#!/usr/bin/env python
# -*- coding: utf-8
"""A script to export a FASTA file of contigs from the contigs database."""

import sys
import argparse

import anvio
import anvio.db as db
import anvio.tables as t
import anvio.fastalib as fastalib
import anvio.terminal as terminal
import anvio.filesnpaths as filesnpaths

from anvio.errors import ConfigError, FilesNPathsError
import anvio.errors


__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):
    filesnpaths.is_output_file_writable(args.output_file)

    contigs_db = db.DB(args.contigs_db, anvio.__contigs__version__)
    contig_sequences_dict = contigs_db.get_table_as_dict(t.contig_sequences_table_name, string_the_key = True)
    contigs_db.disconnect()

    contigs_fasta = fastalib.FastaOutput(args.output_file)

    for contig_name in sorted(contig_sequences_dict.keys()):
        contigs_fasta.write_id(contig_name)
        contigs_fasta.write_seq(contig_sequences_dict[contig_name]['sequence'], split = False)

    run.info('Contigs FASTA', args.output_file)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description="Export contigs from an anvi'o contigs database")

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

    args = parser.parse_args()

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