Python NCBITaxa.get_broken_branches Examples

Example #1

File: phylotree.py Project: F4L2/devoirs

    def ncbi_compare(self, autodetect_duplications=True, cached_content=None):
        if not cached_content:
            cached_content = self.get_cached_content()
        cached_species = set([n.species for n in cached_content[self]])

        if len(cached_species) != len(cached_content[self]):
            print cached_species
            ntrees, ndups, target_trees = self.get_speciation_trees(
                autodetect_duplications=autodetect_duplications,
                map_features=["taxid"])
        else:
            target_trees = [self]

        ncbi = NCBITaxa()
        for t in target_trees:
            ncbi.get_broken_branches(t, cached_content)

Example #2

File: phylotree.py Project: jerryatmda/ete

    def ncbi_compare(self, autodetect_duplications=True, cached_content=None):
        if not cached_content:
            cached_content = self.get_cached_content()
        cached_species = set([n.species for n in cached_content[self]])

        if len(cached_species) != len(cached_content[self]):
            print cached_species
            ntrees, ndups, target_trees = self.get_speciation_trees(
                autodetect_duplications=autodetect_duplications, map_features=["taxid"]
            )
        else:
            target_trees = [self]

        ncbi = NCBITaxa()
        for t in target_trees:
            ncbi.get_broken_branches(t, cached_content)