diff options
| -rw-r--r-- | gn3/db/__init__.py | 15 | ||||
| -rw-r--r-- | gn3/db/phenotypes.py | 59 |
2 files changed, 69 insertions, 5 deletions
diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py index 34a0236..9b1b36a 100644 --- a/gn3/db/__init__.py +++ b/gn3/db/__init__.py @@ -6,27 +6,32 @@ from typing_extensions import Protocol from gn3.db.metadata_audit import MetadataAudit from gn3.db.phenotypes import Phenotype -from gn3.db.phenotypes import PublishXRef +from gn3.db.phenotypes import Probeset from gn3.db.phenotypes import Publication +from gn3.db.phenotypes import PublishXRef + from gn3.db.metadata_audit import metadata_audit_mapping from gn3.db.phenotypes import phenotype_mapping +from gn3.db.phenotypes import probeset_mapping from gn3.db.phenotypes import publication_mapping from gn3.db.phenotypes import publish_x_ref_mapping TABLEMAP = { - "metadata_audit": metadata_audit_mapping, "Phenotype": phenotype_mapping, - "PublishXRef": publish_x_ref_mapping, + "ProbeSet": probeset_mapping, "Publication": publication_mapping, + "PublishXRef": publish_x_ref_mapping, + "metadata_audit": metadata_audit_mapping, } DATACLASSMAP = { - "metadata_audit": MetadataAudit, "Phenotype": Phenotype, - "PublishXRef": PublishXRef, + "ProbeSet": Probeset, "Publication": Publication, + "PublishXRef": PublishXRef, + "metadata_audit": MetadataAudit, } diff --git a/gn3/db/phenotypes.py b/gn3/db/phenotypes.py index 2b93c85..147cbf3 100644 --- a/gn3/db/phenotypes.py +++ b/gn3/db/phenotypes.py @@ -99,3 +99,62 @@ publication_mapping = { "month": "Month", "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 + 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" +} |