Mercurial > repos > yating-l > jbrowsearchivecreator

annotate test/lib/python2.7/codecs.py @ 3:7d1a9a91b989 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
author yating-l
date Thu, 18 May 2017 18:37:28 -0400
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1 """ codecs -- Python Codec Registry, API and helpers.
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2
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3
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4 Written by Marc-Andre Lemburg (mal@lemburg.com).
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6 (c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
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8 """#"
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9
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10 import __builtin__, sys
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12 ### Registry and builtin stateless codec functions
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14 try:
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15 from _codecs import *
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16 except ImportError, why:
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17 raise SystemError('Failed to load the builtin codecs: %s' % why)
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19 __all__ = ["register", "lookup", "open", "EncodedFile", "BOM", "BOM_BE",
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20 "BOM_LE", "BOM32_BE", "BOM32_LE", "BOM64_BE", "BOM64_LE",
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21 "BOM_UTF8", "BOM_UTF16", "BOM_UTF16_LE", "BOM_UTF16_BE",
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22 "BOM_UTF32", "BOM_UTF32_LE", "BOM_UTF32_BE",
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23 "CodecInfo", "Codec", "IncrementalEncoder", "IncrementalDecoder",
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24 "StreamReader", "StreamWriter",
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25 "StreamReaderWriter", "StreamRecoder",
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26 "getencoder", "getdecoder", "getincrementalencoder",
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27 "getincrementaldecoder", "getreader", "getwriter",
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28 "encode", "decode", "iterencode", "iterdecode",
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29 "strict_errors", "ignore_errors", "replace_errors",
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30 "xmlcharrefreplace_errors", "backslashreplace_errors",
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31 "register_error", "lookup_error"]
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32
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33 ### Constants
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35 #
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36 # Byte Order Mark (BOM = ZERO WIDTH NO-BREAK SPACE = U+FEFF)
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37 # and its possible byte string values
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38 # for UTF8/UTF16/UTF32 output and little/big endian machines
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39 #
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41 # UTF-8
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42 BOM_UTF8 = '\xef\xbb\xbf'
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44 # UTF-16, little endian
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45 BOM_LE = BOM_UTF16_LE = '\xff\xfe'
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47 # UTF-16, big endian
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48 BOM_BE = BOM_UTF16_BE = '\xfe\xff'
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49
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50 # UTF-32, little endian
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51 BOM_UTF32_LE = '\xff\xfe\x00\x00'
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52
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53 # UTF-32, big endian
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54 BOM_UTF32_BE = '\x00\x00\xfe\xff'
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55
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56 if sys.byteorder == 'little':
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58 # UTF-16, native endianness
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59 BOM = BOM_UTF16 = BOM_UTF16_LE
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61 # UTF-32, native endianness
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62 BOM_UTF32 = BOM_UTF32_LE
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64 else:
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66 # UTF-16, native endianness
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67 BOM = BOM_UTF16 = BOM_UTF16_BE
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68
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69 # UTF-32, native endianness
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70 BOM_UTF32 = BOM_UTF32_BE
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72 # Old broken names (don't use in new code)
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73 BOM32_LE = BOM_UTF16_LE
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74 BOM32_BE = BOM_UTF16_BE
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75 BOM64_LE = BOM_UTF32_LE
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76 BOM64_BE = BOM_UTF32_BE
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79 ### Codec base classes (defining the API)
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80
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81 class CodecInfo(tuple):
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82 """Codec details when looking up the codec registry"""
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83
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84 # Private API to allow Python to blacklist the known non-Unicode
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85 # codecs in the standard library. A more general mechanism to
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86 # reliably distinguish test encodings from other codecs will hopefully
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87 # be defined for Python 3.5
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88 #
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89 # See http://bugs.python.org/issue19619
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90 _is_text_encoding = True # Assume codecs are text encodings by default
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91
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92 def __new__(cls, encode, decode, streamreader=None, streamwriter=None,
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93 incrementalencoder=None, incrementaldecoder=None, name=None,
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94 _is_text_encoding=None):
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95 self = tuple.__new__(cls, (encode, decode, streamreader, streamwriter))
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96 self.name = name
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97 self.encode = encode
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98 self.decode = decode
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99 self.incrementalencoder = incrementalencoder
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100 self.incrementaldecoder = incrementaldecoder
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101 self.streamwriter = streamwriter
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102 self.streamreader = streamreader
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103 if _is_text_encoding is not None:
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104 self._is_text_encoding = _is_text_encoding
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105 return self
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106
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107 def __repr__(self):
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108 return "<%s.%s object for encoding %s at 0x%x>" % (self.__class__.__module__, self.__class__.__name__, self.name, id(self))
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109
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110 class Codec:
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111
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112 """ Defines the interface for stateless encoders/decoders.
