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jhcepas/sort_alg_by_tree.py

Created March 15, 2017 14:48
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  1. jhcepas created this gist Mar 15, 2017.
    17 changes: 17 additions & 0 deletions sort_alg_by_tree.py
    View file
    Original file line number Diff line number Diff line change
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    import re
    from ete3 import SeqGroup, Tree
    import sys

    alg_file = sys.argv[1] # in fasta format
    tree_file = sys.argv[2] # in newick format

    alg = SeqGroup(alg_file)
    for k,v in alg.name2id.items():
    # converts ilegal newick chars from alg names.
    # Comment this line if not necessary
    k = re.sub('[:,();]','_', k)
    alg.name2id[k] = v

    tree = Tree(tree_file)
    for leaf in tree:
    print ">%s\n%s" %(leaf.name, alg.get_seq(leaf.name))