#!/opt/anaconda1anaconda2anaconda3/bin/python
# File created on 09 Feb 2010
# file filter_otus_by_sample.py

from __future__ import division

__author__ = "Jesse Stombaugh"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jesse Stombaugh"]
__license__ = "GPL"
__version__ = "1.9.1"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"

import os

from skbio.alignment import SequenceCollection
from skbio.sequence import DNA
from skbio.parse.sequences import parse_fasta

from qiime.util import make_option
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.filter_otus_by_sample import filter_samples, process_extract_samples
from qiime.parse import fields_to_dict

options_lookup = get_options_lookup()

# filter_otus_by_sample.py
script_info = {}
script_info[
    'brief_description'] = """Filter OTU mapping file and sequences by SampleIDs"""
script_info[
    'script_description'] = """This filter allows for the removal of sequences and OTUs containing user-specified Sample IDs, for instance, the removal of negative control samples. This script identifies OTUs containing the specified Sample IDs and removes its corresponding sequence from the sequence collection."""
script_info['script_usage'] = []
script_info['script_usage'].append(
    ("""Example:""",
     """The following command can be used, where all options are passed (using the resulting OTU file from pick_otus.py, FASTA file from split_libraries.py and removal of sample 'PC.636') with the resulting data being written to the output directory "filtered_otus/":""",
     """%prog -i seqs_otus.txt -f seqs.fna -s PC.636 -o filtered_otus/"""))
script_info[
    'output_description'] = """As a result a new OTU and sequence file is generated and written to a randomly generated folder where the name of the folder starts with "filter_by_otus" Also included in the folder, is another FASTA file containing the removed sequences, leaving the user with 3 files."""

script_info['required_options'] = [
    options_lookup['otu_map_as_primary_input'],
    options_lookup['input_fasta'],
    make_option('-s', '--samples_to_extract', type='string', help='This is a list of sample \
ids, which should be removed from the OTU file')]

script_info['optional_options'] = [
    options_lookup['output_dir']
]

script_info['version'] = __version__


def main():
    """opens files as necessary based on prefs"""
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    data = {}

    fasta_file = opts.input_fasta_fp

    # load the input alignment
    data['aln'] = SequenceCollection.from_fasta_records(
        parse_fasta(open(fasta_file)), DNA)

    # Load the otu file
    otu_path = opts.otu_map_fp
    otu_f = open(otu_path, 'U')
    otus = fields_to_dict(otu_f)
    otu_f.close()

    data['otus'] = otus
    # Determine which which samples to extract from representative seqs
    # and from otus file
    if opts.samples_to_extract:
        prefs = process_extract_samples(opts.samples_to_extract)

    filepath = opts.input_fasta_fp
    filename = filepath.strip().split('/')[-1]
    filename = filename.split('.')[0]

    if opts.output_dir:
        if os.path.exists(opts.output_dir):
            dir_path = opts.output_dir
        else:
            try:
                os.mkdir(opts.output_dir)
                dir_path = opts.output_dir
            except OSError:
                pass
    else:
        dir_path = './'

    try:
        action = filter_samples
    except NameError:
        action = None
    # Place this outside try/except so we don't mask NameError in action
    if action:
        action(prefs, data, dir_path, filename)

if __name__ == "__main__":
    main()
