cool_seq_tool.app

Provides core CoolSeqTool class, which non-redundantly initializes all Cool-Seq-Tool data handler and mapping resources for straightforward access.

class cool_seq_tool.app.CoolSeqTool(transcript_file_path=TRANSCRIPT_MAPPINGS_PATH, lrg_refseqgene_path=LRG_REFSEQGENE_PATH, mane_data_path=MANE_SUMMARY_PATH, db_url=UTA_DB_URL, sr=None)

Non-redundantly initialize all Cool-Seq-Tool data resources, available under the following attribute names:

• self.seqrepo_access: SeqRepoAccess

• self.transcript_mappings: TranscriptMappings

• self.mane_transcript_mappings: ManeTranscriptMappings

• self.uta_db: UtaDatabase

• self.alignment_mapper: AlignmentMapper

• self.mane_transcript: ManeTranscript

• self.ex_g_coords_mapper: ExonGenomicCoordsMapper

Initialization with default resource locations is straightforward:

>>> from cool_seq_tool.app import CoolSeqTool
>>> cst = CoolSeqTool()

See the configuration section for more information.

__init__(transcript_file_path=TRANSCRIPT_MAPPINGS_PATH, lrg_refseqgene_path=LRG_REFSEQGENE_PATH, mane_data_path=MANE_SUMMARY_PATH, db_url=UTA_DB_URL, sr=None)

Initialize CoolSeqTool class

Parameters:

• transcript_file_path (Path) – The path to transcript_mapping.tsv

• lrg_refseqgene_path (Path) – The path to the LRG_RefSeqGene file

• mane_data_path (Path) – Path to RefSeq MANE summary data

• db_url (str) – PostgreSQL connection URL Format: driver://user:password@host/database/schema

• sr (Optional[SeqRepo]) – SeqRepo instance. If this is not provided, will create a new instance