Matching names in Phylogenetic Trees

[alrichardbollans]

The following is some experimental, unoptimised code for matching names in a phylogenetic tree in newick format:

def substitute_name_in_tree(tree_string: str, old_name: str, new_name: str):
    # Note ape will not read spaces, so add underscores back to names
    tree_string = re.sub(r'\b{}(?=;|:)'.format(old_name), new_name.replace(' ', '_'), tree_string)
    return tree_string

def relabel_tree():
    f = open(tree_file, "r")
    tree_string = f.readline()
    # From https://stackoverflow.com/questions/45668107/python-regex-parsing-newick-format
    rx = r'[(),]+([^;:]+)\b'
    name_list = re.findall(rx, tree_string)
    binomial_names = [get_binomial_from_label(x) for x in name_list]
    zipped = list(zip(name_list, binomial_names))

    df = pd.DataFrame(zipped, columns=['tree_name', 'binomial_name'])

    acc_name_df = get_accepted_info_from_names_in_column(df, 'binomial_name', match_level='fuzzy')
    acc_name_df.to_csv(os.path.join('inputs', 'acc_name_tree.csv'))
    acc_name_df = pd.read_csv(os.path.join('inputs', 'acc_name_tree.csv'), index_col=0)

    # Catch words in tree string by left hand word boundaries (generic) and right hand ; or : characters
    for index, row in acc_name_df.iterrows():
        print(f'{index} out of {len(acc_name_df)}')
        if isinstance(row[wcvp_accepted_columns['name']], str):

            tree_string = substitute_name_in_tree(tree_string, row['tree_name'], row[wcvp_accepted_columns['name']])
        else:
            # If not matched, use old name. This could be changed to a generic string to be dropped later.
            tree_string = substitute_name_in_tree(tree_string, row['tree_name'], row['binomial_name'])

    f = open(standard_tree_file, "w")
    f.writelines([tree_string])

However, in this case resolution requirements may be different depending on planned phylogenetic analyses. For example resolving species with misspelled/unknown species epithets to genera (as in 'full' matching) could cause issues if trying to induce genus-level subtrees.