Mercurial > repos > earlhaminst > ete

diff ete_homology_classifier.py @ 6:f1eca1158f21 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73
author earlhaminst
date Wed, 10 Oct 2018 05:24:04 -0400
parents 817031b8486d
children ed74587a13c8
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line diff
--- a/ete_homology_classifier.py	Thu May 10 06:15:17 2018 -0400
+++ b/ete_homology_classifier.py	Wed Oct 10 05:24:04 2018 -0400
@@ -17,8 +17,13 @@
     if options.genetree is None:
         parser.error("--genetree option must be specified, GeneTree in nhx format")
 
+    with open(options.genetree, 'r') as f:
+        contents = f.read()
+
+    # Remove empty NHX features that can be produced by TreeBest but break ete3
+    contents = contents.replace('[&&NHX]', '')
     # reads single gene tree
-    genetree = PhyloTree(options.genetree)
+    genetree = PhyloTree(contents)
 
     leaves_list = genetree.get_leaf_names()
     # Genetree nodes are required to be in gene_species format