singlecellmultiomics.modularDemultiplexer package

Submodules

singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods module

class singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.DemultiplexingStrategy[source]

Bases: object

demultiplex(records, **kwargs)[source]
getParserSummary()[source]
class singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.IlluminaBaseDemultiplexer(indexFileParser, indexFileAlias='illumina_merged_ThruPlex48S_RP', **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.DemultiplexingStrategy

demultiplex(records, inherited=False, library=None, reason=None, **kwargs)[source]
exception singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.NonMultiplexable[source]

Bases: Exception

class singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.TaggedRecord(tagDefinitions, rawRecord=False, library=None, reason=None, **kwargs)[source]

Bases: object

addTagByTag(tagName, value, isPhred=None, decodePhred=False, cast_type=<class 'str'>, make_safe=True)[source]
asFastq(sequence=None, dirAtt=None, baseQualities=None, format='illumina')[source]
asIlluminaHeader()[source]
fromRawFastq(fastqRecord, indexFileParser=None, indexFileAlias=None)[source]
fromTaggedBamRecord(pysamRecord)[source]
fromTaggedFastq(fastqRecord)[source]
has_tag(tag)[source]
tagPysamRead(read)[source]
class singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.UmiBarcodeDemuxMethod(umiRead=0, umiStart=0, umiLength=6, barcodeRead=0, barcodeStart=6, barcodeLength=8, barcodeFileParser=None, barcodeFileAlias=None, indexFileParser=None, indexFileAlias='illumina_merged_ThruPlex48S_RP', random_primer_read=None, random_primer_length=6, **kwargs)[source]

Bases: singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.IlluminaBaseDemultiplexer

demultiplex(records, **kwargs)[source]
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.fastqHeaderSafeQualitiesToPhred(phred, method=3)[source]
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.fqSafe(string)[source]
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.metaFromRead(read, tag)[source]
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.phredToFastqHeaderSafeQualities(asciiEncodedPhredScores, method=3)[source]

Convert ASCII encoded pred string to fastq safe string. numeric encoded string (method 0), or 65 shifted (method 1) which is safe to use in the fastq header

singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.reverseComplement(seq)[source]

singlecellmultiomics.modularDemultiplexer.demultiplexedFastqConversion module

singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader module

class singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.DemultiplexingStrategyLoader(barcodeParser, moduleSearchDir='demultiplexModules', indexParser=None, ignoreMethods=None, indexFileAlias=None)[source]

Bases: object

demultiplex(fastqfiles, maxReadPairs=None, strategies=None, library=None, targetFile=None, rejectHandle=None, log_handle=None, probe=None)[source]
detectLibYields(libraries, strategies=None, testReads=100000, maxAutoDetectMethods=1, minAutoDetectPct=5, verbose=False)[source]
getAutodetectStrategies()[source]
getDemultiplexingSelectedStrategies()[source]
getSelectedStrategiesFromStringList(strList, verbose=True)[source]
list()[source]
selectedStrategiesBasedOnYield(processedReadPairs, strategyYields, maxAutoDetectMethods=1, minAutoDetectPct=0.05)[source]
strategyYieldsToFormattedReport(processedReadPairs, strategyYields, selectedStrategies=None, maxAutoDetectMethods=1, minAutoDetectPct=5)[source]

singlecellmultiomics.modularDemultiplexer.demux module

Module contents