Merge pull request #23 from andrewjpage/no_operons

inverted operon at terminus falsely giving valid when should be invalid
quadram-institute-bioscience · Oct 12, 2019 · 4e9ff40 · 4e9ff40
2 parents ec78b77 + 08162a9
commit 4e9ff40
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Showing 7 changed files with 117 additions and 252 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-2.2.2
+2.2.3
diff --git a/scripts/socru_lookup b/scripts/socru_lookup
diff --git a/socru/Socru.py b/socru/Socru.py
@@ -74,6 +74,9 @@ def run(self):
                     output_fh.write(str(h)+"\n")
 
     def output_results(self, input_file, profile_type):
+        if profile_type == '':
+            profile_type = "RED\tGS0.0"
+
         if self.output_file is None:
             print(input_file + "\t" + profile_type)
         else:

diff --git a/socru/SocruLookup.py b/socru/SocruLookup.py
diff --git a/socru/ValidateFragments.py b/socru/ValidateFragments.py
@@ -40,24 +40,22 @@ def validate(self):
 
         # forward walk
         for i in range(dnaa_index + 1, len(self.fragments)):
-            if i >= dif_index:
-                # we have reached the end
-                continue
-
             #  direction should be -->
             # if the operon is not forward then its invalid
             if not reorientated_frags[i].operon_forward_start:
                 return False
+            if i >= dif_index:
+                # we have reached the end
+                break
 
         # reverse walk
         for i in range( len(self.fragments) -1, dif_index, -1):
-            if i <= dif_index:
-                # we have reached the end
-                continue
-
             #  direction should be <--
             if reorientated_frags[i].operon_forward_start:
                 return False    
+            if i <= dif_index:
+                # we have reached the end
+                break
 
         return True
 

diff --git a/socru/tests/SocruLookup_test.py b/socru/tests/SocruLookup_test.py