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authorBonfaceKilz2021-07-09 16:50:28 +0300
committerBonfaceKilz2021-07-10 09:09:00 +0300
commitd5c0cdec01ce1888946d09c0df72ea42ad2d2c17 (patch)
tree57c0b82e817edf6ccdd6ba65b3e55201186b7849 /gn3
parentd6715cff2e5a1771b22bb2ce7680347cad501841 (diff)
downloadgenenetwork3-d5c0cdec01ce1888946d09c0df72ea42ad2d2c17.tar.gz
db: phenotypes: Add Probeset data structures
* gn3/db/phenotypes.py (Probeset): New dataclass. (probeset_mapping): New dict. * gn3/db/__init__.py: Add probeset_mapping and Probeset.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/db/__init__.py15
-rw-r--r--gn3/db/phenotypes.py59
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"
+}