Example #1
0
def fetch_and_write_taxon_info(id_list, include_anc, list_tips, output):
    from peyotl.sugar import taxonomy
    for ott_id in id_list:
        info = taxonomy.taxon(ott_id,
                              include_lineage=include_anc,
                              list_terminal_descendants=list_tips,
                              wrap_response=True)
        write_taxon_info(info, include_anc, output)
Example #2
0
def fetch_and_write_taxon_info(id_list, include_anc, list_tips, output):
    from peyotl.sugar import taxonomy
    for ott_id in id_list:
        info = taxonomy.taxon(ott_id,
                              include_lineage=include_anc,
                              list_terminal_descendants=list_tips,
                              wrap_response=True)
        write_taxon_info(info, include_anc, output)
Example #3
0
def fetch_and_write_taxon_info(id_list, include_anc, list_tips, output):
    from peyotl.sugar import taxonomy
    assert(list_tips == False) # args.list_tips once https://github.com/OpenTreeOfLife/taxomachine/issues/89 is fixed @TEMP
    for ott_id in id_list:
        info = taxonomy.taxon(ott_id,
                              include_lineage=include_anc,
                              list_terminal_descendants=list_tips,
                              wrap_response=True)
        write_taxon_info(info, include_anc, output)
Example #4
0
def get_taxonomic_ancestor_ids(ott_id):
    from peyotl.sugar import taxonomy

    info = taxonomy.taxon(ott_id, include_lineage=True, list_terminal_descendants=False, wrap_response=True)
    anc_id_list = []
    while True:
        anc_id_list.append(info.ott_id)
        info = info.parent
        if info is None:
            return anc_id_list
Example #5
0
def get_taxonomic_ancestor_ids(ott_id):
    from peyotl.sugar import taxonomy
    info = taxonomy.taxon(ott_id,
                          include_lineage=True,
                          list_terminal_descendants=False,
                          wrap_response=True)
    anc_id_list = []
    while True:
        anc_id_list.append(info.ott_id)
        info = info.parent
        if info is None:
            return anc_id_list