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-rw-r--r--wqflask/wqflask/do_search.py80
1 files changed, 40 insertions, 40 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 364a3eed..115182e4 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -32,7 +32,7 @@ class DoSearch:
self.search_type = search_type
if self.dataset:
- #Get group information for dataset and the species id
+ # Get group information for dataset and the species id
self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def execute(self, query):
@@ -137,7 +137,7 @@ class MrnaAssaySearch(DoSearch):
return where_clause
- def compile_final_query(self, from_clause = '', where_clause = ''):
+ def compile_final_query(self, from_clause='', where_clause=''):
"""Generates the final query string"""
from_clause = self.normalize_spaces(from_clause)
@@ -153,7 +153,7 @@ class MrnaAssaySearch(DoSearch):
escape(str(self.dataset.id))))
return query
- def run_combined(self, from_clause = '', where_clause = ''):
+ def run_combined(self, from_clause='', where_clause=''):
"""Generates and runs a combined search of an mRNA expression dataset"""
logger.debug("Running ProbeSetSearch")
@@ -218,10 +218,10 @@ class PhenotypeSearch(DoSearch):
def get_where_clause(self):
"""Generate clause for WHERE portion of query"""
- #Todo: Zach will figure out exactly what both these lines mean
- #and comment here
+ # Todo: Zach will figure out exactly what both these lines mean
+ # and comment here
- #if "'" not in self.search_term[0]:
+ # if "'" not in self.search_term[0]:
search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]"
if "_" in self.search_term[0]:
if len(self.search_term[0].split("_")[0]) == 3:
@@ -236,7 +236,7 @@ class PhenotypeSearch(DoSearch):
return where_clause
- def compile_final_query(self, from_clause = '', where_clause = ''):
+ def compile_final_query(self, from_clause='', where_clause=''):
"""Generates the final query string"""
from_clause = self.normalize_spaces(from_clause)
@@ -292,7 +292,7 @@ class PhenotypeSearch(DoSearch):
def run(self):
"""Generates and runs a simple search of a phenotype dataset"""
- query = self.compile_final_query(where_clause = self.get_where_clause())
+ query = self.compile_final_query(where_clause=self.get_where_clause())
return self.execute(query)
@@ -334,7 +334,7 @@ class GenotypeSearch(DoSearch):
return where_clause
- def compile_final_query(self, from_clause = '', where_clause = ''):
+ def compile_final_query(self, from_clause='', where_clause=''):
"""Generates the final query string"""
from_clause = self.normalize_spaces(from_clause)
@@ -344,26 +344,26 @@ class GenotypeSearch(DoSearch):
query = (self.base_query +
"""WHERE Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
- and GenoFreeze.Id = %s"""% (escape(str(self.dataset.id))))
+ and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id))))
else:
query = (self.base_query +
"""WHERE %s
and Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
- and GenoFreeze.Id = %s"""% (where_clause,
+ and GenoFreeze.Id = %s""" % (where_clause,
escape(str(self.dataset.id))))
return query
def run(self):
"""Generates and runs a simple search of a genotype dataset"""
- #Todo: Zach will figure out exactly what both these lines mean
- #and comment here
+ # Todo: Zach will figure out exactly what both these lines mean
+ # and comment here
if self.search_term[0] == "*":
self.query = self.compile_final_query()
else:
- self.query = self.compile_final_query(where_clause = self.get_where_clause())
+ self.query = self.compile_final_query(where_clause=self.get_where_clause())
return self.execute(self.query)
@@ -393,7 +393,7 @@ class RifSearch(MrnaAssaySearch):
class WikiSearch(MrnaAssaySearch):
"""Searches GeneWiki for traits other people have annotated"""
- DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch"
+ DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch"
def get_from_clause(self):
return ", GeneRIF "
@@ -403,7 +403,7 @@ class WikiSearch(MrnaAssaySearch):
and GeneRIF.versionId=0 and GeneRIF.display>0
and (GeneRIF.comment REGEXP '%s' or GeneRIF.initial = '%s')
""" % (self.dataset.type,
- "[[:<:]]"+str(self.search_term[0])+"[[:>:]]",
+ "[[:<:]]" + str(self.search_term[0]) + "[[:>:]]",
str(self.search_term[0]))
return where_clause
@@ -418,7 +418,7 @@ class WikiSearch(MrnaAssaySearch):
class GoSearch(MrnaAssaySearch):
"""Searches for synapse-associated genes listed in the Gene Ontology."""
