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authorLei Yan2014-07-18 17:31:27 +0000
committerLei Yan2014-07-18 17:31:27 +0000
commitee0769c22472ea9dc1addd3886afd62d54ff2c00 (patch)
tree1f9477bd801e7555f0554466d78b13a8e3f77047 /wqflask
parente810ca62b8e39d85974c7fbc4b6bd64638c793a3 (diff)
downloadgenenetwork2-ee0769c22472ea9dc1addd3886afd62d54ff2c00.tar.gz
Correlation table for phenotypes is working
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/data_set.py2
-rwxr-xr-xwqflask/wqflask/correlation/show_corr_results.py6
2 files changed, 2 insertions, 6 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 2a79dc9c..a9a8beb2 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -564,7 +564,7 @@ class DataSet(object):
if self.type == "Publish":
query += """
- WHERE {}XRef.PublicationId = {}Freeze.Id
+ WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId
and {}Freeze.Name = '{}'
and {}.Id = {}XRef.{}Id
order by {}.Id
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 1cc932a0..506610f1 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -98,8 +98,6 @@ class CorrelationResults(object):
with Bench("Doing correlations"):
helper_functions.get_species_dataset_trait(self, start_vars)
- print("TRAIT SYMBOL:", self.this_trait.symbol)
-
self.dataset.group.read_genotype_file()
corr_samples_group = start_vars['corr_samples_group']
@@ -108,7 +106,7 @@ class CorrelationResults(object):
self.corr_type = start_vars['corr_type']
self.corr_method = start_vars['corr_sample_method']
self.get_formatted_corr_type()
- self.return_number = 50
+ self.return_number = int(start_vars['corr_return_results'])
#The two if statements below append samples to the sample list based upon whether the user
#rselected Primary Samples Only, Other Samples Only, or All Samples
@@ -485,8 +483,6 @@ class CorrelationResults(object):
sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
-
-
def do_tissue_corr_for_all_traits_2(self):
"""Comments Possibly Out of Date!!!!!