diff options
Diffstat (limited to 'gn3/db/traits.py')
| -rw-r--r-- | gn3/db/traits.py | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 6c31a4d..fb48fc3 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -43,6 +43,7 @@ def update_sample_data(conn: Any, count: Union[int, str]): """Given the right parameters, update sample-data from the relevant table.""" + # pylint: disable=[R0913, R0914] STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s" PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s " "WHERE StrainId = %s AND Id = %s") @@ -252,6 +253,9 @@ def set_homologene_id_field(trait_type, trait_info, conn): return functions_table[trait_type](trait_info) def load_publish_qtl_info(trait_info, conn): + """ + Load extra QTL information for `Publish` traits + """ query = ( "SELECT PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive " "FROM PublishXRef, PublishFreeze " @@ -264,6 +268,9 @@ def load_publish_qtl_info(trait_info, conn): return {"locus": "", "lrs": "", "additive": ""} def load_probeset_qtl_info(trait_info, conn): + """ + Load extra QTL information for `ProbeSet` traits + """ query = ( "SELECT ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, " "ProbeSetXRef.mean, ProbeSetXRef.additive " @@ -278,6 +285,22 @@ def load_probeset_qtl_info(trait_info, conn): return {"locus": "", "lrs": "", "pvalue": "", "mean": "", "additive": ""} def load_qtl_info(qtl, trait_type, trait_info, conn): + """ + Load extra QTL information for traits + + DESCRIPTION: + Migrated from + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L500-L534 + + PARAMETERS: + qtl: boolean + trait_type: string + The type of the trait in consideration + trait_info: map/dictionary + A dictionary of the trait's key-value pairs + conn: + A database connection object + """ if not qtl: return trait_info qtl_info_functions = { @@ -290,6 +313,9 @@ def load_qtl_info(qtl, trait_type, trait_info, conn): return qtl_info_functions[trait_type](trait_info, conn) def build_trait_name(trait_fullname): + """ + Initialises the trait's name, and other values from the search data provided + """ name_parts = trait_fullname.split("::") assert len(name_parts) >= 2, "Name format error" return { @@ -300,6 +326,9 @@ def build_trait_name(trait_fullname): } def retrieve_probeset_sequence(trait, conn): + """ + Retrieve a 'ProbeSet' trait's sequence information + """ query = ( "SELECT ProbeSet.BlatSeq " "FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef " |