cool_seq_tool.mappers.feature_overlap#

Module for getting feature (gene/exon) overlap

class cool_seq_tool.mappers.feature_overlap.FeatureOverlap(seqrepo_access, mane_refseq_genomic_path=None, from_local=False)[source]#

The class for getting feature overlap

__init__(seqrepo_access, mane_refseq_genomic_path=None, from_local=False)[source]#

Initialize the FeatureOverlap class. Will load RefSeq data and store as df.

Parameters:

  • seqrepo_access (SeqRepoAccess) – Client for accessing SeqRepo data

  • mane_refseq_genomic_path (Optional[Path]) – Path to MANE RefSeq Genomic GFF data

  • from_local (bool) – if True, don’t check for or acquire latest version – just provide most recent locally available file, if possible, and raise error otherwise

get_grch38_mane_gene_cds_overlap(start, end, chromosome=None, identifier=None, coordinate_type=CoordinateType.RESIDUE)[source]#

Given GRCh38 genomic data, find the overlapping MANE features (gene and cds). The genomic data is specified as a sequence location by chromosome, start, end. All CDS regions with which the input sequence location has nonzero base pair overlap will be returned.

Parameters:

  • start (int) – GRCh38 start position

  • end (int) – GRCh38 end position

  • chromosome (Optional[str]) – Chromosome. 1..22, X, or Y. If not provided, must provide identifier. If both chromosome and identifier are provided, chromosome will be used.

  • identifier (Optional[str]) – Genomic identifier on GRCh38 assembly. If not provided, must provide chromosome. If both chromosome and identifier are provided, chromosome will be used.

  • coordinate_type (CoordinateType) – Coordinate type for start and end

Raises:

FeatureOverlapError – If missing required fields or unable to find associated ga4gh identifier

Return type:

Optional[dict[str, list[CdsOverlap]]]

Returns:

MANE feature (gene/cds) overlap data represented as a dict. The dictionary will be keyed by genes which overlap the input sequence location. Each gene contains a list of the overlapping CDS regions with the beginning and end of the input sequence location’s overlap with each

exception cool_seq_tool.mappers.feature_overlap.FeatureOverlapError[source]#

Custom exception for the Feature Overlap class