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113
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114 The .encode()/.decode() methods may use different error
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115 handling schemes by providing the errors argument. These
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116 string values are predefined:
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117
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118 'strict' - raise a ValueError error (or a subclass)
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119 'ignore' - ignore the character and continue with the next
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120 'replace' - replace with a suitable replacement character;
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121 Python will use the official U+FFFD REPLACEMENT
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122 CHARACTER for the builtin Unicode codecs on
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123 decoding and '?' on encoding.
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124 'xmlcharrefreplace' - Replace with the appropriate XML
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125 character reference (only for encoding).
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126 'backslashreplace' - Replace with backslashed escape sequences
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127 (only for encoding).
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128
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129 The set of allowed values can be extended via register_error.
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130
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131 """
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132 def encode(self, input, errors='strict'):
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133
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134 """ Encodes the object input and returns a tuple (output
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135 object, length consumed).
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136
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137 errors defines the error handling to apply. It defaults to
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138 'strict' handling.
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139
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140 The method may not store state in the Codec instance. Use
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141 StreamWriter for codecs which have to keep state in order to
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142 make encoding efficient.
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143
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144 The encoder must be able to handle zero length input and
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145 return an empty object of the output object type in this
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146 situation.
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147
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148 """
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149 raise NotImplementedError
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150
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151 def decode(self, input, errors='strict'):
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152
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153 """ Decodes the object input and returns a tuple (output
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154 object, length consumed).
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155
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156 input must be an object which provides the bf_getreadbuf
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157 buffer slot. Python strings, buffer objects and memory
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158 mapped files are examples of objects providing this slot.
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159
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160 errors defines the error handling to apply. It defaults to
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161 'strict' handling.
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162
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163 The method may not store state in the Codec instance. Use
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164 StreamReader for codecs which have to keep state in order to
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165 make decoding efficient.
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166
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167 The decoder must be able to handle zero length input and
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168 return an empty object of the output object type in this
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169 situation.
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170
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171 """
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172 raise NotImplementedError
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173
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174 class IncrementalEncoder(object):
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175 """
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176 An IncrementalEncoder encodes an input in multiple steps. The input can be
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177 passed piece by piece to the encode() method. The IncrementalEncoder remembers
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178 the state of the Encoding process between calls to encode().
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179 """
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180 def __init__(self, errors='strict'):
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181 """
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182 Creates an IncrementalEncoder instance.
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183
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184 The IncrementalEncoder may use different error handling schemes by
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185 providing the errors keyword argument. See the module docstring
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186 for a list of possible values.
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187 """
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188 self.errors = errors
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189 self.buffer = ""
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190
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191 def encode(self, input, final=False):
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192 """
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193 Encodes input and returns the resulting object.
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194 """
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195 raise NotImplementedError
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196
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197 def reset(self):
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198 """
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199 Resets the encoder to the initial state.
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200 """
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201
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202 def getstate(self):
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203 """
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204 Return the current state of the encoder.
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205 """
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206 return 0
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207
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208 def setstate(self, state):
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209 """
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210 Set the current state of the encoder. state must have been
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211 returned by getstate().
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212 """
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213
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214 class BufferedIncrementalEncoder(IncrementalEncoder):
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215 """
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216 This subclass of IncrementalEncoder can be used as the baseclass for an
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217 incremental encoder if the encoder must keep some of the output in a
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218 buffer between calls to encode().
