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, mane_refseq_genomic, liftover)[source]#

liftover[source]#: Alias for field number 6

lrg_refseqgene[source]#: Alias for field number 4

mane_refseq_genomic[source]#: Alias for field number 5

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, mane_refseq_genomic_path=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
mane_refseq_genomic_path (Optional[str]) – Optional path to MANE RefSeq Genomic GFF data

Return type:

ResourceStatus

Returns:

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