#!/opt/anaconda1anaconda2anaconda3/bin/python
# -*- coding: utf-8
"""Collapses variation for a given list of gene caller ids"""

import sys
import argparse

import anvio
import anvio.variabilityops as variabilityops

from anvio.errors import ConfigError, FilesNPathsError


__author__ = "Developers of anvi'o (see AUTHORS.txt)"
__copyright__ = "Copyleft 2015-2018, the Meren Lab (http://merenlab.org/)"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Collapse variability for a set of genes across samples')

    groupD = parser.add_argument_group('DATABASES', "Declaring relevant anvi'o databases. First things first.")
    groupD.add_argument(*anvio.A('profile-db'), **anvio.K('profile-db'))
    groupD.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db'))

    groupS = parser.add_argument_group('FOCUS', 'What do we want? A consensus sequence for a gene, or a list of\
                                                 genes. From where do we want it? All samples, by default. When\
                                                 do we want it? Whenever it is convenient.')
    groupS.add_argument(*anvio.A('gene-caller-id'), **anvio.K('gene-caller-id'))
    groupS.add_argument(*anvio.A('genes-of-interest'), **anvio.K('genes-of-interest'))
    groupS.add_argument(*anvio.A('samples-of-interest'), **anvio.K('samples-of-interest'))

    groupO = parser.add_argument_group('OUTPUT', 'Output file and output style')
    groupO.add_argument(*anvio.A('output-file'), **anvio.K('output-file', {'default': 'genes.fa', 'help': 'The output\
                                                  file name. The boring default is "%(default)s". You can change\
                                                  the output file format to a TAB-delimited file using teh flag \
                                                  `--tab-delimited`, in which case please do not forget to change the\
                                                  file name, too.'}))
    groupO.add_argument(*anvio.A('tab-delimited'), **anvio.K('tab-delimited'))


    groupE = parser.add_argument_group('EXTRAS', 'Parameters that will help you to do a very precise analysis.\
                                                  If you declare nothing from this bunch, you will get "everything"\
                                                  to play with, which is not necessarily a good thing...')
    groupE.add_argument(*anvio.A('engine'), **anvio.K('engine'))


    args = anvio.get_args(parser)

    try:
        c = variabilityops.ConsensusSequences(args)
        c.process()
        c.report()
    except ConfigError as e:
        print(e)
        sys.exit(1)
    except FilesNPathsError as e:
        print(e)
        sys.exit(2)
