diff options
| -rw-r--r-- | wqflask/utility/helper_functions.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 25 |
2 files changed, 13 insertions, 14 deletions
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py index 920d9ac6..9ecad993 100644 --- a/wqflask/utility/helper_functions.py +++ b/wqflask/utility/helper_functions.py @@ -5,7 +5,7 @@ from base import data_set def get_dataset_and_trait(self, start_vars): #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype" - self.dataset = data_set.create_dataset(start_vars['dataset']) + self.dataset = data_set.create_dataset(start_vars['dataset_name']) self.this_trait = GeneralTrait(dataset=self.dataset.name, name=start_vars['trait_id'], cellid=None) diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 23dd1534..b82f1c59 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -374,7 +374,7 @@ class CorrelationResults(object): #XZ: As of Nov/13/2010, this dataset is 'UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)' self.tissue_probeset_freeze_id = 1 - traitList = self.correlate(self.vals) + traitList = self.correlate() _log.info("Done doing correlation calculation") @@ -823,18 +823,17 @@ Resorting this table <br> """Returns the name of the reference database file with which correlations are calculated. Takes argument cursor which is a cursor object of any instance of a subclass of templatePage Used by correlationPage""" -ROM ProbeSetFreeze WHERE Name = "%s"' % target_db_name - self.cursor.execute(query) - result = self.cursor.fetchone() - Id = result[0] - FullName = result[1] - FullName = FullName.replace(' ','_') - FullName = FullName.replace('/','_') - FileName = 'ProbeSetFreezeId_' + str(Id) + '_FullName_' + FullName + '.txt' + trait_id, full_name = g.db.execute("""SELECT Id, FullName + FROM ProbeSetFreeze + WHERE Name = '%s'""" % target_db_name).fetchone() + for char in [' ', '/']: + full_name = full_name.replace(char, '_') + + file_name = 'ProbeSetFreezeId_' + str(trait_id) + '_FullName_' + full_name + '.txt' + + return file_name - return FileName - query = 'SELECT Id, FullName F #XZ, 01/29/2009: I modified this function. @@ -1262,7 +1261,7 @@ ROM ProbeSetFreeze WHERE Name = "%s"' % target_db_name #_log.info("Using the slow method for correlation") # #_log.info("Fetching from database") - traits = self.fetchAllDatabaseData(species=self.species, GeneId=self.gene_id, GeneSymbol=self.trait_symbol, strains=self.sample_names, db=self.db, method=self.method, returnNumber=self.returnNumber, tissueProbeSetFreezeId= self.tissue_probeset_freeze_id) + traits = self.fetchAllDatabaseData(species=self.dataset.species, GeneId=self.gene_id, GeneSymbol=self.trait.symbol, strains=self.sample_names, db=self.db, method=self.method, returnNumber=self.returnNumber, tissueProbeSetFreezeId= self.tissue_probeset_freeze_id) #_log.info("Done fetching from database") totalTraits = len(traits) #XZ, 09/18/2008: total trait number @@ -1339,7 +1338,7 @@ ROM ProbeSetFreeze WHERE Name = "%s"' % target_db_name #cache_available = db_filename in os.listdir(webqtlConfig.TEXTDIR) # If the cache file exists, do a cached correlation for probeset data - if self.db.type == "ProbeSet": + if self.dataset.type == "ProbeSet": # if self.method in [METHOD_SAMPLE_PEARSON, METHOD_SAMPLE_RANK] and cache_available: # traits = do_parallel_correlation() # |