Mercurial > repos > earlhaminst > ete
comparison 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 |
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date | Wed, 10 Oct 2018 05:24:04 -0400 |
parents | 817031b8486d |
children | ed74587a13c8 |
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5:817031b8486d | 6:f1eca1158f21 |
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15 options, args = parser.parse_args() | 15 options, args = parser.parse_args() |
16 | 16 |
17 if options.genetree is None: | 17 if options.genetree is None: |
18 parser.error("--genetree option must be specified, GeneTree in nhx format") | 18 parser.error("--genetree option must be specified, GeneTree in nhx format") |
19 | 19 |
20 with open(options.genetree, 'r') as f: | |
21 contents = f.read() | |
22 | |
23 # Remove empty NHX features that can be produced by TreeBest but break ete3 | |
24 contents = contents.replace('[&&NHX]', '') | |
20 # reads single gene tree | 25 # reads single gene tree |
21 genetree = PhyloTree(options.genetree) | 26 genetree = PhyloTree(contents) |
22 | 27 |
23 leaves_list = genetree.get_leaf_names() | 28 leaves_list = genetree.get_leaf_names() |
24 # Genetree nodes are required to be in gene_species format | 29 # Genetree nodes are required to be in gene_species format |
25 leaves_list = [_ for _ in leaves_list if '_' in _] | 30 leaves_list = [_ for _ in leaves_list if '_' in _] |
26 | 31 |