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219 """
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220 def __init__(self, errors='strict'):
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221 IncrementalEncoder.__init__(self, errors)
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222 self.buffer = "" # unencoded input that is kept between calls to encode()
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223
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224 def _buffer_encode(self, input, errors, final):
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225 # Overwrite this method in subclasses: It must encode input
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226 # and return an (output, length consumed) tuple
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227 raise NotImplementedError
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228
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229 def encode(self, input, final=False):
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230 # encode input (taking the buffer into account)
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231 data = self.buffer + input
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232 (result, consumed) = self._buffer_encode(data, self.errors, final)
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233 # keep unencoded input until the next call
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234 self.buffer = data[consumed:]
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235 return result
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236
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237 def reset(self):
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238 IncrementalEncoder.reset(self)
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239 self.buffer = ""
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240
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241 def getstate(self):
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242 return self.buffer or 0
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243
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244 def setstate(self, state):
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245 self.buffer = state or ""
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246
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247 class IncrementalDecoder(object):
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248 """
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249 An IncrementalDecoder decodes an input in multiple steps. The input can be
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250 passed piece by piece to the decode() method. The IncrementalDecoder
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251 remembers the state of the decoding process between calls to decode().
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252 """
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253 def __init__(self, errors='strict'):
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254 """
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255 Creates a IncrementalDecoder instance.
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256
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257 The IncrementalDecoder may use different error handling schemes by
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258 providing the errors keyword argument. See the module docstring
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259 for a list of possible values.
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260 """
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261 self.errors = errors
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262
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263 def decode(self, input, final=False):
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264 """
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265 Decodes input and returns the resulting object.
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266 """
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267 raise NotImplementedError
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268
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269 def reset(self):
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270 """
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271 Resets the decoder to the initial state.
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272 """
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273
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274 def getstate(self):
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275 """
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276 Return the current state of the decoder.
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277
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278 This must be a (buffered_input, additional_state_info) tuple.
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279 buffered_input must be a bytes object containing bytes that
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280 were passed to decode() that have not yet been converted.
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281 additional_state_info must be a non-negative integer
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282 representing the state of the decoder WITHOUT yet having
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283 processed the contents of buffered_input. In the initial state
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284 and after reset(), getstate() must return (b"", 0).
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285 """
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286 return (b"", 0)
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287
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288 def setstate(self, state):
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289 """
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290 Set the current state of the decoder.
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291
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292 state must have been returned by getstate(). The effect of
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293 setstate((b"", 0)) must be equivalent to reset().
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294 """
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295
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296 class BufferedIncrementalDecoder(IncrementalDecoder):
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297 """
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298 This subclass of IncrementalDecoder can be used as the baseclass for an
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299 incremental decoder if the decoder must be able to handle incomplete byte
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300 sequences.
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301 """
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302 def __init__(self, errors='strict'):
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303 IncrementalDecoder.__init__(self, errors)
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304 self.buffer = "" # undecoded input that is kept between calls to decode()
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305
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306 def _buffer_decode(self, input, errors, final):
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307 # Overwrite this method in subclasses: It must decode input
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308 # and return an (output, length consumed) tuple
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309 raise NotImplementedError
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310
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311 def decode(self, input, final=False):
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312 # decode input (taking the buffer into account)
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313 data = self.buffer + input
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314 (result, consumed) = self._buffer_decode(data, self.errors, final)
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315 # keep undecoded input until the next call
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316 self.buffer = data[consumed:]
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317 return result
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318
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319 def reset(self):
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320 IncrementalDecoder.reset(self)
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321 self.buffer = ""
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322
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323 def getstate(self):
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324 # additional state info is always 0
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325 return (self.buffer, 0)
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326
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327 def setstate(self, state):
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328 # ignore additional state info
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329 self.buffer = state[0]
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330
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331 #
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332 # The StreamWriter and StreamReader class provide generic working
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333 # interfaces which can be used to implement new encoding submodules
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334 # very easily. See encodings/utf_8.py for an example on how this is
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335 # done.
