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)[source]#
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)[source]#
Initialize CoolSeqTool class
- Parameters:
transcript_file_path (
Path
) – The path totranscript_mapping.tsv
lrg_refseqgene_path (
Path
) – The path to the LRG_RefSeqGene filemane_data_path (
Path
) – Path to RefSeq MANE summary datadb_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