diff --git a/src/cool_seq_tool/resources/status.py b/src/cool_seq_tool/resources/status.py index d43455e..695ca8b 100644 --- a/src/cool_seq_tool/resources/status.py +++ b/src/cool_seq_tool/resources/status.py @@ -24,6 +24,7 @@ DataFile.TRANSCRIPT_MAPPINGS.lower(), DataFile.MANE_SUMMARY.lower(), DataFile.LRG_REFSEQGENE.lower(), + DataFile.MANE_REFSEQ_GENOMIC.lower(), "liftover", ), ) @@ -37,6 +38,7 @@ async def check_status( sr: SeqRepo | None = None, chain_file_37_to_38: str | None = None, chain_file_38_to_37: str | None = None, + mane_refseq_genomic_path: str | None = None, ) -> ResourceStatus: """Perform basic status checks on availability of required data resources. @@ -62,6 +64,7 @@ async def check_status( 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 + :param mane_refseq_genomic_path: Optional path to MANE RefSeq Genomic GFF data :return: boolean description of availability of each resource, given current environment configurations """ @@ -69,19 +72,21 @@ async def check_status( DataFile.TRANSCRIPT_MAPPINGS.lower(): transcript_file_path, DataFile.LRG_REFSEQGENE.lower(): lrg_refseqgene_path, DataFile.MANE_SUMMARY.lower(): mane_data_path, + DataFile.MANE_REFSEQ_GENOMIC.lower(): mane_refseq_genomic_path, } status = { DataFile.TRANSCRIPT_MAPPINGS.lower(): False, DataFile.LRG_REFSEQGENE.lower(): False, DataFile.MANE_SUMMARY.lower(): False, + DataFile.MANE_REFSEQ_GENOMIC.lower(): False, "liftover": False, "uta": False, "seqrepo": False, } for r in list(DataFile): name_lower = r.lower() - declared_path = file_path_params[name_lower] + declared_path = file_path_params.get(name_lower) if declared_path and declared_path.exists() and declared_path.is_file(): status[name_lower] = True continue