format_silva_to_gg.py

import argparse
import re
import sys
import os

p = argparse.ArgumentParser(description="This script is used to transform the taxonomy derived from Silva to GreenGene")
p.add_argument('-i', '--input', dest='input', metavar='<path>', help='Taxonomic qza')
p.add_argument('-c', '--only-clean-tax', dest='clean', action='store_true',
               help='supply this to clean the tax only, but keep the levels name')
p.add_argument('-o', '--output', dest='output', metavar='<directory>', default='./', help='Given an output directory')
options = p.parse_args()

if not os.path.exists(options.output):
    os.makedirs(options.output)


def clean_tax(tax):
    for ambi in ['uncultured', 'Ambiguous', 'unidentified', 'unassigned', 'unclassified']:
        tax = re.sub(';[^;]*' + ambi + '.*', '', tax, flags=re.I)
    tax = re.sub('; ', ';', tax)
    tax = re.sub(r'[\-| ]+', '_', tax)
    tax = re.sub(';$', '', tax)
    return(tax)


def trans(tar):
    level = {"D_0": "k", "D_1": "p", "D_2": "c", "D_3": "o", "D_4": "f", "D_5": "g", "D_6": "s"}
    for t in level.keys():
        tar = re.sub(t, level[t], tar)
    tar = re.sub('; *D_7.+', '', tar)
#    for keyword in ['uncultured', 'Ambiguous', 'unidentified', 'unassigned', 'unclassified']:
#        tar = re.sub(';[^;]*%s.*' % (keyword), '', tar, flags=re.I)
    tar = clean_tax(tar)
    return(tar)


os.system('qiime tools export --input-path %s --output-path %s' % (options.input, options.output))

with open(options.output + '/' + 'taxonomy.tsv', 'r') as infile, open(options.output + '/' + 'transformed_taxonomy.tsv', 'w') as outfile:
    for line in enumerate(infile):
        if line[0] == 0:
            outfile.write(line[1])
        else:
            line = re.split('\t', line[1].strip())
            if options.clean:
                line[1] = clean_tax(line[1])
            else:
                print('changing D_0...D_6 to k..s')
                line[1] = trans(line[1])
            outfile.write('\t'.join(line) + '\n')


os.system('qiime tools import --input-format TSVTaxonomyFormat --output-path %s/%s --input-path %s/transformed_taxonomy.tsv --type FeatureData[Taxonomy]' % (
    options.output, options.input.split("/")[-1], options.output))