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-rw-r--r--wqflask/wqflask/do_search.py153
1 files changed, 118 insertions, 35 deletions
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index c7dbc972..b0ca5ced 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -1,6 +1,8 @@
from __future__ import print_function, division
import string
+import requests
+import json
from flask import Flask, g
@@ -11,6 +13,7 @@ import sys
# sys.path.append("..") Never in a running webserver
from db import webqtlDatabaseFunction
+from utility.tools import GN2_BASE_URL
import logging
from utility.logger import getLogger
@@ -22,17 +25,19 @@ class DoSearch(object):
# Used to translate search phrases into classes
search_types = dict()
- def __init__(self, search_term, search_operator=None, dataset=None):
+ def __init__(self, search_term, search_operator=None, dataset=None, search_type=None):
self.search_term = search_term
# Make sure search_operator is something we expect
assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator"
self.search_operator = search_operator
self.dataset = dataset
+ self.search_type = search_type
if self.dataset:
logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
logger.debug("self.dataset.group is: ", pf(self.dataset.group))
#Get group information for dataset and the species id
+
self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def execute(self, query):
@@ -44,8 +49,8 @@ class DoSearch(object):
def handle_wildcard(self, str):
keyword = str.strip()
- keyword.replace("*",".*")
- keyword.replace("?",".")
+ keyword = keyword.replace("*",".*")
+ keyword = keyword.replace("?",".")
return keyword
@@ -69,7 +74,7 @@ class DoSearch(object):
logger.debug("search_types are:", pf(cls.search_types))
search_type_string = search_type['dataset_type']
- if 'key' in search_type:
+ if 'key' in search_type and search_type['key'] != None:
search_type_string += '_' + search_type['key']
logger.debug("search_type_string is:", search_type_string)
@@ -105,18 +110,34 @@ class MrnaAssaySearch(DoSearch):
'Max LRS Location',
'Additive Effect']
+ def get_alias_where_clause(self):
+ search_string = escape(self.search_term[0])
+
+ if self.search_term[0] != "*":
+ match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (search_string)
+ else:
+ match_clause = ""
+
+ where_clause = (match_clause +
+ """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ and ProbeSetXRef.ProbeSetFreezeId = %s
+ """ % (escape(str(self.dataset.id))))
+
+ return where_clause
+
def get_where_clause(self):
+ search_string = escape(self.search_term[0])
if self.search_term[0] != "*":
- match_clause = """(MATCH (ProbeSet.Name,
+ match_clause = """((MATCH (ProbeSet.Name,
ProbeSet.description,
ProbeSet.symbol,
alias,
GenbankId,
UniGeneId,
Probe_Target_Description)
- AGAINST ('%s' IN BOOLEAN MODE)) and
- """ % (escape(self.search_term[0]))
+ AGAINST ('%s' IN BOOLEAN MODE))) AND
+ """ % (search_string)
else:
match_clause = ""
@@ -198,6 +219,7 @@ class PhenotypeSearch(DoSearch):
header_fields = ['Index',
'Record',
'Description',
+ 'Mean',
'Authors',
'Year',
'Max LRS',
@@ -209,8 +231,12 @@ class PhenotypeSearch(DoSearch):
#Todo: Zach will figure out exactly what both these lines mean
#and comment here
- if "'" not in self.search_term[0]:
- search_term = "[[:<:]]" + self.handle_wildcard(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:
+ search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0].split("_")[1]) + "[[:>:]]"
# This adds a clause to the query that matches the search term
# against each field in the search_fields tuple
@@ -232,7 +258,8 @@ class PhenotypeSearch(DoSearch):
WHERE PublishXRef.InbredSetId = %s
and PublishXRef.PhenotypeId = Phenotype.Id
and PublishXRef.PublicationId = Publication.Id
- and PublishFreeze.Id = %s""" % (
+ and PublishFreeze.Id = %s
+ ORDER BY PublishXRef.Id""" % (
from_clause,
escape(str(self.dataset.group.id)),
escape(str(self.dataset.id))))
@@ -243,7 +270,8 @@ class PhenotypeSearch(DoSearch):
and PublishXRef.InbredSetId = %s
and PublishXRef.PhenotypeId = Phenotype.Id
and PublishXRef.PublicationId = Publication.Id
- and PublishFreeze.Id = %s""" % (
+ and PublishFreeze.Id = %s
+ ORDER BY PublishXRef.Id""" % (
from_clause,
where_clause,
escape(str(self.dataset.group.id)),
@@ -444,15 +472,18 @@ class LrsSearch(DoSearch):
"""
- DoSearch.search_types['LRS'] = 'LrsSearch'
+ for search_key in ('LRS', 'LOD'):
+ DoSearch.search_types[search_key] = "LrsSearch"
def get_from_clause(self):
- #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 len(self.search_term) > 2 and "Chr" in self.search_term[2]:
- chr_num = self.search_term[2].replace("Chr", "")
- self.search_term[2] = chr_num
+ converted_search_term = []
+ for value in self.search_term:
+ try:
+ converted_search_term.append(float(value))
+ except:
+ converted_search_term.append(value)
- self.search_term = [float(value) for value in self.search_term]
+ self.search_term = converted_search_term
if len(self.search_term) > 2:
from_clause = ", Geno"
@@ -465,6 +496,9 @@ class LrsSearch(DoSearch):
if self.search_operator == "=":
