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from __future__ import absolute_import, print_function, division
import collections
from flask import g
from utility import dbtools
from uitility import Bunch
from MySQLdb import escape_string as escape
class MrnaAssayTissueData(object):
def __init__(self, gene_symbols=None):
self.gene_symbols = gene_symbols
self.have_data = False
if self.gene_symbols == None:
self.gene_symbols = []
self.data = collections.defaultdict(Bunch)
#self.gene_id_dict ={}
#self.data_id_dict = {}
#self.chr_dict = {}
#self.mb_dict = {}
#self.desc_dict = {}
#self.probe_target_desc_dict = {}
query = '''select t.Symbol, t.GeneId, t.DataId,t.Chr, t.Mb, t.description, t.Probe_Target_Description
from (
select Symbol, max(Mean) as maxmean
from TissueProbeSetXRef
where TissueProbeSetFreezeId=1 and '''
# Note that inner join is necessary in this query to get distinct record in one symbol group
# with highest mean value
# Due to the limit size of TissueProbeSetFreezeId table in DB,
# performance of inner join is acceptable.
if len(gene_symbols) == 0:
query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''
else:
in_clause = dbtools.create_in_clause(gene_symbols)
query += ''' Symbol in {} group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''.format(in_clause)
results = g.db.execute(query).fetchall()
for result in results:
symbol = item[0]
gene_symbols.append(symbol)
symbol = symbol.lower()
self.data[symbol].gene_id = result.GeneId
self.data[symbol].data_id = result.DataId
self.data[symbol].chr = result.Chr
self.data[symbol].mb = result.Mb
self.data[symbol].description = result.description
self.data[symbol].probe_target_description = result.Probe_Target_Description
###########################################################################
#Input: cursor, symbolList (list), dataIdDict(Dict)
#output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
# key is symbol, value is one list of expression values of one probeSet;
#function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
#Attention! All keys are lower case!
###########################################################################
def get_symbol_value_pairs(self):
id_list = [self.tissue_data[symbol.lower()].data_id for item in self.tissue_data]
symbol_value_pairs = {}
value_list=[]
query = """SELECT value, id
FROM TissueProbeSetData
WHERE Id IN {}""".format(create_in_clause(id_list))
try :
results = g.db.execute(query).fetchall()
for result in results:
value_list.append(result.value)
symbol_value_pairs[symbol] = value_list
except:
symbol_value_pairs[symbol] = None
#for symbol in symbol_list:
# if tissue_data.has_key(symbol):
# data_id = tissue_data[symbol].data_id
#
# query = """select value, id
# from TissueProbeSetData
# where Id={}""".format(escape(data_id))
# try :
# results = g.db.execute(query).fetchall()
# for item in results:
# item = item[0]
# value_list.append(item)
# symbol_value_pairs[symbol] = value_list
# value_list=[]
# except:
# symbol_value_pairs[symbol] = None
return symbol_value_pairs
########################################################################################################
#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
# key is symbol, value is one list of expression values of one probeSet.
#function: wrapper function for getSymbolValuePairDict function
# build gene symbol list if necessary, cut it into small lists if necessary,
# then call getSymbolValuePairDict function and merge the results.
########################################################################################################
def get_trait_symbol_and_tissue_values(symbol_list=None):
tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
#symbolList,
#geneIdDict,
#dataIdDict,
#ChrDict,
#MbDict,
#descDict,
#pTargetDescDict = getTissueProbeSetXRefInfo(
# GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
if len(tissue_data.gene_symbols):
return get_symbol_value_pairs(tissue_data)
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