# 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):


import itertools
import os.path
import re
import shutil
import tempfile
from Bio.Alphabet import generic_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from anoisetools import sff
    def __init__(self, fp):
        self._fp = (i.rstrip('\n') for i in fp)
        header = next(self._fp)
        count, barcode, fname = header.split(None, 2)
        self.count = int(count)
        self.barcode = barcode
        self.fname = fname

    def __iter__(self):
        while True:
            header = next(self._fp)[1:]
            split_line = next(self._fp).split()
            flow_length = int(split_line[0])
            flows = split_line[1:]
            flows = map(float, flows)
            bases = sff.flow_to_seq(flows)
            sequence = Seq(bases, generic_dna)
            record = SeqRecord(sequence, id=header)
            # Add flows and clip as annotations
            record.annotations['flow_values'] = [int(i * 100) for i in flows]
            record.annotations['clip_flow_right'] = flow_length
            yield record


def _record_to_anoise_raw(seq_record):
    """
    Generates a string suitable for using as input to AmpliconNoise,
    consisting of the identifier, a newline, the integer length of the
    flow, a space, and the float flow readings.
    """

# 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
import itertools
import os.path
import re
import shutil
import tempfile
from Bio.Alphabet import generic_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from anoisetools import sff

    def __init__(self, fp):
        self._fp = (i.rstrip('\n') for i in fp)
        header = next(self._fp)
        count, barcode, fname = header.split(None, 2)
        self.count = int(count)
        self.barcode = barcode
        self.fname = fname

    def __iter__(self):
        while True:
            header = next(self._fp)[1:]
            split_line = next(self._fp).split()
            flow_length = int(split_line[0])
            flows = split_line[1:]
            flows = map(float, flows)
            bases = sff.flow_to_seq(flows)
            sequence = Seq(bases, generic_dna)
            record = SeqRecord(sequence, id=header)
            # Add flows and clip as annotations
            record.annotations['flow_values'] = [int(i * 100) for i in flows]
            record.annotations['clip_flow_right'] = flow_length
            yield record


def _record_to_anoise_raw(seq_record):
    """
    Generates a string suitable for using as input to AmpliconNoise,
    consisting of the identifier, a newline, the integer length of the
    flow, a space, and the float flow readings.
    """

    l, r = sff.find_clip(seq_record)