#!/opt/anaconda1anaconda2anaconda3/bin/python
# File created on 25 May 2010
from __future__ import division

__author__ = "Antonio Gonzalez Pena"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Antonio Gonzalez Pena", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1"
__maintainer__ = "Antonio Gonzalez Pena"
__email__ = "antgonza@gmail.com"

from os.path import isfile
from sys import stderr

from biom.table import Table

from qiime.util import (make_option, write_biom_table,
                        parse_command_line_parameters, get_options_lookup)
from qiime.parse import parse_trflp

options_lookup = get_options_lookup()

script_info = {}
script_info[
    'brief_description'] = """Convert TRFLP text file to an OTU table"""
script_info[
    'script_description'] = """The input for this script is a TRLFP text file. The output of this script is an OTU table text file that can be use with QIIME for further analysis """
script_info['script_usage'] = [
    ("""Usage:""", """You need to pass a TRFLP text, the script will remove not wanted chars sample and otus names, and will add zeros as need it""",
     """%prog -i trflp_in.txt -o otu_table.biom""")
]
script_info['output_description'] = ""
script_info['required_options'] = [
    make_option('-i', '--input_path',
                type='existing_filepath',
                help='input path: TRFLP text file'),
    make_option('-o', '--output_path',
                type='new_filepath',
                help="output file: OTU table"),
]
script_info['optional_options'] = []
script_info['version'] = __version__


def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    if not isfile(opts.input_path):
        raise IOError(
            "Input path (%s) not valid.  Does it exist?" %
            opts.input_path)

    samples, otus, data = parse_trflp(open(opts.input_path, 'U'))

    t = Table(data, otus, samples)
    write_biom_table(t, opts.output_path)


if __name__ == "__main__":
    main()
