last iteration will keep all meme output and write it to a final resu…

…lts file for evaluation
baliga-lab · Jul 1, 2014 · 1071a2d · 1071a2d
1 parent 1b759e4
commit 1071a2d
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Showing 2 changed files with 12 additions and 10 deletions.
diff --git a/cmonkey/cmonkey_run.py b/cmonkey/cmonkey_run.py
@@ -679,14 +679,15 @@ def run_iterations(self, row_scoring, col_scoring):
             self.write_stats(iteration_result)
             self.update_iteration(iteration)
 
-            if 'dump_results' in self['debug']:
-                # write complete result into a cmresults.tsv
-                conn = self.__dbconn()
-                path =  os.path.join(self['output_dir'], 'cmresults-postproc.tsv.bz2')
-                with bz2.BZ2File(path, 'w') as outfile:
-                    debug.write_iteration(conn, outfile,
-                                          self['num_iterations'] + 1,
-                                          self['num_clusters'], self['output_dir'])
+            # default behaviour:
+            # always write complete result into a cmresults.tsv for R/cmonkey
+            # compatibility
+            conn = self.__dbconn()
+            path =  os.path.join(self['output_dir'], 'cmresults-postproc.tsv.bz2')
+            with bz2.BZ2File(path, 'w') as outfile:
+                debug.write_iteration(conn, outfile,
+                                      self['num_iterations'] + 1,
+                                      self['num_clusters'], self['output_dir'])
 
 
         self.write_finish_info()

diff --git a/cmonkey/meme.py b/cmonkey/meme.py
@@ -119,7 +119,8 @@ def background_file():
 
         # run mast
         meme_outfile = None
-        if 'keep_memeout' in params.debug:
+        is_last_iteration = params.iteration > params.num_iterations
+        if 'keep_memeout' in params.debug or is_last_iteration:
             meme_outfile = os.path.join(params.outdir,
                                         'meme-out-%04d-%04d' % (params.iteration, params.cluster))
             with open(meme_outfile, 'w') as outfile:
@@ -158,7 +159,7 @@ def background_file():
                 except:
                     logging.warn("could not remove tmp file: '%s'", seqfile)
                 try:
-                    if 'keep_memeout' not in params.debug:
+                    if 'keep_memeout' not in params.debug and not is_last_iteration:
                         os.remove(meme_outfile)
                 except:
                     logging.warn("could not remove tmp file: '%s'", meme_outfile)