#!/usr/bin/env python
# -*- coding: utf-8

"""Return short reads from BAM files mapping to gene."""

import sys

import anvio
import anvio.terminal as terminal

from anvio.dbops import ContigsSuperclass
from anvio.errors import ConfigError, FilesNPathsError
from anvio.bamops import ReadsMappingToARange


__author__ = "A. Murat Eren"
__copyright__ = "Copyright 2015, The anvio Project"
__credits__ = []
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "A. Murat Eren"
__email__ = "a.murat.eren@gmail.com"


run = terminal.Run()


def main(args):
    c = ContigsSuperclass(args)

    if args.gene_caller_id not in c.genes_in_contigs_dict:
        raise ConfigError, "The gene id you provided does not seem to be in the contigs\
                            database."

    gene_call = c.genes_in_contigs_dict[args.gene_caller_id]
    mapping_range_start = gene_call['start'] + args.leeway
    mapping_range_stop = gene_call['stop'] - args.leeway

    gene_length = gene_call['stop'] - gene_call['start']
    run.info('Contig', gene_call['contig'])
    run.info('Gene id', args.gene_caller_id)
    run.info('Gene length', gene_length)
    run.info('Leeway', args.leeway)
    run.info('Mapping range start in contig', mapping_range_start)
    run.info('Mapping range end in contig', mapping_range_stop)
    run.info('Actual length of mapping window', mapping_range_stop - mapping_range_start)


    r = ReadsMappingToARange()
    r.process_range(args.input_files, gene_call['contig'], mapping_range_start, mapping_range_stop)
    r.report(args.output_file)


if __name__ == '__main__':
    import argparse

    parser = argparse.ArgumentParser(description='Access reads in contigs and positions in a BAM file')

    parser.add_argument('-i', '--input-files', metavar = 'INPUT_BAM(S)', nargs='+', default = None, required = True,
                        help = 'Sorted and indexed BAM files to analyze. It is essential that all BAM files must be\
                                the result of mappings against the same contigs.')

    parser.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db', {'required': True}))
    parser.add_argument(*anvio.A('gene-caller-id'), **anvio.K('gene-caller-id', {'required': True}))
    parser.add_argument(*anvio.A('output-file'), **anvio.K('output-file', {'required': True}))
    parser.add_argument(*anvio.A('leeway'), **anvio.K('leeway'))

    args = parser.parse_args()

    try:
        main(args)
    except ConfigError, e:
        print e
        sys.exit(-1)
    except FilesNPathsError, e:
        print e
        sys.exit(-2)
  
