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b/singlecellmultiomics/modularDemultiplexer/demultiplexModules/NLAIII.py |
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from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import UmiBarcodeDemuxMethod, NonMultiplexable |
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# NLAIII, 96 well format with 3bp UMI |
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class NLAIII_96w_c8_u3(UmiBarcodeDemuxMethod): |
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def __init__(self, barcodeFileParser, **kwargs): |
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self.barcodeFileAlias = 'lennart96NLA' |
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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=3, |
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random_primer_read=1, |
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random_primer_length=6, |
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barcodeRead=0, |
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barcodeStart=3, |
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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 = 'NLAIII96C8U3' |
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self.longName = 'NLAIII, 96well CB: 8bp UMI: 3bp RP: 6bp' |
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self.autoDetectable = True |
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self.description = '96 well format. 3bp umi followed by 8bp barcode. R2 starts with a 6bp random primer' |
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# NLAIII, 384 well format with 3bp UMI |
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class NLAIII_384w_c8_u3(UmiBarcodeDemuxMethod): |
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def __init__(self, barcodeFileParser, **kwargs): |
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self.barcodeFileAlias = 'maya_384NLA' |
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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=3, |
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barcodeRead=0, |
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barcodeStart=3, |
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barcodeLength=8, |
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random_primer_read=1, |
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random_primer_length=6, |
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barcodeFileAlias=self.barcodeFileAlias, |
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barcodeFileParser=barcodeFileParser, |
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**kwargs) |
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self.shortName = 'NLAIII384C8U3' |
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self.longName = 'NLAIII, 384well CB: 8bp UMI: 3bp RP:6bp' |
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self.autoDetectable = True |
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self.description = '384 well format. 3bp umi followed by 8bp barcode. R2 starts with a 6bp random primer' |
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def demultiplex(self, records, **kwargs): |
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if kwargs.get('probe') and records[0].sequence[self.barcodeLength + \ |
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self.umiLength: self.barcodeLength + self.umiLength + 4] != 'CATG': |
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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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# NLAIII, 384 well format with 3bp UMI, single end, because? Why? Lets make ourselves unable to deduplicate IVT |
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class NLAIII_384w_c8_u3_SINGLE_END(UmiBarcodeDemuxMethod): |
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def __init__(self, barcodeFileParser, **kwargs): |
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self.barcodeFileAlias = 'maya_384NLA' |
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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=3, |
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barcodeRead=0, |
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barcodeStart=3, |
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barcodeLength=8, |
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random_primer_read=None, |
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random_primer_length=None, |
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barcodeFileAlias=self.barcodeFileAlias, |
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barcodeFileParser=barcodeFileParser, |
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**kwargs) |
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self.shortName = 'NLAIII384C8U3SE' |
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self.longName = 'NLAIII, 384well CB: 8bp UMI: 3bp RP:6bp, single ended' |
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self.autoDetectable = True |
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self.description = '384 well format. 3bp umi followed by 8bp barcode. Single end: R2 is sadly missing' |
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def demultiplex(self, records, **kwargs): |
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if kwargs.get('probe') and records[0].sequence[self.barcodeLength + \ |
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self.umiLength: self.barcodeLength + self.umiLength + 4] != 'CATG' or len(records)!=1: |
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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 NLAIII_96w_c8_u3_SINGLE_END(UmiBarcodeDemuxMethod): |
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def __init__(self, barcodeFileParser, **kwargs): |
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self.barcodeFileAlias = 'lennart96NLA' |
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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=3, |
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barcodeRead=0, |
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barcodeStart=3, |
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barcodeLength=8, |
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random_primer_read=None, |
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random_primer_length=None, |
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barcodeFileAlias=self.barcodeFileAlias, |
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barcodeFileParser=barcodeFileParser, |
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**kwargs) |
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self.shortName = 'NLAIII96C8U3SE' |
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self.longName = 'NLAIII, 96 well CB: 8bp UMI: 3bp RP:6bp, single ended' |
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self.autoDetectable = True |
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self.description = '96 well format. 3bp umi followed by 8bp barcode. Single end: R2 is missing' |
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def demultiplex(self, records, **kwargs): |
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if kwargs.get('probe') and records[0].sequence[self.barcodeLength + \ |
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self.umiLength: self.barcodeLength + self.umiLength + 4] != 'CATG' or len(records)!=1: |
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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 |