# Path: anoisetools/sff.py
# FLOW_ORDER = 'TACG'
# READ_BEGIN = 'TCAG'
# def cumsum(iterable):
# def find_clip(seqrecord):
# def flow_to_seq(flowgram, flow_order=FLOW_ORDER):
# def bases_from_flows(seq_record):
# def flows_to_string(seq_record):
# 
# 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/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 argparse
import math
import re
import shutil
import sys
import tempfile
from anoisetools import sff, anoiseio, util
            clip_right = a['clip_flow_right']
            flows = a['flow_values']
            flows = [float(i) / 100.0 for  i in flows]
            trim_flows = flows[:clip_right]
            trim_flows = self.filter_record(trim_flows)
            trimmed_reading = sff.flow_to_seq(trim_flows)

            m = self.primer_re.match(trimmed_reading)
            if (self.min_flows is None or len(trim_flows) >= self.min_flows) and m:
                sequence = m.group(1)

                # Truncate the flow result to a maximum length
                # Note that the FASTA result is unchanged
                flow_result = trim_flows[:self.max_flows]

                # AmpliconNoise reports flowgram lengths to the nearest power of 4
                trim_len = int(math.ceil(len(flow_result) / 4.0)) * 4

                self.passed += 1
                yield (record.id, sequence, trim_len, flows[:self.max_flows])
            else:
                self.failed += 1


def invoke(reader, fa_handle, dat_path, primer, min_flows, max_flows,
        max_empty):
    """
    Main routine. Loop over the records in reader, write good results to
    fa_handle and dat_handle respectively.
    """

# Path: anoisetools/sff.py
# FLOW_ORDER = 'TACG'
# READ_BEGIN = 'TCAG'
# def cumsum(iterable):
# def find_clip(seqrecord):
# def flow_to_seq(flowgram, flow_order=FLOW_ORDER):
# def bases_from_flows(seq_record):
# def flows_to_string(seq_record):
# 
# 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/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/clean.py
import argparse
import math
import re
import shutil
import sys
import tempfile
from anoisetools import sff, anoiseio, util

            clip_right = a['clip_flow_right']
            flows = a['flow_values']
            flows = [float(i) / 100.0 for  i in flows]
            trim_flows = flows[:clip_right]
            trim_flows = self.filter_record(trim_flows)
            trimmed_reading = sff.flow_to_seq(trim_flows)

            m = self.primer_re.match(trimmed_reading)
            if (self.min_flows is None or len(trim_flows) >= self.min_flows) and m:
                sequence = m.group(1)

                # Truncate the flow result to a maximum length
                # Note that the FASTA result is unchanged
                flow_result = trim_flows[:self.max_flows]

                # AmpliconNoise reports flowgram lengths to the nearest power of 4
                trim_len = int(math.ceil(len(flow_result) / 4.0)) * 4

                self.passed += 1
                yield (record.id, sequence, trim_len, flows[:self.max_flows])
            else:
                self.failed += 1


def invoke(reader, fa_handle, dat_path, primer, min_flows, max_flows,
        max_empty):
    """
    Main routine. Loop over the records in reader, write good results to
    fa_handle and dat_handle respectively.
    """

    primer_re = re.compile(r'^{0}.*?({1}.*)'.format(sff.READ_BEGIN, primer))