annotate ete_genetree_splitter.py @ 9:b29ee6a16524 draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 17c65045b726d0695814bfe761e534f6521786f1"

from __future__ import print_function

import optparse

from ete3 import PhyloTree


def main():
    usage = "usage: %prog --genetree <genetree-file> --speciestree <speciestree-file> [options]"
    parser = optparse.OptionParser(usage=usage)
    parser.add_option('--genetree', help='GeneTree in nhx format')
    parser.add_option('--speciestree', help='Species Tree in nhx format')
    parser.add_option('--species_format', type='int', default=8, help='Species Tree input format (0-9)')
    parser.add_option('--gene_node', type='int', default=0, help='Gene node format 0=gene_species, 1=species_gene')
    parser.add_option('--gainlose', action='store_true', default=False, help='Find out gene gain/lose')
    parser.add_option('--split', type='choice', choices=['dups', 'treeko'], dest="split", default='dups', help='Choose GeneTree splitting algorithms')
    parser.add_option('--output_format', type='int', default=9, help='GeneTree output format (0-9)')
    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)

    # sets species naming function
    if options.gene_node == 0:
        genetree.set_species_naming_function(parse_sp_name)

    # reconcile species tree with gene tree to help find out gene gain/lose
    if options.gainlose:

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

        # reads species tree
        speciestree = PhyloTree(options.speciestree, format=options.species_format)

        # Removes '*' from Species names comes from Species tree configrured for TreeBest
        for leaf in speciestree:
            leaf.name = leaf.name.strip('*')

        genetree, events = genetree.reconcile(speciestree)

    if options.split == "dups":
        # splits tree by duplication events which returns the list of all subtrees resulting from splitting current tree by its duplication nodes.
        for cluster_id, node in enumerate(genetree.split_by_dups(), 1):
            outfile = str(cluster_id) + '_genetree.nhx'
            with open(outfile, 'w') as f:
                f.write(node.write(format=options.output_format))
    elif options.split == "treeko":
        # splits tree using the TreeKO algorithm.
        ntrees, ndups, sptrees = genetree.get_speciation_trees()

        cluster_id = 0
        for spt in sptrees:
            cluster_id = cluster_id + 1
            outfile = str(cluster_id) + '_genetree.nhx'
            with open(outfile, 'w') as f:
                f.write(spt.write(format=options.output_format))


def parse_sp_name(node_name):
    return node_name.split("_")[1]


if __name__ == "__main__":
    main()