diff options
| -rw-r--r-- | gn3/db/correlations.py | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py index d94759a..06b3310 100644 --- a/gn3/db/correlations.py +++ b/gn3/db/correlations.py @@ -339,3 +339,43 @@ def fetch_tissue_correlations(# pylint: disable=R0913 return { trait_name: (tiss_corr, tiss_p_val) for trait_name, tiss_corr, tiss_p_val in results} + +def check_for_literature_info(conn: Any, geneid: int) -> bool: + """ + Checks the database to find out whether the trait with `geneid` has any + associated literature. + + This is a migration of the + `web.webqtl.correlation.CorrelationPage.checkForLitInfo` function in + GeneNetwork1. + """ + query = "SELECT 1 FROM LCorrRamin3 WHERE GeneId1=%s LIMIT 1" + with conn.cursor() as cursor: + cursor.execute(query, geneid) + result = cursor.fetchone() + if result: + return True + + return False + +def check_symbol_for_tissue_correlation( + conn: Any, tissue_probeset_freeze_id: int, symbol: str = "") -> bool: + """ + Checks whether a symbol has any associated tissue correlations. + + This is a migration of the + `web.webqtl.correlation.CorrelationPage.checkSymbolForTissueCorr` function + in GeneNetwork1. + """ + query = ( + "SELECT 1 FROM TissueProbeSetXRef " + "WHERE TissueProbeSetFreezeId=%(probeset_freeze_id)s " + "AND Symbol=%(symbol)s LIMIT 1") + with conn.cursor() as cursor: + cursor.execute( + query, probeset_freeze_id=tissue_probeset_freeze_id, symbol=symbol) + result = cursor.fetchone() + if result: + return True + + return False |