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| author | Frederick Muriuki Muriithi | 2024-01-10 07:16:55 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-10 08:02:51 +0300 |
| commit | 0d0b284a76bee863b97c46e8275cd62e02552a93 (patch) | |
| tree | 39206b15683a9a943add843dc262758cb495e1cd | |
| parent | dd50c620e77561b4b507ed8ed73b2fd5cdab31ef (diff) | |
| download | gn-uploader-0d0b284a76bee863b97c46e8275cd62e02552a93.tar.gz | |
Cross-reference genotype data to the dataset.
| -rw-r--r-- | scripts/rqtl2/install_genotypes.py | 15 |
1 files changed, 14 insertions, 1 deletions
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py index 63e6113..a555d46 100644 --- a/scripts/rqtl2/install_genotypes.py +++ b/scripts/rqtl2/install_genotypes.py @@ -106,6 +106,18 @@ def insert_genotype_data(dbconn: mdb.Connection, "markerid": row["markerid"] } for row in data) +def cross_reference_genotypes(dbconn: mdb.Connection, + datasetid: int, + dataids: tuple[int, ...]) -> int: + """Cross-reference the data to the relevant dataset.""" + with dbconn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "INSERT INTO GenoXRef(GenoFreezeId, GenoId, DataId) " + "VALUES(%(datasetid)s, %(markerid)s, %(dataid)s) " + "ON DUPLICATE KEY UPDATE GenoFreezeId=GenoFreezeId", + tuple({**row, "datasetid": datasetid} for row in dataids)) + return cursor.rowcount + def install_genotypes(dbconn: mdb.Connection, speciesid: int, populationid: int, @@ -141,8 +153,9 @@ def install_genotypes(dbconn: mdb.Connection, insert_individuals(dbconn, speciesid, individuals) cross_reference_individuals( dbconn, speciesid, populationid, individuals) - _num_rows, data_ids = insert_genotype_data( + _num_rows, dataids = insert_genotype_data( dbconn, speciesid, batch, individuals) + cross_reference_genotypes(dbconn, datasetid, dataids) count = count + len(batch) if "gmap" in cdata: |