- DoSearch.search_types['ProbeSet_GO'] = "GoSearch"
+ DoSearch.search_types['ProbeSet_GO'] = "GoSearch"
def get_from_clause(self):
from_clause = """, db_GeneOntology.term as GOterm,
@@ -429,7 +429,7 @@ class GoSearch(MrnaAssaySearch):
def get_where_clause(self):
field = 'GOterm.acc'
- go_id = 'GO:' + ('0000000'+self.search_term[0])[-7:]
+ go_id = 'GO:' + ('0000000' + self.search_term[0])[-7:]
statements = ("""%s.symbol=GOgene_product.symbol and
GOassociation.gene_product_id=GOgene_product.id and
@@ -448,7 +448,7 @@ class GoSearch(MrnaAssaySearch):
return self.execute(query)
-#ZS: Not sure what the best way to deal with LRS searches is
+# ZS: Not sure what the best way to deal with LRS searches is
class LrsSearch(DoSearch):
"""Searches for genes with a QTL within the given LRS values
@@ -486,8 +486,8 @@ class LrsSearch(DoSearch):
assert isinstance(self.search_term, (list, tuple))
lrs_min, lrs_max = self.search_term[:2]
if self.search_type == "LOD":
- lrs_min = lrs_min*4.61
- lrs_max = lrs_max*4.61
+ lrs_min = lrs_min * 4.61
+ lrs_max = lrs_max * 4.61
where_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s """ % self.mescape(self.dataset.type,
@@ -496,7 +496,7 @@ class LrsSearch(DoSearch):
max(lrs_min, lrs_max))
if len(self.search_term) > 2:
- #If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats
+ # If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats
chr_num = self.search_term[2]
if "chr" in self.search_term[2].lower():
chr_num = self.search_term[2].lower().replace("chr", "")
@@ -518,7 +518,7 @@ class LrsSearch(DoSearch):
logger.debug("self.search_term is:", self.search_term)
lrs_val = self.search_term[0]
if self.search_type == "LOD":
- lrs_val = lrs_val*4.61
+ lrs_val = lrs_val * 4.61
where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
@@ -546,7 +546,7 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause)
+ self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -560,7 +560,7 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause)
+ self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -599,7 +599,7 @@ class CisTransLrsSearch(DoSearch):
lrs_max = lrs_max * 4.61
sub_clause = """ %sXRef.LRS > %s and
- %sXRef.LRS < %s and """ % (
+ %sXRef.LRS < %s and """ % (
escape(self.dataset.type),
escape(str(min(lrs_min, lrs_max))),
escape(self.dataset.type),
@@ -607,7 +607,7 @@ class CisTransLrsSearch(DoSearch):
)
else:
# Deal with >, <, >=, and <=
- sub_clause = """ %sXRef.LRS %s %s and """ % (
+ sub_clause = """ %sXRef.LRS %s %s and """ % (
escape(self.dataset.type),
escape(self.search_operator),
escape(self.search_term[0])
@@ -667,7 +667,7 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
for search_key in ('LRS', 'LOD'):
- DoSearch.search_types['ProbeSet_CIS'+search_key] = "CisLrsSearch"
+ DoSearch.search_types['ProbeSet_CIS' + search_key] = "CisLrsSearch"
def get_where_clause(self):
return CisTransLrsSearch.get_where_clause(self, "cis")
@@ -697,7 +697,7 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
for search_key in ('LRS', 'LOD'):
- DoSearch.search_types['ProbeSet_TRANS'+search_key] = "TransLrsSearch"
+ DoSearch.search_types['ProbeSet_TRANS' + search_key] = "TransLrsSearch"
def get_where_clause(self):
return CisTransLrsSearch.get_where_clause(self, "trans")
@@ -740,7 +740,7 @@ class MeanSearch(MrnaAssaySearch):
self.where_clause = self.get_where_clause()
logger.debug("where_clause is:", pf(self.where_clause))
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -775,7 +775,7 @@ class RangeSearch(MrnaAssaySearch):
def run(self):
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -815,7 +815,7 @@ class PositionSearch(DoSearch):
def run(self):
self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -823,12 +823,12 @@ class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
"""Searches for genes located within a specified range on a specified chromosome"""
for search_key in ('POSITION', 'POS', 'MB'):
- DoSearch.search_types['ProbeSet_'+search_key] = "MrnaPositionSearch"
+ DoSearch.search_types['ProbeSet_' + search_key] = "MrnaPositionSearch"
def run(self):
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -836,12 +836,12 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch):
"""Searches for genes located within a specified range on a specified chromosome"""
for search_key in ('POSITION', 'POS', 'MB'):
- DoSearch.search_types['Geno_'+search_key] = "GenotypePositionSearch"
+ DoSearch.search_types['Geno_' + search_key] = "GenotypePositionSearch"
def run(self):
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -873,7 +873,7 @@ class PvalueSearch(MrnaAssaySearch):
logger.debug("where_clause is:", pf(self.where_clause))
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
logger.sql(self.query)
return self.execute(self.query)
@@ -888,7 +888,7 @@ class AuthorSearch(PhenotypeSearch):
self.where_clause = """ Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" and
""" % (self.search_term[0])
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -924,8 +924,8 @@ def get_aliases(symbol, species):
return filtered_aliases
if __name__ == "__main__":
- ### Usually this will be used as a library, but call it from the command line for testing
- ### And it runs the code below
+ # Usually this will be used as a library, but call it from the command line for testing
+ # And it runs the code below
import MySQLdb
import sys
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 04:52:44 +0000