diff options
Diffstat (limited to 'wqflask/base/mrna_assay_tissue_data.py')
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 39 |
1 files changed, 34 insertions, 5 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index f1929518..0220d73b 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -6,6 +6,7 @@ from utility import db_tools from utility import Bunch from utility.db_tools import escape +from gn3.db_utils import database_connector from utility.logger import getLogger @@ -44,16 +45,42 @@ class MrnaAssayTissueData(object): and t.Mean = x.maxmean; '''.format(in_clause) - results = g.db.execute(query).fetchall() - lower_symbols = [] + # lower_symbols = [] + lower_symbols = {} for gene_symbol in gene_symbols: + # lower_symbols[gene_symbol.lower()] = True if gene_symbol != None: - lower_symbols.append(gene_symbol.lower()) - + lower_symbols[gene_symbol.lower()] = True + + import time + # initial_time = time.time() + # conn,cursor = database_connector() + # cursor.execute(query) + # for result in cursor.fetchall(): + # symbol = result[0] + # self.data[symbol].gene_id = result[1] + # self.data[symbol].data_id = result[2] + # self.data[symbol].chr = result[3] + # self.data[symbol].mb = result[4] + # self.data[symbol].description = result[5] + # self.data[symbol].probe_target_description = result[6] + + + # print("my loop takes>>>>",time.time()-initial_time) + # conn.close() + # r + + # takes 5 seconds + initial_time = time.time() + results = list(g.db.execute(query).fetchall()) for result in results: symbol = result[0] - if symbol.lower() in lower_symbols: + # if symbol is not None + # exists = lower_symbols.get(symbol.lower()) + # if symbol.lower() in lower_symbols: + if symbol is not None and lower_symbols.get(symbol.lower()): + symbol = symbol.lower() self.data[symbol].gene_id = result.GeneId @@ -62,6 +89,7 @@ class MrnaAssayTissueData(object): self.data[symbol].mb = result.Mb self.data[symbol].description = result.description self.data[symbol].probe_target_description = result.Probe_Target_Description + print("time taken in the loop is",time.time()-initial_time) ########################################################################### #Input: cursor, symbolList (list), dataIdDict(Dict) @@ -82,6 +110,7 @@ class MrnaAssayTissueData(object): WHERE TissueProbeSetData.Id IN {} and TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) + results = g.db.execute(query).fetchall() for result in results: if result.Symbol.lower() not in symbol_values_dict: |