comparison ete_homology_classifier.py @ 6:f1eca1158f21 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 133bb57feca9672734d664e6b34e428488cf2e73

5:817031b8486d

    options, args = parser.parse_args()

    if options.genetree is None:
        parser.error("--genetree option must be specified, GeneTree in nhx format")

    # reads single gene tree
    genetree = PhyloTree(options.genetree)

    leaves_list = genetree.get_leaf_names()
    # Genetree nodes are required to be in gene_species format
    leaves_list = [_ for _ in leaves_list if '_' in _]

6:f1eca1158f21

    options, args = parser.parse_args()

    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(contents)

    leaves_list = genetree.get_leaf_names()
    # Genetree nodes are required to be in gene_species format
    leaves_list = [_ for _ in leaves_list if '_' in _]