singlecellmultiomics.modularDemultiplexer package¶
Subpackages¶
- singlecellmultiomics.modularDemultiplexer.demultiplexModules package
- Submodules
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.BULK_ILLUMINA module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq1 module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.CELSeq2 module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.Hexamer module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.MSPJI module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.NLAIII module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.restrictionbisulfite module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.scCHIC module
- singlecellmultiomics.modularDemultiplexer.demultiplexModules.scartrace module
- Module contents
Submodules¶
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods module¶
-
class
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.
DemultiplexingStrategy
[source]¶ Bases:
object
-
class
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.
IlluminaBaseDemultiplexer
(indexFileParser, indexFileAlias='illumina_merged_ThruPlex48S_RP', **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.DemultiplexingStrategy
-
exception
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.
NonMultiplexable
[source]¶ Bases:
Exception
-
class
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.
TaggedRecord
(tagDefinitions, rawRecord=False, library=None, reason=None, **kwargs)[source]¶ Bases:
object
-
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, random_primer_end=False, **kwargs)[source]¶ Bases:
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.IlluminaBaseDemultiplexer
-
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.
fastqHeaderSafeQualitiesToPhred
(phred, method=3)[source]¶
-
singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods.
fqSafe
(string) → str[source]¶ Convert input string into a representation which can be stored in a fastq header
- Input:
- string(str) : string to clean
Returns: cleaned(str)
singlecellmultiomics.modularDemultiplexer.demultiplexedFastqConversion module¶
singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader module¶
-
class
singlecellmultiomics.modularDemultiplexer.demultiplexingStrategyLoader.
DemultiplexingStrategyLoader
(barcodeParser, moduleSearchDir='demultiplexModules', indexParser=None, ignoreMethods=None, only_detect_methods=None, indexFileAlias=None)[source]¶ Bases:
object
-
demultiplex
(fastqfiles, maxReadPairs=None, strategies=None, library=None, targetFile=None, rejectHandle=None, log_handle=None, probe=None)[source]¶
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detectLibYields
(libraries, strategies=None, testReads=100000, maxAutoDetectMethods=1, minAutoDetectPct=5, verbose=False)[source]¶
-