cool_seq_tool.resources.status#

Enable quick status check of Cool-Seq-Tool resources.

class cool_seq_tool.resources.status.ResourceStatus(uta, seqrepo, transcript_mappings, mane_summary, lrg_refseqgene, liftover)[source]#
liftover[source]#

Alias for field number 5

lrg_refseqgene[source]#

Alias for field number 4

mane_summary[source]#

Alias for field number 3

seqrepo[source]#

Alias for field number 1

transcript_mappings[source]#

Alias for field number 2

uta[source]#

Alias for field number 0

async cool_seq_tool.resources.status.check_status(transcript_file_path=None, lrg_refseqgene_path=None, mane_data_path=None, db_url=UTA_DB_URL, sr=None, chain_file_37_to_38=None, chain_file_38_to_37=None)[source]#

Perform basic status checks on availability of required data resources.

Arguments are intended to mirror arguments to cool_seq_tool.app.CoolSeqTool.__init__().

Additional arguments are available for testing paths to specific chainfiles (same signature as cool_seq_tool.mappers.liftover.LiftOver.__init__()).

>>> from cool_seq_tool.resources.status import check_status
>>> await check_status()
ResourceStatus(uta=True, seqrepo=True, transcript_mappings=True, mane_summary=True, lrg_refseqgene=True, liftover=True)
Parameters:

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

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

  • mane_data_path (Optional[Path]) – Path to RefSeq MANE summary data

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

  • chain_file_37_to_38 (Optional[str]) – Optional path to chain file for 37 to 38 assembly. This is used for agct. If this is not provided, will check to see if LIFTOVER_CHAIN_37_TO_38 env var is set. If neither is provided, will allow agct to download a chain file from UCSC

  • chain_file_38_to_37 (Optional[str]) – Optional path to chain file for 38 to 37 assembly. This is used for agct. If this is not provided, will check to see if LIFTOVER_CHAIN_38_TO_37 env var is set. If neither is provided, will allow agct to download a chain file from UCSC

Return type:

ResourceStatus

Returns:

boolean description of availability of each resource, given current environment configurations