Mercurial > repos > earlhaminst > ete
diff ete_homology_classifier.py @ 6:f1eca1158f21 draft
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 |
line wrap: on
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