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authorMuriithi Frederick Muriuki2021-08-09 11:44:47 +0300
committerMuriithi Frederick Muriuki2021-08-09 11:44:47 +0300
commit667e67bae832ca5083f3319ada4fda67aca41f44 (patch)
treec733219f180fbe4448baee80b3ced13176518182 /gn3/db/traits.py
parent4bc516beea37b0cc0a54f42d93cf5606f073abbf (diff)
downloadgenenetwork3-667e67bae832ca5083f3319ada4fda67aca41f44.tar.gz
Fix linting errors
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * Add module, class and function docstrings * Deactivate some irrelevant pylint errors * Fix indentations and line-lengths
Diffstat (limited to 'gn3/db/traits.py')
-rw-r--r--gn3/db/traits.py29
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 "