1, 1: Read 2 etc
self.umiStart = umiStart # First base
self.umiLength = umiLength
self.shortName = 'RB'
self.longName = 'base class for restriction bisulfite'
self.illumina_mux = IlluminaBaseDemultiplexer(
indexFileParser=indexFileParser,
indexFileAlias='illumina_merged_ThruPlex48S_RP')
self.barcodeRead = barcodeRead
self.barcodeStart = barcodeStart
self.barcodeLength = barcodeLength
self.enzymeRead = enzymeRead
self.enzymeStart = enzymeStart
self.enzymeLength = enzymeLength
self.ispcrRead = ispcrRead
self.ispcrStart = ispcrStart
self.ispcrLength = ispcrLength
self.autoDetectable = False
self.sequenceCapture = [slice(None), slice(None)] # ranges
# TAKE OUT IF STATEMENT
if umiLength == 0:
# if there is a barcode only
if barcodeStart != 0:
raise NotImplementedError(
'Complicated slice where we need to capture around a region')
self.sequenceCapture[barcodeRead] = slice(barcodeLength, None)
else:
if umiRead != barcodeRead:
raise NotImplementedError()
if not(umiStart == 0 or barcodeStart == 0):
raise NotImplementedError(
'Complicated slice where we need to capture around a region')
self.sequenceCapture[barcodeRead] = slice(
barcodeLength + umiLength + enzymeLength + ispcrLength, None)