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336 #
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337
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338 class StreamWriter(Codec):
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339
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340 def __init__(self, stream, errors='strict'):
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341
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342 """ Creates a StreamWriter instance.
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343
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344 stream must be a file-like object open for writing
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345 (binary) data.
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346
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347 The StreamWriter may use different error handling
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348 schemes by providing the errors keyword argument. These
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349 parameters are predefined:
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350
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351 'strict' - raise a ValueError (or a subclass)
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352 'ignore' - ignore the character and continue with the next
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353 'replace'- replace with a suitable replacement character
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354 'xmlcharrefreplace' - Replace with the appropriate XML
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355 character reference.
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356 'backslashreplace' - Replace with backslashed escape
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357 sequences (only for encoding).
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358
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359 The set of allowed parameter values can be extended via
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360 register_error.
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361 """
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362 self.stream = stream
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363 self.errors = errors
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364
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365 def write(self, object):
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366
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367 """ Writes the object's contents encoded to self.stream.
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368 """
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369 data, consumed = self.encode(object, self.errors)
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370 self.stream.write(data)
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371
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372 def writelines(self, list):
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373
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374 """ Writes the concatenated list of strings to the stream
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375 using .write().
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376 """
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377 self.write(''.join(list))
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diff changeset
378
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379 def reset(self):
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diff changeset
380
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381 """ Flushes and resets the codec buffers used for keeping state.
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diff changeset
382
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383 Calling this method should ensure that the data on the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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384 output is put into a clean state, that allows appending
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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385 of new fresh data without having to rescan the whole
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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386 stream to recover state.
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diff changeset
387
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yating-l
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388 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
389 pass
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
390
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parents:
diff changeset
391 def seek(self, offset, whence=0):
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392 self.stream.seek(offset, whence)
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diff changeset
393 if whence == 0 and offset == 0:
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yating-l
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394 self.reset()
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yating-l
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diff changeset
395
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diff changeset
396 def __getattr__(self, name,
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diff changeset
397 getattr=getattr):
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yating-l
parents:
diff changeset
398
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
399 """ Inherit all other methods from the underlying stream.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
400 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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401 return getattr(self.stream, name)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
402
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yating-l
parents:
diff changeset
403 def __enter__(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
404 return self
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
405
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yating-l
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diff changeset
406 def __exit__(self, type, value, tb):
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diff changeset
407 self.stream.close()
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yating-l
parents:
diff changeset
408
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
409 ###
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
410
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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parents:
diff changeset
411 class StreamReader(Codec):
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yating-l
parents:
diff changeset
412
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yating-l
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diff changeset
413 def __init__(self, stream, errors='strict'):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
414
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yating-l
parents:
diff changeset
415 """ Creates a StreamReader instance.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
416
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
417 stream must be a file-like object open for reading
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
418 (binary) data.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
419
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yating-l
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diff changeset
420 The StreamReader may use different error handling
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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421 schemes by providing the errors keyword argument. These
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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422 parameters are predefined:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
423
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yating-l
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diff changeset
424 'strict' - raise a ValueError (or a subclass)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
425 'ignore' - ignore the character and continue with the next
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
426 'replace'- replace with a suitable replacement character;
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
427
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
428 The set of allowed parameter values can be extended via
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
429 register_error.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
430 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
431 self.stream = stream
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diff changeset
432 self.errors = errors
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diff changeset
433 self.bytebuffer = ""
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yating-l
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434 # For str->str decoding this will stay a str
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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435 # For str->unicode decoding the first read will promote it to unicode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
436 self.charbuffer = ""
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diff changeset
437 self.linebuffer = None
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yating-l
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diff changeset
438
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
439 def decode(self, input, errors='strict'):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
440 raise NotImplementedError
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diff changeset
441
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yating-l
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diff changeset
442 def read(self, size=-1, chars=-1, firstline=False):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
443
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
444 """ Decodes data from the stream self.stream and returns the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
445 resulting object.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
446
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
447 chars indicates the number of characters to read from the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
448 stream. read() will never return more than chars
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
449 characters, but it might return less, if there are not enough
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
450 characters available.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
451
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
452 size indicates the approximate maximum number of bytes to
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
453 read from the stream for decoding purposes. The decoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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454 can modify this setting as appropriate. The default value
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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455 -1 indicates to read and decode as much as possible. size
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
456 is intended to prevent having to decode huge files in one
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
457 step.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
458
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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459 If firstline is true, and a UnicodeDecodeError happens
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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460 after the first line terminator in the input only the first line
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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461 will be returned, the rest of the input will be kept until the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
462 next call to read().
