# HG changeset patch
# User greg
# Date 1448370940 18000
# Node ID 2e0ddcc726f9a26be456178d97c640cba55427af
# Parent  9ed566138ecb24660d45b3b4057c762122815133
Uploaded

diff -r 9ed566138ecb -r 2e0ddcc726f9 cwpair2_util.py
--- a/cwpair2_util.py	Sat Nov 21 09:01:46 2015 -0500
+++ b/cwpair2_util.py	Tue Nov 24 08:15:40 2015 -0500
@@ -225,7 +225,7 @@
 
 
 def process_file(dataset_path, galaxy_hid, method, threshold, up_distance,
-                 down_distance, binsize, output_files, sort_chromosome, sort_score):
+                 down_distance, binsize, output_files, sort_score):
     if method == 'all':
         match_methods = METHODS.keys()
     else:
@@ -240,7 +240,6 @@
                                 down_distance,
                                 binsize,
                                 output_files,
-                                sort_chromosome,
                                 sort_score)
         statistics.append(stats)
     if output_files == 'all' and method == 'all':
@@ -251,7 +250,7 @@
 
 
 def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance,
-                    down_distance, binsize, output_files, sort_chromosome, sort_score):
+                    down_distance, binsize, output_files, sort_score):
     output_details = output_files in ["all", "simple_orphan_detail"]
     output_plots = output_files in ["all"]
     output_orphans = output_files in ["all", "simple_orphan", "simple_orphan_detail"]
@@ -367,27 +366,12 @@
                 orphan_output.writerow((cname, cpeak[0], cpeak[1], cpeak[2], cpeak[3]))
         # Keep track of orphans for statistics.
         orphans += len(crick)
-    # Sort output by chromosome if specified.
-    if sort_chromosome == "asc":
-        try:
-            x.sort(key=lambda data: int(data[3]))
-            x.sort(key=lambda data: int(data[0]))
-        except:
-            # Cannot sort because chromosome number is not a numeric.
-            pass
-    elif sort_chromosome == "desc":
-        try:
-            x.sort(key=lambda data: int(data[0]), reverse=True)
-            x.sort(key=lambda data: int(data[3]), reverse=True)
-        except:
-            # Cannot sort because chromosome number is not a numeric.
-            pass
     # Sort output by score if specified.
     if sort_score == "desc":
         x.sort(key=lambda data: float(data[5]), reverse=True)
     elif sort_score == "asc":
         x.sort(key=lambda data: float(data[5]))
-    # Writing a summary to txt or gff format file
+    # Writing a summary to gff format file
     for row in x:
         row_tmp = list(row)
         # Dataset in tuple cannot be modified in Python, so row will