jwdebelius

import os
import biom
import numpy as np
import pandas as pd


def _parse_sample_lines(line):
    """
    Extracts the sample name from the kraken identifier
    """

jwdebelius

import pandas as pd

def tidy_taxon_silva(x):
    """
    A very ugly script for cleaning taxonomy.

    The script will take the string, and parse it into seven taxonomic levels
    if they are avalaible. If lower levels are unavalaible (i.e. they could
    not be classified accurately), then they will inheriet a designation
    from the last classified level. Then, ambigious or uncultured organisms