message about invalid outgroups

nickjcroucher · Jan 23, 2015 · 6499829 · 6499829
1 parent 404203e
commit 6499829
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diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.1.0
+1.1.1
diff --git a/debian/changelog b/debian/changelog
@@ -1,3 +1,14 @@
+gubbins (1.1.1~trusty1) trusty; urgency=low
+
+ * Message to tell user theres a problem with outgroups not a clade
+
+ -- Andrew Page <ap13@sanger.ac.uk> Fri, 23 Jan 2015 16:02 gubbins (1.1.0~trusty1) trusty; urgency=low
+
+ * Allow for multiple outgroups
+
+ -- Andrew Page <ap13@sanger.ac.uk> Fri, 23 Jan 2015 15:05:00 +0000
+:00 +0000
+
 gubbins (1.1.0~trusty1) trusty; urgency=low
 
  * Allow for multiple outgroups

diff --git a/python/gubbins/common.py b/python/gubbins/common.py
@@ -399,6 +399,7 @@ def get_monophyletic_outgroup(tree_name, outgroups):
 
  for leaf_node in tree.mrca(taxon_labels=outgroups).leaf_nodes():
  if leaf_node.taxon.label not in outgroups:
+ print "Your outgroups do not form a clade.\n Using the first taxon "+str(outgroups[0])+" as the outgroup.\n Taxon "+str(leaf_node.taxon.label)+" is in the clade but not in your list of outgroups."
  return [outgroups[0]]
 
  return outgroups