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b/singlecellmultiomics/modularDemultiplexer/demultiplexModules/scartrace.py |
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from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import UmiBarcodeDemuxMethod, NonMultiplexable |
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# ScarTrace |
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class ScartraceR1(UmiBarcodeDemuxMethod): |
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def __init__(self, barcodeFileParser, **kwargs): |
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self.barcodeFileAlias = 'scartrace' |
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UmiBarcodeDemuxMethod.__init__( |
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self, |
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umiRead=0, |
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umiStart=0, |
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umiLength=0, |
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barcodeRead=0, |
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barcodeStart=0, |
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barcodeLength=8, |
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barcodeFileAlias=self.barcodeFileAlias, |
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barcodeFileParser=barcodeFileParser, |
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**kwargs) |
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self.shortName = 'SCARC8R1' |
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self.longName = 'Scartrace, CB: 8bp' |
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self.description = '384 well format. Scar amplicon demultiplexing, cell barcode in read 1' |
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self.autoDetectable = True |
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class ScartraceR2(UmiBarcodeDemuxMethod): |
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def __init__(self, barcodeFileParser, **kwargs): |
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self.barcodeFileAlias = 'scartrace' |
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UmiBarcodeDemuxMethod.__init__( |
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self, |
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umiRead=0, |
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umiStart=0, |
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umiLength=0, |
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barcodeRead=1, |
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barcodeStart=0, |
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barcodeLength=8, |
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barcodeFileAlias=self.barcodeFileAlias, |
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barcodeFileParser=barcodeFileParser, |
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**kwargs) |
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self.shortName = 'SCARC8R2' |
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self.longName = 'Scartrace, CB: 8bp' |
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self.description = '384 well format. Scar amplicon demultiplexing, cell barcode in read 2' |
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self.autoDetectable = True |
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def demultiplex(self, records, **kwargs): |
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if kwargs.get( |
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'probe') and not records[0].sequence.startswith('CCTTGAACTTCTGGTTGTAG'): |
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raise NonMultiplexable |
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taggedRecords = UmiBarcodeDemuxMethod.demultiplex( |
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self, records, **kwargs) |
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return taggedRecords |
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class ScartraceR2RP4(UmiBarcodeDemuxMethod): |
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def __init__(self, barcodeFileParser, **kwargs): |
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self.barcodeFileAlias = 'scartrace' |
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UmiBarcodeDemuxMethod.__init__( |
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self, |
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umiRead=0, |
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umiStart=0, |
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umiLength=0, |
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barcodeRead=1, |
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barcodeStart=0, |
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barcodeLength=8, |
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barcodeFileAlias=self.barcodeFileAlias, |
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barcodeFileParser=barcodeFileParser, |
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random_primer_end=False, |
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random_primer_read=0, |
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random_primer_length=4, |
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**kwargs) |
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self.shortName = 'SCARC8R2R4' |
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self.longName = 'Scartrace, CB: 8bp, with 4bp random sequence in read 1' |
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self.description = '384 well format. Scar amplicon demultiplexing, cell barcode in read , 4bp random sequence in R1' |
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self.autoDetectable = True |
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def demultiplex(self, records, **kwargs): |
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if kwargs.get( |
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'probe') and not records[0].sequence[4:].startswith('CCTTGAACTTCTGGTTGTAG'): |
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raise NonMultiplexable |
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taggedRecords = UmiBarcodeDemuxMethod.demultiplex( |
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self, records, **kwargs) |
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return taggedRecords |