# Path: simdna/simdnautil/util.py
# DEFAULT_LETTER_TO_INDEX = {'A': 0, 'C': 1, 'G': 2, 'T': 3}
# DEFAULT_BACKGROUND_FREQ = OrderedDict(
#     [('A', 0.3), ('C', 0.2), ('G', 0.2), ('T', 0.3)])
# DEFAULT_DINUC_FREQ = OrderedDict([
#  ('AA',0.095),
#  ('AC',0.050),
#  ('AG',0.071),
#  ('AT',0.075),
#  ('CA',0.073),
#  ('CC',0.054),
#  ('CG',0.010),
#  ('CT',0.072),
#  ('GA',0.060),
#  ('GC',0.044),
#  ('GG',0.054),
#  ('GT',0.050),
#  ('TA',0.064),
#  ('TC',0.060),
#  ('TG',0.073),
#  ('TT',0.095),
# ])
# DEFAULT_BASE_DISCRETE_DISTRIBUTION = DiscreteDistribution(
#     DEFAULT_BACKGROUND_FREQ)
# class DiscreteDistribution(object):
# class VariableWrapper():
#     class Enum(object):
# class FileNameParts(object):
# class ArgumentToAdd(object):
# class FloatArgument(ArgumentToAdd):
# class BooleanArgument(ArgumentToAdd):
# class CoreFileNameArgument(ArgumentToAdd):
# class ArrArgument(ArgumentToAdd):
# class ArrOfFileNamesArgument(ArrArgument):
#     def __init__(self, valToFreq):
#     def sample(self):
# def get_file_handle(filename, mode="r"):
# def default_tab_seppd(s):
# def trim_newline(s):
# def perform_action_on_each_line_of_file(
#     file_handle, action, transformation=default_tab_seppd, ignore_input_title=False):
# def process_line(line, i, ignore_input_title,
#                  transformation, action):
#     def __init__(self, var):
# def enum(**enums):
# def combine_enums(*enums):
# def sampleFromProbsArr(arrWithProbs):
# def reverseComplement(sequence):
# def sampleWithoutReplacement(arr, numToSample):
# def swapIndices(arr, idx1, idx2):
# def get_file_name_parts(file_name):
#     def __init__(self, directory, core_file_name, extension):
#     def get_full_path(self):
#     def get_core_file_name_and_extension(self):
#     def get_transformed_core_file_name(self, transformation, extension=None):
#     def get_transformed_file_path(self, transformation, extension=None):
# def format_as_json(jsonable_data):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def transform(self):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+", toStringFunc=str):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+"):
# def addArguments(string, args, joiner="_"):


import re
import os
import gzip
            import os.path
        import numpy as np
from simdna.simdnautil import util
    from collections import OrderedDict
                    indicesToCareAboutWrapper.var.append(
                        indicesLookup[labelToUse])
            return columnOrdering
        else:
            # regular line processing
            key = "_".join(inp[x] for x in keyColumns)
            if (subsetOfRowsToUseMembershipDict is None or (key in subsetOfRowsToUseMembershipDict)):
                if (indicesToCareAboutWrapper.var is None):
                    arrToAdd = [contentType(x)
                                for x in inp[contentStartIndex:]]
                else:
                    arrToAdd = [contentType(inp[x])
                                for x in indicesToCareAboutWrapper.var]
                return key, arrToAdd
            return None
    return titledMappingAction


def readTitledMapping(fileHandle, contentType=float, contentStartIndex=1, subsetOfColumnsToUseOptions=None, subsetOfRowsToUse=None, progressUpdate=None, keyColumns=[0]):
    """
        returns an instance of util.TitledMapping.
            util.TitledMapping has functions:
                - getTitledArrForKey(key): returns an instance of util.TitledArr which has: getCol(colName) and setCol(colName)
                - getArrForKey(key): returns the array for the key
                - keyPresenceCheck(key): throws an error if the key is absent
                Is also iterable! Returns an iterator of util.TitledArr
        subsetOfColumnsToUseOptions: instance of SubsetOfColumnsToUseOptions
        subsetOfRowsToUse: something that has a subset of row ids to be considered
    """


