diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 6 | ||||
| -rw-r--r-- | gn3/db/partial_correlations.py | 18 |
2 files changed, 15 insertions, 9 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 1cc969c..3633a59 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -628,6 +628,12 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911] return { "status": "not-found", "message": "None of the requested control traits were found."} + for trait in cntrl_traits: + if trait["haveinfo"] == False: + warnings.warn( + (f"Control traits {trait['trait_fullname']} was not found " + "- continuing without it."), + category=UserWarning) group = primary_trait["db"]["group"] primary_trait_data = all_traits_data[primary_trait["trait_name"]] diff --git a/gn3/db/partial_correlations.py b/gn3/db/partial_correlations.py index 0931f09..0075cad 100644 --- a/gn3/db/partial_correlations.py +++ b/gn3/db/partial_correlations.py @@ -347,10 +347,11 @@ def probeset_traits_info( "probe_set_note_by_rw", "flag") query = ( "SELECT ProbeSet.Name AS trait_name, {columns} " - "FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef " - "WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " - "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id " - "AND ProbeSetFreeze.Name IN ({dataset_names}) " + "FROM ProbeSet INNER JOIN ProbeSetXRef " + "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id " + "INNER JOIN ProbeSetFreeze " + "ON ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId " + "WHERE ProbeSetFreeze.Name IN ({dataset_names}) " "AND ProbeSet.Name IN ({trait_names})").format( columns=", ".join(["ProbeSet.{}".format(x) for x in keys]), dataset_names=", ".join(["%s"] * len(dataset_names)), @@ -376,11 +377,10 @@ def geno_traits_info( "SELECT " "Geno.Name AS trait_name, {columns} " "FROM " - "Geno, GenoFreeze, GenoXRef " - "WHERE " - "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND " - "GenoFreeze.Name IN ({dataset_names}) AND " - "Geno.Name IN ({trait_names})").format( + "Geno INNER JOIN GenoXRef ON GenoXRef.GenoId = Geno.Id " + "INNER JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId " + "WHERE GenoFreeze.Name IN ({dataset_names}) " + "AND Geno.Name IN ({trait_names})").format( columns=", ".join(["Geno.{}".format(x) for x in keys]), dataset_names=", ".join(["%s"] * len(dataset_names)), trait_names=", ".join(["%s"] * len(traits))) |