`ngs_tools.chemistry.SpatialChemistry`

Module Contents

Classes

`SpatialResolution`	Typed version of namedtuple.
`SpatialChemistry`	Extends `Chemistry` to be able to handle spatial chemistries.
`SpatialSequencingChemistry`	Extends `SequencingChemistry` to be able to handle common spatial chemistries.

Attributes

`_SLIDESEQ_V2`
`_VISIUM`
`_STEREOSEQ`
`_COSMX`
`_SEQSCOPE_HDMI_DRAI`
`_SEQSCOPE_HDMI32_DRA1`
`_STARMAP`
`_SEQFISH`
`_MERFISH`
`_SEQUENCING_SPATIAL_CHEMISTRIES`
`_INSITU_SPATIAL_CHEMISTRIES`
`SPATIAL_CHEMISTRIES`

class ngs_tools.chemistry.SpatialChemistry.SpatialResolution

Bases: NamedTuple

Typed version of namedtuple.

Usage in Python versions >= 3.6:

class Employee(NamedTuple):
    name: str
    id: int

This is equivalent to:

Employee = collections.namedtuple('Employee', ['name', 'id'])

The resulting class has extra __annotations__ and _field_types attributes, giving an ordered dict mapping field names to types. __annotations__ should be preferred, while _field_types is kept to maintain pre PEP 526 compatibility. (The field names are in the _fields attribute, which is part of the namedtuple API.) Alternative equivalent keyword syntax is also accepted:

Employee = NamedTuple('Employee', name=str, id=int)

In Python versions <= 3.5 use:

Employee = NamedTuple('Employee', [('name', str), ('id', int)])

scale: float = 1.0

unit: Optional[typing_extensions.Literal[nm, um, mm]]

exception ngs_tools.chemistry.SpatialChemistry.SpatialChemistryError

Bases: Exception

Common base class for all non-exit exceptions.

class ngs_tools.chemistry.SpatialChemistry.SpatialChemistry(resolution: SpatialResolution, *args, **kwargs)

Bases: ngs_tools.chemistry.Chemistry.Chemistry

Extends Chemistry to be able to handle spatial chemistries.

property resolution: SpatialResolution: Get the spatial resolution as a SpatialResolution object.

class ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry(name: str, description: str, resolution: SpatialResolution, n: int, strand: ngs_tools.chemistry.Chemistry.SequencingStrand, cdna_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser, spot_barcode_parser: Optional[ngs_tools.chemistry.Chemistry.SubSequenceParser] = None, umi_parser: Optional[ngs_tools.chemistry.Chemistry.SubSequenceParser] = None, whitelist_path: Optional[str] = None)

Bases: SpatialChemistry, ngs_tools.chemistry.Chemistry.SequencingChemistry

Extends SequencingChemistry to be able to handle common spatial chemistries.

property spot_barcode_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser: Get the spot barcode parser

property barcode_parser: ngs_tools.chemistry.Chemistry.SubSequenceParser: Get the spot 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_spot_barcode: bool: Whether the chemistry has a spot barcode

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

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

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

property whitelist_path: Optional[str]: Path to the whitelist. None if it does not exist.

ngs_tools.chemistry.SpatialChemistry._SLIDESEQ_V2

ngs_tools.chemistry.SpatialChemistry._VISIUM

ngs_tools.chemistry.SpatialChemistry._STEREOSEQ

ngs_tools.chemistry.SpatialChemistry._COSMX

ngs_tools.chemistry.SpatialChemistry._SEQSCOPE_HDMI_DRAI

ngs_tools.chemistry.SpatialChemistry._SEQSCOPE_HDMI32_DRA1

ngs_tools.chemistry.SpatialChemistry._STARMAP

ngs_tools.chemistry.SpatialChemistry._SEQFISH

ngs_tools.chemistry.SpatialChemistry._MERFISH

ngs_tools.chemistry.SpatialChemistry._SEQUENCING_SPATIAL_CHEMISTRIES

ngs_tools.chemistry.SpatialChemistry._INSITU_SPATIAL_CHEMISTRIES

ngs_tools.chemistry.SpatialChemistry.SPATIAL_CHEMISTRIES

ngs_tools.chemistry.SpatialChemistry

Module Contents

Classes

Attributes

`ngs_tools.chemistry.SpatialChemistry`