#!/opt/anaconda1anaconda2anaconda3/bin/python
# File created on 09 Feb 2010
from __future__ import division

__author__ = "Rob Knight"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Daniel McDonald", "Kyle Bittinger"]
__license__ = "GPL"
__version__ = "1.9.1"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"


from qiime.util import make_option

from qiime.make_per_library_sff import make_per_library_sffs
from qiime.util import parse_command_line_parameters


# make_per_library_sff.py
script_info = {}
script_info[
    'brief_description'] = """Make per-library sff files from ID lists"""
script_info['script_description'] = """This script generates per-library sff files using a directory of text files, one per library, which list read ID's to be included.

The ID list files should contain one read ID per line. If a line contains multiple words (separated by whitespace), then only the first word is used. A '>' character is stripped from the beginning of the line, if present. Blank lines in the file are skipped.
"""
script_info['script_usage'] = []
script_info['script_usage'].append(
    ("""Example:""",
     """Make per-library sff files using input.sff and a directory of libs where each file in the directory contains the id lists for each library:""",
     """make_per_library_sff.py -i input.sff -l libs"""))
script_info[
    'output_description'] = """The result of this script generates sff files for each library."""

script_info['required_options'] = [
    make_option("-i", "--input_sff", type='existing_filepaths',
                help="Input sff file (separate multiple files w/ comma)"),
    make_option("-l", "--libdir", type='existing_dirpath',
                help="Directory containing ID list text files, one per library"),
]

script_info['optional_options'] = [
    make_option("-p", "--sfffile_path", type='string',
                help="Path to sfffile binary [default: use sfffile in $PATH]"),
    make_option('--use_sfftools', action='store_true', default=False,
                help=('Use external sfffile program instead of equivalent Python '
                      'routines.')),
    make_option('--debug', action='store_true', default=False,
                help="Print debugging output to stdout [default: %default]"),
]
script_info['version'] = __version__


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

    sff_fps = opts.input_sff
    make_per_library_sffs(
        sff_fps,
        opts.libdir,
        opts.use_sfftools,
        opts.sfffile_path,
        opts.debug,
    )

if __name__ == "__main__":
    main()
