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Diffstat (limited to 'gn3/db/phenotypes.py')
-rw-r--r-- | gn3/db/phenotypes.py | 59 |
1 files changed, 0 insertions, 59 deletions
diff --git a/gn3/db/phenotypes.py b/gn3/db/phenotypes.py index 605ca73..e8b0b0b 100644 --- a/gn3/db/phenotypes.py +++ b/gn3/db/phenotypes.py @@ -105,65 +105,6 @@ publication_mapping = { "year": "Year", } - -@dataclass(frozen=True) -class Probeset: - """Data Type that represents a Probeset""" - id_: Optional[int] = None - name: Optional[str] = None - symbol: Optional[str] = None - description: Optional[str] = None - probe_target_description: Optional[str] = None - chr_: Optional[str] = None - mb: Optional[float] = None # pylint: disable=C0103 - alias: Optional[str] = None - geneid: Optional[str] = None - homologeneid: Optional[str] = None - unigeneid: Optional[str] = None - omim: Optional[str] = None - refseq_transcriptid: Optional[str] = None - blatseq: Optional[str] = None - targetseq: Optional[str] = None - strand_probe: Optional[str] = None - probe_set_target_region: Optional[str] = None - probe_set_specificity: Optional[float] = None - probe_set_blat_score: Optional[float] = None - probe_set_blat_mb_start: Optional[float] = None - probe_set_blat_mb_end: Optional[float] = None - probe_set_strand: Optional[str] = None - probe_set_note_by_rw: Optional[str] = None - flag: Optional[str] = None - - -# Mapping from the Phenotype dataclass to the actual column names in the -# database -probeset_mapping = { - "id_": "Id", - "name": "Name", - "symbol": "symbol", - "description": "description", - "probe_target_description": "Probe_Target_Description", - "chr_": "Chr", - "mb": "Mb", - "alias": "alias", - "geneid": "GeneId", - "homologeneid": "HomoloGeneID", - "unigeneid": "UniGeneId", - "omim": "OMIM", - "refseq_transcriptid": "RefSeq_TranscriptId", - "blatseq": "BlatSeq", - "targetseq": "TargetSeq", - "strand_probe": "Strand_Probe", - "probe_set_target_region": "Probe_set_target_region", - "probe_set_specificity": "Probe_set_specificity", - "probe_set_blat_score": "Probe_set_BLAT_score", - "probe_set_blat_mb_start": "Probe_set_Blat_Mb_start", - "probe_set_blat_mb_end": "Probe_set_Blat_Mb_end", - "probe_set_strand": "Probe_set_strand", - "probe_set_note_by_rw": "Probe_set_Note_by_RW", - "flag": "flag" -} - def fetch_trait(conn: DBConnection, dataset_id: int, trait_name: str) -> dict: """Fetch phenotype 'traits' by `dataset_id` and `trait_name`.""" query = ( |