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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
'''
Created on May 13, 2014
@author: namphuon
'''
import argparse
import os
from argparse import Namespace
import sepp.config
import tipp.metagenomics
import sepp
def parse_args():
parser = argparse.ArgumentParser(
description='Performs various tools for TIPP.')
parser.add_argument(
"-g", "--gene",
dest="gene", metavar="GENE",
default=None,
type=str,
help="use GENE\'s reference package")
parser.add_argument(
"-o", "--output",
dest="output", metavar="OUTPUT",
default="output",
type=sepp.config.valid_file_prefix,
help="output files with prefix OUTPUT. [default: %(default)s]")
parser.add_argument(
"-d", "--outdir",
dest="outdir", metavar="OUTPUT_DIR",
default=os.path.curdir,
type=sepp.config.valid_dir_path,
help="output to OUTPUT_DIR directory. full-path required. "
"[default: %(default)s]")
parser.add_argument(
"-i", "--input",
dest="input", metavar="INPUT",
default=None,
type=str,
help="input file. full-path required. "
"(_classification.txt file from running run_tipp.py)")
parser.add_argument(
"-t", "--threshold",
dest="threshold", metavar="THRESHOLD",
default=0.95,
type=float,
help="Threshold for classification [default: 0.95]")
return parser.parse_args()
def profile(inputf, gene, output, prefix, threshold):
home = os.path.expanduser("~")
if os.path.isfile(home + "/.tipp/tipp.config"):
tipp_config_path = home + "/.tipp/tipp.config"
else:
tipp_config_path = "/etc/tipp/tipp.config"
sepp.config.set_main_config_path(tipp_config_path)
opts = Namespace()
sepp.config._read_config_file(open(tipp_config_path, 'r'), opts)
(taxon_map, level_map, key_map) = tipp.metagenomics.load_taxonomy(
"%s/%s.refpkg/all_taxon.taxonomy" % (opts.reference.path, gene))
gene_classification = tipp.metagenomics.generate_classification(
inputf, threshold)
tipp.metagenomics.remove_unclassified_level(gene_classification)
tstr = str("%d" % (threshold * 100))
cfile = str("%s/%s.classification_%s.txt" % (output, prefix, tstr))
tipp.metagenomics.write_classification(gene_classification, cfile)
tipp.metagenomics.write_abundance(gene_classification, output)
def main():
args = parse_args()
profile(args.input, args.gene, args.outdir, args.output,
args.threshold)
if __name__ == "__main__":
main()
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