gunz_cm package

Subpackages

Submodules

gunz_cm.consts module

Defines shared constants, enumerations, and data structures for the library.

This module centralizes common values used throughout the application, including DataFrame column names, data types, supported file formats, and standard genomic build information. Using this module ensures consistency and simplifies maintenance.

Examples

class gunz_cm.consts.Backend(value)[source]

Bases: BaseStrEnum

Enumeration for interaction matrix loader backends.

Examples

COOLER = 'cooler'
HICSTRAW = 'hicstraw'
HICTK = 'hictk'
STRAW = 'straw'
class gunz_cm.consts.Balancing(value)[source]

Bases: BaseStrEnum

Enumeration for matrix balancing (normalization) methods.

Examples

KR = 'KR'
NONE = 'NONE'
VC = 'VC'
VC_SQRT = 'VC_SQRT'
class gunz_cm.consts.BpFrag(value)[source]

Bases: BaseStrEnum

Enumeration for binning units (Base Pairs vs. Fragments).

Examples

BP = 'BP'
FRAG = 'FRAG'
class gunz_cm.consts.Counts(value)[source]

Bases: BaseStrEnum

Enumeration for different types of interaction counts.

Examples

EXPECTED = 'expected'
OBSERVED = 'observed'
OE = 'oe'
gunz_cm.consts.DS

alias of DataStructure

class gunz_cm.consts.DataStructure(value)[source]

Bases: BaseStrEnum

Enumeration for in-memory data representations.

Examples

COO = 'coo'
DF = 'df'
RC = 'rc'
RCV = 'rcv'
class gunz_cm.consts.Format(value)[source]

Bases: BaseStrEnum

Enumeration for supported file formats.

Uses BaseStrEnum for case-insensitivity and aliases.

Examples

COO = 'coo'
COOLER = 'cooler'
CSV = 'csv'
GINTERACTIONS = 'ginteractions'
HIC = 'hic'
MCOO = 'mcoo'
MCSV = 'mcsv'
MEMMAP = 'npdat'
NPY = 'npy'
PICKLE = 'pickle'
TSV = 'tsv'
class gunz_cm.consts.GenomeBuild(value)[source]

Bases: BaseStrEnum

Enumeration for standard genome builds.

Examples

HG19 = 'hg19'
HG38 = 'hg38'
MM10 = 'mm10'
MM9 = 'mm9'

gunz_cm.exceptions module

Custom exception classes for the gunz_cm package.

Examples

exception gunz_cm.exceptions.ConversionFailedError(region: str, message: str = 'Conversion failed')[source]

Bases: ConverterError

Exception raised when a conversion process fails.

regionstr

The region string for which the conversion failed.

messagestr, optional

A custom error message (default is “Conversion failed”).

Examples

exception gunz_cm.exceptions.ConverterError[source]

Bases: GunzCMError

Base class for exceptions in the converters module.

Examples

exception gunz_cm.exceptions.DataResolutionError[source]

Bases: LoaderError

Exception raised when there’s an issue with data resolution.

Examples

exception gunz_cm.exceptions.DatasetError[source]

Bases: GunzCMError

Base class for exceptions in the datasets module.

Examples

exception gunz_cm.exceptions.FormatError[source]

Bases: LoaderError

Exception raised for format-related errors.

Examples

exception gunz_cm.exceptions.GunzCMError[source]

Bases: Exception

Base class for all custom exceptions in the gunz_cm package.

Examples

exception gunz_cm.exceptions.IOError[source]

Bases: GunzCMError

Base class for exceptions related to input/output operations.

Examples

exception gunz_cm.exceptions.InvalidRegionFormatError(region: str, message: str = 'Invalid region format')[source]

Bases: LoaderError

Exception raised for errors in the input region format.

regionstr

The invalid region string that caused the error.

messagestr, optional

A custom error message (default is “Invalid region format”).

Examples

exception gunz_cm.exceptions.LoaderError[source]

Bases: GunzCMError

Base class for exceptions in the loaders module.

Examples

exception gunz_cm.exceptions.MetricError[source]

Bases: GunzCMError

Base class for exceptions in the metrics module.

Examples

exception gunz_cm.exceptions.PreprocError[source]

Bases: GunzCMError

Base class for exceptions in the preprocs module.

Examples

exception gunz_cm.exceptions.ReconstructionError[source]

Bases: GunzCMError

Base class for exceptions in the reconstructions module.

Examples

exception gunz_cm.exceptions.UnsupportedLoaderFeatureError(feature: str, loader_name: str)[source]

Bases: LoaderError

Exception raised when a loader does not support a requested feature.

featurestr

The name of the unsupported feature.

loader_namestr

The name of the loader that does not support the feature.

Examples

gunz_cm.matrix module

Module contents