Fix imports and finalisation for tools, resolves #325

davidemms · Feb 6, 2020 · b588cf5 · b588cf5
1 parent 074c5e7
commit b588cf5
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/tools/convert_orthofinder_tree_ids.py b/tools/convert_orthofinder_tree_ids.py
@@ -8,8 +8,9 @@
 
 if __name__ == "__main__" and __package__ is None:   
     sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
+    print(sys.path[-1])
 
-from orthofinder.scripts import tree, util
+from scripts_of import tree, util
 
 def ReplaceFileWithNewIDs(idsMap, treeFilename, newTreeFilename):     
     qHaveSupport = False
@@ -50,7 +51,7 @@ def GetSpeciesSequenceIDsDict(sequenceIDsFilename, speciesIDsFN = None):
         idsDict = {seqID:speciesDict[seqID.split("_")[0]] + "_" + name for seqID, name in idsDict.items()}
     return idsDict
 
-def main():
+def main_convert():
     with util.Finalise():
         parser = argparse.ArgumentParser(description="Takes a tree with OrthoFinder IDs and outputs a tree with gene accessions")
         parser.add_argument("TreeInput", help="Tree filename or directory")
@@ -76,4 +77,4 @@ def main():
             print("")
 
 if __name__ == "__main__":
-    main()
+    main_convert()
diff --git a/tools/make_ultrametric.py b/tools/make_ultrametric.py
@@ -9,7 +9,7 @@
 if __name__ == "__main__" and __package__ is None:
     sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 
-from orthofinder.scripts import tree
+from scripts_of import tree, util
 
 def AveDist(node):
     return np.average([node.get_distance(l) for l in node.get_leaf_names()]) 
@@ -69,4 +69,5 @@ def main():
     print("\nUltrametric tree written to: %s\n" % outfn)
 
 if __name__ == "__main__":
-    main()
+    with util.Finalise():
+        main()