# Path: simdna/simdnautil/util.py
# DEFAULT_LETTER_TO_INDEX = {'A': 0, 'C': 1, 'G': 2, 'T': 3}
# DEFAULT_BACKGROUND_FREQ = OrderedDict(
#     [('A', 0.3), ('C', 0.2), ('G', 0.2), ('T', 0.3)])
# DEFAULT_DINUC_FREQ = OrderedDict([
#  ('AA',0.095),
#  ('AC',0.050),
#  ('AG',0.071),
#  ('AT',0.075),
#  ('CA',0.073),
#  ('CC',0.054),
#  ('CG',0.010),
#  ('CT',0.072),
#  ('GA',0.060),
#  ('GC',0.044),
#  ('GG',0.054),
#  ('GT',0.050),
#  ('TA',0.064),
#  ('TC',0.060),
#  ('TG',0.073),
#  ('TT',0.095),
# ])
# DEFAULT_BASE_DISCRETE_DISTRIBUTION = DiscreteDistribution(
#     DEFAULT_BACKGROUND_FREQ)
# class DiscreteDistribution(object):
# class VariableWrapper():
#     class Enum(object):
# class FileNameParts(object):
# class ArgumentToAdd(object):
# class FloatArgument(ArgumentToAdd):
# class BooleanArgument(ArgumentToAdd):
# class CoreFileNameArgument(ArgumentToAdd):
# class ArrArgument(ArgumentToAdd):
# class ArrOfFileNamesArgument(ArrArgument):
#     def __init__(self, valToFreq):
#     def sample(self):
# def get_file_handle(filename, mode="r"):
# def default_tab_seppd(s):
# def trim_newline(s):
# def perform_action_on_each_line_of_file(
#     file_handle, action, transformation=default_tab_seppd, ignore_input_title=False):
# def process_line(line, i, ignore_input_title,
#                  transformation, action):
#     def __init__(self, var):
# def enum(**enums):
# def combine_enums(*enums):
# def sampleFromProbsArr(arrWithProbs):
# def reverseComplement(sequence):
# def sampleWithoutReplacement(arr, numToSample):
# def swapIndices(arr, idx1, idx2):
# def get_file_name_parts(file_name):
#     def __init__(self, directory, core_file_name, extension):
#     def get_full_path(self):
#     def get_core_file_name_and_extension(self):
#     def get_transformed_core_file_name(self, transformation, extension=None):
#     def get_transformed_file_path(self, transformation, extension=None):
# def format_as_json(jsonable_data):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def __init__(self, val, argumentName=None, argNameAndValSep="-"):
#     def argNamePrefix(self):
#     def transform(self):
#     def transform(self):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+", toStringFunc=str):
#     def transform(self):
#     def __init__(self, val, argumentName, sep="+"):
# def addArguments(string, args, joiner="_"):


# Path: simdna/simdnautil/fileProcessing.py
import re
import os
import gzip
            import os.path
        import numpy as np
from simdna.simdnautil import util
    from collections import OrderedDict

                    indicesToCareAboutWrapper.var.append(
                        indicesLookup[labelToUse])
            return columnOrdering
        else:
            # regular line processing
            key = "_".join(inp[x] for x in keyColumns)
            if (subsetOfRowsToUseMembershipDict is None or (key in subsetOfRowsToUseMembershipDict)):
                if (indicesToCareAboutWrapper.var is None):
                    arrToAdd = [contentType(x)
                                for x in inp[contentStartIndex:]]
                else:
                    arrToAdd = [contentType(inp[x])
                                for x in indicesToCareAboutWrapper.var]
                return key, arrToAdd
            return None
    return titledMappingAction


def readTitledMapping(fileHandle, contentType=float, contentStartIndex=1, subsetOfColumnsToUseOptions=None, subsetOfRowsToUse=None, progressUpdate=None, keyColumns=[0]):
    """
        returns an instance of util.TitledMapping.
            util.TitledMapping has functions:
                - getTitledArrForKey(key): returns an instance of util.TitledArr which has: getCol(colName) and setCol(colName)
                - getArrForKey(key): returns the array for the key
                - keyPresenceCheck(key): throws an error if the key is absent
                Is also iterable! Returns an iterator of util.TitledArr
        subsetOfColumnsToUseOptions: instance of SubsetOfColumnsToUseOptions
        subsetOfRowsToUse: something that has a subset of row ids to be considered
    """


    titledMappingWrapper = util.VariableWrapper(None)