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
where_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s """ % self.mescape(self.dataset.type,
@@ -473,8 +507,12 @@ 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
chr_num = self.search_term[2]
- where_clause += """ and Geno.Chr = %s """ % (chr_num)
+ if "chr" in self.search_term[2].lower():
+ chr_num = self.search_term[2].lower().replace("chr", "")
+ self.search_term[2] = chr_num
+ where_clause += """ and Geno.Chr = '%s' """ % (chr_num)
if len(self.search_term) == 5:
mb_low, mb_high = self.search_term[3:]
where_clause += """ and Geno.Mb > %s and
@@ -489,6 +527,10 @@ class LrsSearch(DoSearch):
else:
# Deal with >, <, >=, and <=
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
+
where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
self.search_term[0])
@@ -505,12 +547,13 @@ class LrsSearch(DoSearch):
return self.execute(self.query)
+
class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
- DoSearch.search_types['ProbeSet_LRS'] = 'MrnaLrsSearch'
+ for search_key in ('LRS', 'LOD'):
+ DoSearch.search_types['ProbeSet_' + search_key] = "MrnaLrsSearch"
def run(self):
-
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
@@ -520,7 +563,8 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
- DoSearch.search_types['Publish_LRS'] = 'PhenotypeLrsSearch'
+ for search_key in ('LRS', 'LOD'):
+ DoSearch.search_types['Publish_' + search_key] = "PhenotypeLrsSearch"
def run(self):
@@ -532,31 +576,39 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
return self.execute(self.query)
-
class CisTransLrsSearch(DoSearch):
def get_from_clause(self):
return ", Geno"
def get_where_clause(self, cis_trans):
- self.search_term = [float(value) for value in self.search_term]
self.mb_buffer = 5 # default
+ chromosome = None
if cis_trans == "cis":
the_operator = "<"
else:
the_operator = ">"
if self.search_operator == "=":
+ if len(self.search_term) == 2 or len(self.search_term) == 3:
+ self.search_term = [float(value) for value in self.search_term]
if len(self.search_term) == 2:
lrs_min, lrs_max = self.search_term
#[int(value) for value in self.search_term]
-
elif len(self.search_term) == 3:
lrs_min, lrs_max, self.mb_buffer = self.search_term
-
+ elif len(self.search_term) == 4:
+ lrs_min, lrs_max, self.mb_buffer = [float(value) for value in self.search_term[:3]]
+ chromosome = self.search_term[3]
+ if "Chr" in chromosome or "chr" in chromosome:
+ chromosome = int(chromosome[3:])
else:
SomeError
+ if self.search_type == "CISLOD" or self.search_type == "TRANSLOD":
+ lrs_min = lrs_min * 4.61
+ lrs_max = lrs_max * 4.61
+
sub_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s and """ % (
escape(self.dataset.type),
@@ -586,18 +638,24 @@ class CisTransLrsSearch(DoSearch):
escape(self.dataset.type)
)
else:
+ if chromosome:
+ location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type),
+ chromosome,
+ escape(self.dataset.type),
+ escape(self.dataset.type),
+ the_operator,
+ escape(str(self.mb_buffer)),
+ escape(self.dataset.type),
+ chromosome)
+ else:
+ location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type))
where_clause = sub_clause + """
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
- ((ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or
- (%s.Chr != Geno.Chr))""" % (
+ (%s)""" % (
escape(self.dataset.type),
escape(str(self.species_id)),
- escape(self.dataset.type),
- the_operator,
- escape(str(self.mb_buffer)),
- escape(self.dataset.type),
- escape(self.dataset.type)
+ location_clause
)
return where_clause
@@ -619,7 +677,8 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
- DoSearch.search_types['ProbeSet_CISLRS'] = 'CisLrsSearch'
+ for search_key in ('LRS', 'LOD'):
+ DoSearch.search_types['ProbeSet_CIS'+search_key] = "CisLrsSearch"
def get_where_clause(self):
return CisTransLrsSearch.get_where_clause(self, "cis")
@@ -648,7 +707,8 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
- DoSearch.search_types['ProbeSet_TRANSLRS'] = 'TransLrsSearch'
+ for search_key in ('LRS', 'LOD'):
+ DoSearch.search_types['ProbeSet_TRANS'+search_key] = "TransLrsSearch"
def get_where_clause(self):
return CisTransLrsSearch.get_where_clause(self, "trans")
@@ -742,7 +802,7 @@ class PositionSearch(DoSearch):
self.chr = str(chr).lower()
self.get_chr()
- where_clause = """ %s.Chr = %s and
+ where_clause = """ %s.Chr = '%s' and
%s.Mb > %s and
%s.Mb < %s """ % self.mescape(self.dataset.type,
self.chr,
@@ -851,6 +911,29 @@ def is_number(s):
except ValueError:
return False
+def get_aliases(symbol, species):
+ if species == "mouse":
+ symbol_string = symbol.capitalize()
+ elif species == "human":
+ symbol_string = symbol.upper()
+ else:
+ return []
+
+ filtered_aliases = []
+ response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string)
+ if response:
+ alias_list = json.loads(response.content)
+
+ seen = set()
+ for item in alias_list:
+ if item in seen:
+ continue
+ else:
+ filtered_aliases.append(item)
+ seen.add(item)
+
+ 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-25 04:07:51 +0000