# 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

    with runner:
        # Clean
        logging.info("Extracting clean flows")
        raw_file = runner.path_join(arguments.stub + '.raw')
        with open(raw_file, 'w') as fp:
            sff2raw.sff_to_raw(arguments.sff_file, fp)
        clean_dat = runner.path_join(arguments.stub + '.dat')
        with open(raw_file) as raw_fp:
            reader = anoiseio.AnoiseRawReader(raw_fp)
            with open(runner.path_join(arguments.stub + '.fa'), 'w') as fa_fp:
                passed, failed = clean.invoke(reader, fa_fp, clean_dat,
                        arguments.primer, arguments.min_flows,
                        arguments.max_flows, arguments.max_empty)

                if not passed:
                    raise AssertionError(
                            "No sequences passed flowgram cleaning!")

        logging.info("Starting PyroNoise")
        run_pyronoise(runner, clean_dat, arguments.sigma,
                arguments.cutoff, arguments.stub, arguments.use_m,
                lookup_name=arguments.lookup_file)


def run_pyronoise(runner, dat_path, sigma, cutoff, output_stub, use_m=False,
        lookup_name=None):
    m = run.executable_transformer(use_m)
    pnoise_stub = output_stub + '-pnoise'
    runner.run(['PyroDist', '-in', dat_path, '-out', output_stub])

# 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


    with runner:
        # Clean
        logging.info("Extracting clean flows")
        raw_file = runner.path_join(arguments.stub + '.raw')
        with open(raw_file, 'w') as fp:
            sff2raw.sff_to_raw(arguments.sff_file, fp)
        clean_dat = runner.path_join(arguments.stub + '.dat')
        with open(raw_file) as raw_fp:
            reader = anoiseio.AnoiseRawReader(raw_fp)
            with open(runner.path_join(arguments.stub + '.fa'), 'w') as fa_fp:
                passed, failed = clean.invoke(reader, fa_fp, clean_dat,
                        arguments.primer, arguments.min_flows,
                        arguments.max_flows, arguments.max_empty)

                if not passed:
                    raise AssertionError(
                            "No sequences passed flowgram cleaning!")

        logging.info("Starting PyroNoise")
        run_pyronoise(runner, clean_dat, arguments.sigma,
                arguments.cutoff, arguments.stub, arguments.use_m,
                lookup_name=arguments.lookup_file)


def run_pyronoise(runner, dat_path, sigma, cutoff, output_stub, use_m=False,
        lookup_name=None):
    m = run.executable_transformer(use_m)
    pnoise_stub = output_stub + '-pnoise'
    runner.run(['PyroDist', '-in', dat_path, '-out', output_stub])

    runner.run([m('FCluster'), '-in', output_stub + '.fdist',