# Path: anoisetools/scripts/clean.py
# DEFAULT_MIN_FLOWS = 360
# DEFAULT_MAX_FLOWS = 720
# FLOWGRAM_SIZE = 4
# def build_parser(subparsers):
#     def __init__(self, primer_re=None, high_signal_cutoff=9.49,
#             low_signal_cutoff=0.7, signal_start=0.5, max_empty=0, min_flows =
#             DEFAULT_MIN_FLOWS, max_flows=DEFAULT_MAX_FLOWS):
#     def is_empty(self, flowgram):
#     def is_high(self, flowgram):
#     def is_ambiguous(self, flowgram):
#     def is_valid(self, flowgram):
#     def _clean_flow_iter(self, flows):
#     def filter_record(self, flows):
#     def filter_records(self, records):
# def invoke(reader, fa_handle, dat_path, primer, min_flows, max_flows,
#         max_empty):
# def main(parsed):
# class FlowgramFilter(object):
# 
# Path: anoisetools/scripts/sff2raw.py
# def build_parser(subparsers):
# def sff_to_raw(infile, outfile, identifier=None):
# def main(parsed):
# 
# Path: anoisetools/anoiseio.py
# class AnoiseRawReader(object):
# class AnoiseRawWriter(object):
#     def __init__(self, fp):
#     def __iter__(self):
# def _record_to_anoise_raw(seq_record):
#     def __init__(self, fp, identifier):
#     def _header(self):
#     def write(self, record):
#     def write_records(self, records):
#     def _copy_to_output(self):
#     def close(self):
# def _read_count(read_name):
# def read_mapping(fp):
# def merge_mapping(snoise_map, pnoise_map):
# 
# Path: anoisetools/run.py
# def run(self, command, mpi=True, suppress_stdout=True,
#         suppress_stderr=True, **kwargs):
#     """
#     Run the specified command
#     """
# 
#     if not (self.temp_dir and os.path.isdir(self.temp_dir)):
#         raise ValueError("Missing temporary directory: "
#                 "{0}".format(self.temp_dir))
# 
#     if mpi:
#         command = self._mpi_command(command)
# 
#     outputs = [i for i in ('stderr', 'stdout') if i not in kwargs]
#     for i in ('stderr', 'stdout'):
#         if not i in kwargs:
#             kwargs[i] = tempfile.SpooledTemporaryFile()
# 
#     # Convert args to strings
#     command = map(str, command)
# 
#     logging.info("Running: %s", " ".join(command))
#     try:
#         p = subprocess.Popen(command, cwd=self.temp_dir, **kwargs)
#         p.wait()
#         if p.returncode:
#             raise subprocess.CalledProcessError("Error", p.returncode)
#     except subprocess.CalledProcessError, e:
#         if 'stderr' in outputs:
#             kwargs['stderr'].seek(0)
#             stderr = kwargs['stderr'].read()
#         else:
#             stderr = ''
#         if 'stdout' in outputs:
#             kwargs['stdout'].seek(0)
#             stdout = kwargs['stdout'].read()
#         else:
#             stdout = ''
# 
#         logging.error("Error running '%s': returned with %s.\nstdout:\n%s\nstderr:%s",
#                 ' '.join(command), p.returncode, stdout, stderr)
#         raise SystemExit(1)
# 
# Path: anoisetools/util.py
# _AMBIGUOUS_MAP = {
#        'R': '[GA]',
#        'Y': '[TC]',
#        'K': '[GT]',
#        'M': '[AC]',
#        'S': '[GC]',
#        'W': '[AT]',
#        'B': '[GTC]',
#        'D': '[GAT]',
#        'H': '[ACT]',
#        'V': '[GCA]',
#        'N': '[AGCT]',
# }
# def ambiguous_pattern(sequence_str):
# def ambiguous_regex(sequence_str):


import logging
import os
import os.path
from anoisetools.scripts import clean, sff2raw
from anoisetools import anoiseio, run, util




def build_parser(subparsers):
    parser = subparsers.add_parser("pyronoise", help="Run PyroNoise",
            parents=[run.base_parser()])

    pnoise_opts = parser.add_argument_group("PyroNoise Options")
    pnoise_opts.add_argument('-s', '--sigma', type=float,
            default=60.0, help="""Initial cluster size (see Quince et al)
            [default: %(default)s]""")
    pnoise_opts.add_argument('-c', '--cutoff', type=float,
            default=0.01, help="""Initial cutoff (see Quince et al) [default:
            %(default)s]""")
    pnoise_opts.add_argument('-rin', '--lookup-file',
            help="""Lookup file""")

    parser.add_argument('sff_file', help="""SFF file""")
    parser.add_argument('-v', '--verbose', default=logging.INFO,
            action="store_const", const=logging.DEBUG)

    clean_group = parser.add_argument_group("Cleaning parameters")
    clean_group.add_argument('--min-flows', default=320, type=int,
            help="""Minimum flow count [default: %(default)s]""")
    clean_group.add_argument('--max-flows', default=720, type=int,
            help="""Maximum flow count [default: %(default)s]""")
    clean_group.add_argument('--max-empty', default=0, type=int,
            help="""Maximum empty flowgrams to accept before truncation
            [default: %(default)s]""")

