Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acenteno

1 files changed, 11 insertions, 3 deletions

diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index b1e41e9a..e964c8ed 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -23,10 +23,12 @@ def get_cursor():
     cursor = con.cursor()
     return cursor
 
+
 def show_progress(process, counter):
     if counter % 1000 == 0:
         print("{}: {}".format(process, counter))
 
+
 def get_strains(cursor):
     cursor.execute("""select Strain.Name
                       from Strain, StrainXRef, InbredSet
@@ -42,6 +44,7 @@ def get_strains(cursor):
 
     return strains
 
+
 def get_probeset_vals(cursor, dataset_name):
     cursor.execute(""" select ProbeSet.Id, ProbeSet.Name
                 from ProbeSetXRef,
@@ -77,6 +80,7 @@ def get_probeset_vals(cursor, dataset_name):
 
     return probeset_vals
 
+
 def trim_strains(strains, probeset_vals):
     trimmed_strains = []
     #print("probeset_vals is:", pf(probeset_vals))
@@ -89,6 +93,7 @@ def trim_strains(strains, probeset_vals):
     print("trimmed_strains:", pf(trimmed_strains))
     return trimmed_strains
 
+
 def write_data_matrix_file(strains, probeset_vals, filename):
     with open(filename, "wb") as fh:
         csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL)
@@ -103,10 +108,12 @@ def write_data_matrix_file(strains, probeset_vals, filename):
             csv_writer.writerow(row_data)
             show_progress("Writing", counter)
 
+
 def main():
-    filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
-                "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
-                "(Oct08)_RankInv_Beta.txt")
+    filename = os.path.expanduser(
+        "~/gene/wqflask/maintenance/"
+        "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2"
+        "(Oct08)_RankInv_Beta.txt")
     dataset_name = "Eye_AXBXA_1008_RankInv"
 
     cursor = get_cursor()
@@ -117,5 +124,6 @@ def main():
     trimmed_strains = trim_strains(strains, probeset_vals)
     write_data_matrix_file(trimmed_strains, probeset_vals, filename)
 
+
 if __name__ == '__main__':
     main()