Mercurial > repos > earlhaminst > ete
changeset 7:6a5282f71f82 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 55116304ad98416757ad689c9a885dd0967f120e
| author | earlhaminst |
|---|---|
| date | Thu, 11 Oct 2018 11:52:28 -0400 |
| parents | f1eca1158f21 |
| children | 16e925bf567e |
| files | ete_genetree_splitter.py |
| diffstat | 1 files changed, 7 insertions(+), 1 deletions(-) [+] |
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--- a/ete_genetree_splitter.py Wed Oct 10 05:24:04 2018 -0400 +++ b/ete_genetree_splitter.py Thu Oct 11 11:52:28 2018 -0400 @@ -19,8 +19,14 @@ 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) # sets species naming function if options.gene_node == 0: