Merge pull request #168 from genenetwork/staging

Staging

8 files changed, 33 insertions, 33 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 444c71c9..063de387 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -282,11 +282,11 @@ def gpercentile(lst2, np):
 
 def find_outliers(vals):
     """Calculates the upper and lower bounds of a set of sample/case values
-    
-    
+
+
     >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537])
     (11.252500000000001, 0.5364999999999993)
-    
+
     >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8])
     (32.0, -8.0)
 
@@ -294,7 +294,7 @@ def find_outliers(vals):
     which code that calls it will have to deal with.
     >>> find_outliers([])
     (None, None)
-    
+
     """
 
     print("xerxes vals is:", pf(vals))
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 182187ae..d5b32703 100755
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -7,7 +7,7 @@ import time
 
 class Bench(object):
     entries = collections.OrderedDict()
-    
+
     def __init__(self, name=None):
         self.name = name
 
@@ -26,10 +26,10 @@ class Bench(object):
 
         time_taken = time.time() - self.start_time
         print("  %s took: %f seconds" % (name, (time_taken)))
-        
+
         if self.name:
             Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken
-            
+
 
     @classmethod
     def report(cls):
@@ -39,7 +39,7 @@ class Bench(object):
             percent = int(round((time_taken/total_time) * 100))
             print("[{}%] {}: {}".format(percent, name, time_taken))
         print()
-        
+
     def reset(cls):
         """Reset the entries"""
         cls.entries = collections.OrderedDict()
\ No newline at end of file
diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py
index 9565fb96..b0e33c08 100644
--- a/wqflask/utility/chunks.py
+++ b/wqflask/utility/chunks.py
@@ -6,21 +6,21 @@ import time
 
 def divide_into_chunks(the_list, number_chunks):
     """Divides a list into approximately number_chunks smaller lists
-    
+
     >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3)
     [[1, 2, 7], [3, 22, 8], [5, 22, 333]]
-    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4)                                                                                                                                                     
+    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4)
     [[1, 2, 7], [3, 22, 8], [5, 22, 333]]
-    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5)                                                                                                                                                     
+    >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5)
     [[1, 2], [7, 3], [22, 8], [5, 22], [333]]
     >>>
-    
+
     """
     length = len(the_list)
 
     if length == 0:
         return [[]]
-    
+
     if length <= number_chunks:
         number_chunks = length
 
diff --git a/wqflask/utility/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py
index a253026c..ef644d85 100755
--- a/wqflask/utility/corr_result_helpers.py
+++ b/wqflask/utility/corr_result_helpers.py
@@ -1,16 +1,16 @@
 def normalize_values(a_values, b_values):
     """
     Trim two lists of values to contain only the values they both share
-    
+
     Given two lists of sample values, trim each list so that it contains
     only the samples that contain a value in both lists. Also returns
     the number of such samples.
-    
+
     >>> normalize_values([2.3, None, None, 3.2, 4.1, 5], [3.4, 7.2, 1.3, None, 6.2, 4.1])
     ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3)
-    
+
     """
-    
+
     min_length = min(len(a_values), len(b_values))
     a_new = []
     b_new = []
@@ -18,10 +18,10 @@ def normalize_values(a_values, b_values):
         if a_values[counter] and b_values[counter]:
             a_new.append(a_values[counter])
             b_new.append(b_values[counter])
-        
+
     num_overlap = len(a_new)
     assert num_overlap == len(b_new), "Lengths should be the same"
-    
+
     return a_new, b_new, num_overlap
 
 
@@ -37,16 +37,16 @@ def common_keys(a_samples, b_samples):
 
 def normalize_values_with_samples(a_samples, b_samples):
     common_samples = common_keys(a_samples, b_samples)
-    
+
     a_new = {}
     b_new = {}
     for sample in common_samples:
         a_new[sample] = a_samples[sample]
         b_new[sample] = b_samples[sample]
-        
+
     num_overlap = len(a_new)
     assert num_overlap == len(b_new), "Lengths should be the same"
-    
+
     return a_new, b_new, num_overlap
 
 
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 67b84dc9..7149e560 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -28,10 +28,10 @@ class ConvertGenoFile(object):
     self.mb_exists = False
     self.cm_exists = False
     self.markers = []
-    
+
     self.latest_row_pos = None
     self.latest_col_pos = None
-    
+
     self.latest_row_value = None
     self.latest_col_value = None
     self.input_fh = open(input_file)
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 004d45c6..5bf700c9 100755
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -4,16 +4,16 @@ from redis import Redis
 import simplejson as json
 
 class TempData(object):
-    
+
     def __init__(self, temp_uuid):
         self.temp_uuid = temp_uuid
         self.redis = Redis()
         self.key = "tempdata:{}".format(self.temp_uuid)
-        
+
     def store(self, field, value):
         self.redis.hset(self.key, field, value)
         self.redis.expire(self.key, 60*15)  # Expire in 15 minutes
-        
+
     def get_all(self):
         return self.redis.hgetall(self.key)
 
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index dd8c4a1e..11441d7a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -35,7 +35,7 @@ def get_setting(command_id,guess=None):
             return command
         else:
             return None
-    
+
     # ---- Check whether environment exists
     sys.stderr.write("Looking for "+command_id+"\n")
     command = value(os.environ.get(command_id))
@@ -128,7 +128,7 @@ def locate_ignore_error(name, subdir=None):
 def tempdir():
     return valid_path(get_setting("TEMPDIR","/tmp"))
 
-    
+
 # Cached values
 PYLMM_COMMAND = pylmm_command()
 GEMMA_COMMAND = gemma_command()
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 1108614b..4fc978f5 100755
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -129,7 +129,7 @@ def inverseCumul(p):
         return None
 
     if p>0 and p < 1:
-        e = 0.5 * erfcc(-x/sqrt(2)) - p 
+        e = 0.5 * erfcc(-x/sqrt(2)) - p
         u = e * sqrt(2*pi) * exp(x*x/2)
         x = x - u/(1 + x*u/2)
         return x
@@ -318,10 +318,10 @@ def FloatList2String(lst):
 
 def ListNotNull(lst):
     '''Obsolete - Use built in function any (or all or whatever)
-    
-    
+
+
     Determine if the elements in a list are all null
-    
+
     '''
     for item in lst:
         if item is not None: