diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/sample_data.py | 25 |
1 files changed, 25 insertions, 0 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index 4062705..d8232cb 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -57,6 +57,31 @@ def __extract_actions( ) return result +def get_trait_sample_data( + conn: Any, trait_name: int, phenotype_id: int +) -> str: + """Fetch a trait's sample data and return it as a dict""" + with conn.cursor() as cursor: + cursor.execute(""" +SELECT st.Name, ifnull(pd.value, 'x'), ifnull(ps.error, 'x'), ifnull(ns.count, 'x') +FROM PublishFreeze pf JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId + JOIN PublishData pd ON pd.Id = px.DataId JOIN Strain st ON pd.StrainId = st.Id + LEFT JOIN PublishSE ps ON ps.DataId = pd.Id AND ps.StrainId = pd.StrainId + LEFT JOIN NStrain ns ON ns.DataId = pd.Id AND ns.StrainId = pd.StrainId + AND px.Id = %s AND px.PhenotypeId = %s +ORDER BY st.Name""", (trait_name, phenotype_id)) + + sample_data = {} + for data in cursor.fetchall(): + this_data = {} + sample, value, error, n_cases = data + sample_data[sample] = { + 'value': value, + 'error': error, + 'n_cases:': n_cases + } + + return sample_data def get_trait_csv_sample_data( conn: Any, trait_name: int, phenotype_id: int |