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| author | Frederick Muriuki Muriithi | 2024-01-16 06:52:49 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-16 06:52:49 +0300 |
| commit | 0b8bd607645bf32e1713841e4c68dbc7ea60c0a2 (patch) | |
| tree | 484fde6110ec739bafd4befa7a72308f9f5e34b5 | |
| parent | fc27d0447c189bfd9222c7e8ccc14074cfd6adce (diff) | |
| download | gn-uploader-0b8bd607645bf32e1713841e4c68dbc7ea60c0a2.tar.gz | |
Filter out items with values of `None`.
The ProbeSetData table does not allow `NULL` for the `value` column
for good reason - if there is no value, just don't have a record for
that particular sample.
| -rw-r--r-- | scripts/rqtl2/install_phenos.py | 5 |
1 files changed, 3 insertions, 2 deletions
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py index 4fdf428..5c25866 100644 --- a/scripts/rqtl2/install_phenos.py +++ b/scripts/rqtl2/install_phenos.py @@ -54,12 +54,13 @@ def insert_probeset_data(dbconn: mdb.Connection, data = tuple( {**row, "psdid": lastid + idx} for idx, row in enumerate( - ({ + (item for item in ({ "sampleid": sampleids[innerrow["id"]], "value": innerrow[pheno], "pheno": pheno } for innerrow in phenos for pheno in - (key for key in innerrow.keys() if key != "id")), + (key for key in innerrow.keys() if key != "id")) + if item["value"] is not None), start=1)) cursor.executemany( "INSERT INTO ProbeSetData(Id, StrainId, value) " |