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authorZachary Sloan2013-01-22 17:24:26 -0600
committerZachary Sloan2013-01-22 17:24:26 -0600
commit01283a27bf9cc78653059236fa55d6063558ab21 (patch)
tree97013d79c7c1734bb86b18ef5b8116caa683ce7f
parent8aeff9b91d078a40a50d13f6393a1f1dabf62aa4 (diff)
downloadgenenetwork2-01283a27bf9cc78653059236fa55d6063558ab21.tar.gz
Pushed through a few errors in getting the correlation page running
-rw-r--r--wqflask/utility/helper_functions.py2
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py25
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()
#