import sys

import anvio

from anvio.errors import ConfigError, FilesNPathsError

from anvio.bamops import GetReadsFromBAM

__copyright__ = "Copyleft 2015-2024, The Anvi'o Project (http://anvio.org/)"

__credits__ = []

__license__ = "GPL 3.0"

__version__ = anvio.__version__

__authors__ = ['meren', 'ekiefl']

__requires__ = ['profile-db', 'contigs-db', 'bin', 'bam-file']

__provides__ = ['short-reads-fasta']

__description__ = ("Get short reads back from a BAM file with options for compression, splitting of "

"forward and reverse reads, etc")

if __name__ == '__main__':

from anvio.argparse import ArgumentParser

parser = ArgumentParser(description=__description__)

parser.add_argument('input_bams', metavar = 'BAM FILE[S]', nargs='+',

help = 'BAM file(s) to access to recover short reads')

output_file_kwargs = {'help': 'File path(s) to store results. Multiple files should be separated by commas (no spaces).'}

groupA = parser.add_argument_group('INPUT OPTION #1', "Work with good'ol anvi'o databases, collections, and bins, and get all the reads from "

"one or more BAM files that match to the contigs matching to your selections.")

groupA.add_argument(*anvio.A('profile-db'), **anvio.K('profile-db', {'required': False}))

groupA.add_argument(*anvio.A('contigs-db'), **anvio.K('contigs-db', {'required': False}))

groupA.add_argument(*anvio.A('collection-name'), **anvio.K('collection-name'))

groupA.add_argument(*anvio.A('bin-id'), **anvio.K('bin-id'))

groupA.add_argument(*anvio.A('bin-ids-file'), **anvio.K('bin-ids-file'))

groupB = parser.add_argument_group('INPUT OPTION #2', "Target a specific contig and/or specific start/stop positions to get all the matching "

"reads from your BAM file(s).")

groupB.add_argument(*anvio.A('target-contig'), **anvio.K('target-contig'))

groupB.add_argument(*anvio.A('target-region-start'), **anvio.K('target-region-start'))

groupB.add_argument(*anvio.A('target-region-end'), **anvio.K('target-region-end'))

groupC = parser.add_argument_group('FILTERS', 'Choose which reads to work (or not to work) with like a pro.')

groupC.add_argument(*anvio.A('fetch-filter'), **anvio.K('fetch-filter'))

groupD = parser.add_argument_group('OUTPUT', 'Output options')

groupD.add_argument(*anvio.A('output-file'), **anvio.K('output-file'))

groupD.add_argument(*anvio.A('output-file-prefix'), **anvio.K('output-file-prefix'))

groupD.add_argument(*anvio.A('gzip-output'), **anvio.K('gzip-output'))

groupD.add_argument(*anvio.A('split-R1-and-R2'), **anvio.K('split-R1-and-R2'))

args = parser.get_args(parser)

try:

r = GetReadsFromBAM(args)

r.store_short_reads()

except ConfigError as e:

print(e)

sys.exit(-1)

except FilesNPathsError as e:

print(e)

sys.exit(-2)