diff options
Diffstat (limited to 'gn2/base/trait.py')
| -rw-r--r-- | gn2/base/trait.py | 31 |
1 files changed, 31 insertions, 0 deletions
diff --git a/gn2/base/trait.py b/gn2/base/trait.py index 701958d7..24288ba1 100644 --- a/gn2/base/trait.py +++ b/gn2/base/trait.py @@ -611,3 +611,34 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): f"{repr(trait.name)} information is not found in the database " f"for dataset '{dataset.name}' with id '{dataset.id}'.") return trait + +def fetch_symbols(trait_db_list): + """ + Fetch list of trait symbols + + From a list of traits and datasets (where each item has + the trait and dataset name separated by a colon), return + + """ + + trimmed_trait_list = [trait_db for trait_db in trait_db_list + if 'Publish' not in trait_db and 'Geno' not in trait_db.split(":")[1]] + + symbol_list = [] + with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: + for trait_db in trimmed_trait_list: + symbol_query = """ + SELECT ps.Symbol + FROM ProbeSet as ps + INNER JOIN ProbeSetXRef psx ON psx.ProbeSetId = ps.Id + INNER JOIN ProbeSetFreeze psf ON psx.ProbeSetFreezeId = psf.Id + WHERE + ps.Name = %(trait_name)s AND + psf.Name = %(db_name)s + """ + + cursor.execute(symbol_query, {'trait_name': trait_db.split(":")[0], + 'db_name': trait_db.split(":")[1]}) + symbol_list.append(cursor.fetchone()[0]) + + return "+".join(symbol_list)
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