# Path: anoisetools/scripts/clean.py
# DEFAULT_MIN_FLOWS = 360
# DEFAULT_MAX_FLOWS = 720
# FLOWGRAM_SIZE = 4
# def build_parser(subparsers):
#     def __init__(self, primer_re=None, high_signal_cutoff=9.49,
#             low_signal_cutoff=0.7, signal_start=0.5, max_empty=0, min_flows =
#             DEFAULT_MIN_FLOWS, max_flows=DEFAULT_MAX_FLOWS):
#     def is_empty(self, flowgram):
#     def is_high(self, flowgram):
#     def is_ambiguous(self, flowgram):
#     def is_valid(self, flowgram):
#     def _clean_flow_iter(self, flows):
#     def filter_record(self, flows):
#     def filter_records(self, records):
# def invoke(reader, fa_handle, dat_path, primer, min_flows, max_flows,
#         max_empty):
# def main(parsed):
# class FlowgramFilter(object):
# 
# Path: anoisetools/scripts/sff2raw.py
# def build_parser(subparsers):
# def sff_to_raw(infile, outfile, identifier=None):
# def main(parsed):
# 
# Path: anoisetools/anoiseio.py
# class AnoiseRawReader(object):
# class AnoiseRawWriter(object):
#     def __init__(self, fp):
#     def __iter__(self):
# def _record_to_anoise_raw(seq_record):
#     def __init__(self, fp, identifier):
#     def _header(self):
#     def write(self, record):
#     def write_records(self, records):
#     def _copy_to_output(self):
#     def close(self):
# def _read_count(read_name):
# def read_mapping(fp):
# def merge_mapping(snoise_map, pnoise_map):
# 
# Path: anoisetools/run.py
# def run(self, command, mpi=True, suppress_stdout=True,
#         suppress_stderr=True, **kwargs):
#     """
#     Run the specified command
#     """
# 
#     if not (self.temp_dir and os.path.isdir(self.temp_dir)):
#         raise ValueError("Missing temporary directory: "
#                 "{0}".format(self.temp_dir))
# 
#     if mpi:
#         command = self._mpi_command(command)
# 
#     outputs = [i for i in ('stderr', 'stdout') if i not in kwargs]
#     for i in ('stderr', 'stdout'):
#         if not i in kwargs:
#             kwargs[i] = tempfile.SpooledTemporaryFile()
# 
#     # Convert args to strings
#     command = map(str, command)
# 
#     logging.info("Running: %s", " ".join(command))
#     try:
#         p = subprocess.Popen(command, cwd=self.temp_dir, **kwargs)
#         p.wait()
#         if p.returncode:
#             raise subprocess.CalledProcessError("Error", p.returncode)
#     except subprocess.CalledProcessError, e:
#         if 'stderr' in outputs:
#             kwargs['stderr'].seek(0)
#             stderr = kwargs['stderr'].read()
#         else:
#             stderr = ''
#         if 'stdout' in outputs:
#             kwargs['stdout'].seek(0)
#             stdout = kwargs['stdout'].read()
#         else:
#             stdout = ''
# 
#         logging.error("Error running '%s': returned with %s.\nstdout:\n%s\nstderr:%s",
#                 ' '.join(command), p.returncode, stdout, stderr)
#         raise SystemExit(1)
# 
# Path: anoisetools/util.py
# _AMBIGUOUS_MAP = {
#        'R': '[GA]',
#        'Y': '[TC]',
#        'K': '[GT]',
#        'M': '[AC]',
#        'S': '[GC]',
#        'W': '[AT]',
#        'B': '[GTC]',
#        'D': '[GAT]',
#        'H': '[ACT]',
#        'V': '[GCA]',
#        'N': '[AGCT]',
# }
# def ambiguous_pattern(sequence_str):
# def ambiguous_regex(sequence_str):


# Path: anoisetools/scripts/pyronoise.py
import logging
import os
import os.path
from anoisetools.scripts import clean, sff2raw
from anoisetools import anoiseio, run, util





def build_parser(subparsers):
    parser = subparsers.add_parser("pyronoise", help="Run PyroNoise",
            parents=[run.base_parser()])

    pnoise_opts = parser.add_argument_group("PyroNoise Options")
    pnoise_opts.add_argument('-s', '--sigma', type=float,
            default=60.0, help="""Initial cluster size (see Quince et al)
            [default: %(default)s]""")
    pnoise_opts.add_argument('-c', '--cutoff', type=float,
            default=0.01, help="""Initial cutoff (see Quince et al) [default:
            %(default)s]""")
    pnoise_opts.add_argument('-rin', '--lookup-file',
            help="""Lookup file""")

    parser.add_argument('sff_file', help="""SFF file""")
    parser.add_argument('-v', '--verbose', default=logging.INFO,
            action="store_const", const=logging.DEBUG)

    clean_group = parser.add_argument_group("Cleaning parameters")
    clean_group.add_argument('--min-flows', default=320, type=int,
            help="""Minimum flow count [default: %(default)s]""")
    clean_group.add_argument('--max-flows', default=720, type=int,
            help="""Maximum flow count [default: %(default)s]""")
    clean_group.add_argument('--max-empty', default=0, type=int,
            help="""Maximum empty flowgrams to accept before truncation
            [default: %(default)s]""")

    clean_group.add_argument('--primer', default='.',