`ngs_tools.chemistry.SingleCellChemistry`

Module Contents

Classes

SingleCellChemistry

Extends SequencingChemistry to be able to handle common single-cell

Attributes

`_10X_V1`
`_10X_V2`
`_10X_V3`
`_10X_V3_ULTIMA`
`_10X_FB`
`_10X_ATAC`
`_DROPSEQ`
`_CELSEQ_V1`
`_CELSEQ_V2`
`_INDROPS_V1`
`_INDROPS_V2`
`_INDROPS_V3`
`_SCRBSEQ`
`_SURECELL`
`_SMARTSEQ_V2`
`_SMARTSEQ_V3`
`_STORMSEQ`
`_SCI_FATE`
`_BDWTA`
`_SPLITSEQ`
`_PLATE_SINGLE_CELL_CHEMISTRIES`
`_DROPLET_SINGLE_CELL_CHEMISTRIES`
`_OTHER_SINGLE_CELL_CHEMISTRIES`
`SINGLE_CELL_CHEMISTRIES`

exception ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistryError

Bases: Exception

Common base class for all non-exit exceptions.

class ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry(name: str, description: str, n: int, strand: ngs_tools.chemistry.Chemistry.SequencingStrand, cdna_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser, cell_barcode_parser: Optional[ngs_tools.chemistry.Chemistry.SubSequenceParser] = None, umi_parser: Optional[ngs_tools.chemistry.Chemistry.SubSequenceParser] = None, whitelist_path: Optional[str] = None)

Bases: ngs_tools.chemistry.Chemistry.SequencingChemistry

Extends SequencingChemistry to be able to handle common single-cell chemistries.

property cell_barcode_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser: Get the cell barcode parser

property barcode_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser: Get the cell barcode parser

property umi_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser: Get the UMI parser

property cdna_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser: Get the cDNA parser

property has_cell_barcode: bool: Whether the chemistry has a cell barcode

property has_barcode: bool: Whether the chemistry has a cell barcode

property has_umi: bool: Whether the chemistry has a UMI

property has_whitelist: bool: Whether the chemistry has a fixed predefined cell barcode whitelist

property whitelist_path: str: Path to the whitelist

ngs_tools.chemistry.SingleCellChemistry._10X_V1

ngs_tools.chemistry.SingleCellChemistry._10X_V2

ngs_tools.chemistry.SingleCellChemistry._10X_V3

ngs_tools.chemistry.SingleCellChemistry._10X_V3_ULTIMA

ngs_tools.chemistry.SingleCellChemistry._10X_FB

ngs_tools.chemistry.SingleCellChemistry._10X_ATAC

ngs_tools.chemistry.SingleCellChemistry._DROPSEQ

ngs_tools.chemistry.SingleCellChemistry._CELSEQ_V1

ngs_tools.chemistry.SingleCellChemistry._CELSEQ_V2

ngs_tools.chemistry.SingleCellChemistry._INDROPS_V1

ngs_tools.chemistry.SingleCellChemistry._INDROPS_V2

ngs_tools.chemistry.SingleCellChemistry._INDROPS_V3

ngs_tools.chemistry.SingleCellChemistry._SCRBSEQ

ngs_tools.chemistry.SingleCellChemistry._SURECELL

ngs_tools.chemistry.SingleCellChemistry._SMARTSEQ_V2

ngs_tools.chemistry.SingleCellChemistry._SMARTSEQ_V3

ngs_tools.chemistry.SingleCellChemistry._STORMSEQ

ngs_tools.chemistry.SingleCellChemistry._SCI_FATE

ngs_tools.chemistry.SingleCellChemistry._BDWTA

ngs_tools.chemistry.SingleCellChemistry._SPLITSEQ

ngs_tools.chemistry.SingleCellChemistry._PLATE_SINGLE_CELL_CHEMISTRIES

ngs_tools.chemistry.SingleCellChemistry._DROPLET_SINGLE_CELL_CHEMISTRIES

ngs_tools.chemistry.SingleCellChemistry._OTHER_SINGLE_CELL_CHEMISTRIES

ngs_tools.chemistry.SingleCellChemistry.SINGLE_CELL_CHEMISTRIES

ngs_tools.chemistry.SingleCellChemistry

Module Contents

Classes

Attributes

`ngs_tools.chemistry.SingleCellChemistry`