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-rw-r--r--gn3/db/phenotypes.py59
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 = (