Core Types API

This module contains the core enumerations and basic data models used throughout SeqNado.

seqnado.core

Assay

Bases: Enum

Supported sequencing assay types.

clean_name property

clean_name

Return a short name for the assay.

all_assays classmethod

all_assays()

Return all supported assays.

Source code in seqnado/core.py

@classmethod
def all_assays(cls):
    """Return all supported assays."""
    return list(cls)

from_clean_name classmethod

from_clean_name(clean_name)

Return the assay type from a short name.

Source code in seqnado/core.py

@classmethod
def from_clean_name(cls, clean_name):
    """Return the assay type from a short name."""
    for assay in cls:
        if assay.clean_name == clean_name:
            return assay
    raise ValueError(f"Unknown clean name: {clean_name}")

all_assay_clean_names classmethod

all_assay_clean_names()

Return a list of all clean names for assays.

Source code in seqnado/core.py

@classmethod
def all_assay_clean_names(cls):
    """Return a list of all clean names for assays."""
    return [assay.clean_name for assay in cls]

non_multiomics_assays classmethod

non_multiomics_assays()

Return assays that are not multiomics.

Source code in seqnado/core.py

@classmethod
def non_multiomics_assays(cls):
    """Return assays that are not multiomics."""
    return [assay for assay in cls if assay != cls.MULTIOMICS]

non_ip_assays classmethod

non_ip_assays()

Return assays that don't require IP (immunoprecipitation).

Source code in seqnado/core.py

@classmethod
def non_ip_assays(cls):
    """Return assays that don't require IP (immunoprecipitation)."""
    ip_assays = {cls.CHIP, cls.CAT}
    return [assay for assay in cls if assay not in ip_assays]

ip_assays classmethod

ip_assays()

Return assays that require IP (immunoprecipitation).

Source code in seqnado/core.py

@classmethod
def ip_assays(cls):
    """Return assays that require IP (immunoprecipitation)."""
    return [cls.CHIP, cls.CAT]

FileType

Bases: Enum

Supported file types.

PileupMethod

Bases: Enum

Methods for creating pileup files.

DataScalingTechnique

Bases: Enum

Methods for scaling genomic data.

PeakCallingMethod

Bases: Enum

Methods for calling peaks.

MotifMethod

Bases: Enum

Methods for motif analysis.

PCRDuplicateHandling

Bases: Enum

Methods for handling PCR duplicates.

SpikeInMethod

Bases: Enum

Methods for spike-in normalization.

SNPCallingMethod

Bases: Enum

Methods for SNP calling.

QuantificationMethod

Bases: Enum

Methods for quantification.

MethylationMethod

Bases: Enum

Methods for methylation calling.

Organism

Bases: Enum

Supported organisms.

LibraryType

Bases: Enum

Supported library types.

GenomicCoordinate

Bases: BaseModel

Configuration for genomic coordinates.

from_string classmethod

from_string(coord_str: str) -> GenomicCoordinate

Create a GenomicCoordinate instance from a string representation.

Source code in seqnado/core.py

@classmethod
def from_string(cls, coord_str: str) -> "GenomicCoordinate":
    """
    Create a GenomicCoordinate instance from a string representation.
    """
    chromosome, positions = coord_str.split(":")
    start, end = map(int, positions.split("-"))
    return cls(chromosome=chromosome, start=start, end=end)

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