API Reference

Core Modules

cool_seq_tool.app	Provides core CoolSeqTool class, which non-redundantly initializes all Cool-Seq-Tool data handler and mapping resources for straightforward access.
cool_seq_tool.schemas	Defines attribute constants, useful object structures, and API response schemas.
cool_seq_tool.utils	Provide a small set of general helper functions.
cool_seq_tool.data.data_downloads	Handle acquisition of external data.

Data Sources

cool_seq_tool.sources.mane_transcript_mappings	Provide fast tabular access to MANE summary file.
cool_seq_tool.sources.transcript_mappings	Provide mappings between gene symbols and RefSeq + Ensembl transcript accessions.
cool_seq_tool.sources.uta_database	Provide transcript lookup and metadata tools via the UTA database.

Data Handlers

cool_seq_tool.handlers.seqrepo_access

Wrap SeqRepo to provide additional lookup and identification methods on top of basic dereferencing functions.

Data Mappers

cool_seq_tool.mappers.alignment	Module containing alignment methods for translating to and from different reference sequences.
cool_seq_tool.mappers.exon_genomic_coords	Provide mapping capabilities between transcript exon and genomic coordinates.
cool_seq_tool.mappers.mane_transcript	Retrieve MANE transcript from a location on p./c./g.