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authorLei Yan2013-05-28 23:10:22 +0000
committerLei Yan2013-05-28 23:10:22 +0000
commitcb639316fe007c8bcad731976e8b095dee59115e (patch)
tree3a5240a457f3c16679311dc9fb0c66b12ecfd9b5 /wqflask/base
parent8d0c6166a297d2cc89394649b8f56d8c6bf5d0f7 (diff)
downloadgenenetwork2-cb639316fe007c8bcad731976e8b095dee59115e.tar.gz
Have correlation values appearing in a table in the template
Use scipy to calculate pearson correlation instead of old GN code
Diffstat (limited to 'wqflask/base')
-rwxr-xr-xwqflask/base/data_set.py34
1 files changed, 3 insertions, 31 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index edee6685..c2380f8c 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -78,7 +78,7 @@ def create_in_clause(items):
def mescape(*items):
"""Multiple escape"""
- escaped = [escape(item) for item in items]
+ escaped = [escape(str(item)) for item in items]
#print("escaped is:", escaped)
return escaped
@@ -634,12 +634,6 @@ class MrnaAssayDataSet(DataSet):
def get_trait_data(self):
self.samplelist = self.group.samplelist + self.group.parlist + self.group.f1list
- #query_samplelist = ', '.join("'{}'".format(x) for x in mescape(*samplelist))
- #query_samplelist = '( ' + query_samplelist + ' )'
- #query_samplelist = create_in(samplelist)
-
- print("self.samplelist is:", self.samplelist)
-
query = """
SELECT Strain.Name, Strain.Id FROM Strain, Species
WHERE Strain.Name IN {}
@@ -647,29 +641,13 @@ class MrnaAssayDataSet(DataSet):
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
results = dict(g.db.execute(query).fetchall())
- print("results are:", results)
- print("type results are:", type(results))
-
- #sample_ids = []
- #for item in self.samplelist:
- # sample_ids.append(results[item])
-
sample_ids = [results[item] for item in self.samplelist]
- print("sample_ids are:", sample_ids)
-
- #for sample in self.samplelist:
- # pass
-
- #for index in range(len(results)):
- # sample_ids.append(results[index][0])
# MySQL limits the number of tables that can be used in a join to 61,
# so we break the sample ids into smaller chunks
# Postgres doesn't have that limit, so we can get rid of this after we transition
chunk_size = 50
-
number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
-
trait_sample_data = []
for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
@@ -687,12 +665,6 @@ class MrnaAssayDataSet(DataSet):
# method=method,
# returnNumber=returnNumber)
- #for step in range(int(n)):
- #temp = []
- #sample_ids_step = sample_ids[step*chunk_size:min(len(sample_ids), (step+1)*chunk_size)]
- #for item in sample_ids_step:
- # temp.append('T%s.value' % item)
-
temp = ['T%s.value' % item for item in sample_ids_step]
query = "SELECT {}.Name,".format(escape(self.type))
data_start_pos = 1
@@ -722,10 +694,10 @@ class MrnaAssayDataSet(DataSet):
# trait names and values are lists of sample values
for j in range(trait_count):
trait_name = trait_sample_data[0][j][0]
- for i in range(int(n)):
+ for i in range(int(number_chunks)):
self.trait_data[trait_name] += trait_sample_data[i][j][data_start_pos:]
-
+
def get_trait_info(self, trait_list=None, species=''):
# Note: setting trait_list to [] is probably not a great idea.