peyotl/__init__.py

#!/usr/bin/env python
'''
Small library for conducting operations over the
entire set of NexSON files in one or more phylesystem
repositories.
'''
# Some imports to help our py2 code behave like py3
from __future__ import absolute_import, print_function, division
from peyotl.utility import get_config_setting_kwargs, \
                           get_config_object, \
                           expand_path, \
                           get_logger
from peyotl.utility.input_output import pretty_dict_str
from peyotl.nexson_syntax import can_convert_nexson_forms, \
                                 convert_nexson_format, \
                                 detect_nexson_version, \
                                 get_ot_study_info_from_nexml, \
                                 write_as_json, \
                                 write_obj_as_nexml, \
                                 _is_by_id_hbf
from peyotl.phylesystem.phylesystem_umbrella import Phylesystem
from peyotl.utility.str_util import UNICODE, is_str_type

def gen_otu_dict(nex_obj, nexson_version=None):
    '''Takes a NexSON object and returns a dict of
    otu_id -> otu_obj
    '''
    if nexson_version is None:
        nexson_version = detect_nexson_version(nex_obj)
    if _is_by_id_hbf(nexson_version):
        otus = nex_obj['nexml']['otusById']
        if len(otus) > 1:
            d = {}
            for v in otus.values():
                d.update(v['otuById'])
            return d
        else:
            return otus.values()[0]['otuById']
    o_dict = {}
    for ob in nex_obj.get('otus', []):
        for o in ob.get('otu', []):
            oid = o['@id']
            o_dict[oid] = o
    return o_dict

def iter_tree(nex_obj):
    '''Generator over each tree object in the NexSON object.'''
    for tb in nex_obj.get('trees', []):
        for tree in tb.get('tree', []):
            yield tree

def iter_node(tree):
    '''Generator over each node object in the tree object.'''
    for nd in tree.get('nodeById', {}).items():
        yield nd

__all__ = ['utility',
           'api',
           'nexson_proxy',
           'nexson_syntax',
           'nexson_validation',
           'ott',
           'phylesystem',
           'phylografter',
           'string',
           'sugar',
           'test',
           'utility',
           'external',
           'manip',
           'struct_diff',
           'evaluate_tree',
          ]