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
463
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diff changeset
464 The method should use a greedy read strategy meaning that
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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465 it should read as much data as is allowed within the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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466 definition of the encoding and the given size, e.g. if
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467 optional encoding endings or state markers are available
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yating-l
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diff changeset
468 on the stream, these should be read too.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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469 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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470 # If we have lines cached, first merge them back into characters
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
471 if self.linebuffer:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
472 self.charbuffer = "".join(self.linebuffer)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
473 self.linebuffer = None
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
474
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
475 # read until we get the required number of characters (if available)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
476 while True:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
477 # can the request be satisfied from the character buffer?
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
478 if chars >= 0:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
479 if len(self.charbuffer) >= chars:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
480 break
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
481 elif size >= 0:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
482 if len(self.charbuffer) >= size:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
483 break
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
484 # we need more data
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
485 if size < 0:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
486 newdata = self.stream.read()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
487 else:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
488 newdata = self.stream.read(size)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
489 # decode bytes (those remaining from the last call included)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
490 data = self.bytebuffer + newdata
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
491 try:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
492 newchars, decodedbytes = self.decode(data, self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
493 except UnicodeDecodeError, exc:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
494 if firstline:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
495 newchars, decodedbytes = self.decode(data[:exc.start], self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
496 lines = newchars.splitlines(True)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
497 if len(lines)<=1:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
498 raise
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
499 else:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
500 raise
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
501 # keep undecoded bytes until the next call
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
502 self.bytebuffer = data[decodedbytes:]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
503 # put new characters in the character buffer
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
504 self.charbuffer += newchars
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
505 # there was no data available
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
506 if not newdata:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
507 break
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
508 if chars < 0:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
509 # Return everything we've got
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
510 result = self.charbuffer
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
511 self.charbuffer = ""
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
512 else:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
513 # Return the first chars characters
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
514 result = self.charbuffer[:chars]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
515 self.charbuffer = self.charbuffer[chars:]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
516 return result
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
517
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
518 def readline(self, size=None, keepends=True):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
519
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
520 """ Read one line from the input stream and return the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
521 decoded data.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
522
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
523 size, if given, is passed as size argument to the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
524 read() method.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
525
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
526 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
527 # If we have lines cached from an earlier read, return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
528 # them unconditionally
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
529 if self.linebuffer:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
530 line = self.linebuffer[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
531 del self.linebuffer[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
532 if len(self.linebuffer) == 1:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
533 # revert to charbuffer mode; we might need more data
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
534 # next time
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
535 self.charbuffer = self.linebuffer[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
536 self.linebuffer = None
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
537 if not keepends:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
538 line = line.splitlines(False)[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
539 return line
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
540
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
541 readsize = size or 72
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
542 line = ""
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
543 # If size is given, we call read() only once
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
544 while True:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
545 data = self.read(readsize, firstline=True)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
546 if data:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
547 # If we're at a "\r" read one extra character (which might
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
548 # be a "\n") to get a proper line ending. If the stream is
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
549 # temporarily exhausted we return the wrong line ending.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
550 if data.endswith("\r"):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
551 data += self.read(size=1, chars=1)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
552
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
553 line += data
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
554 lines = line.splitlines(True)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
555 if lines:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
556 if len(lines) > 1:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
557 # More than one line result; the first line is a full line
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
558 # to return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
559 line = lines[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
560 del lines[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
561 if len(lines) > 1:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
562 # cache the remaining lines
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
563 lines[-1] += self.charbuffer
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
564 self.linebuffer = lines
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
565 self.charbuffer = None
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
566 else:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
567 # only one remaining line, put it back into charbuffer
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
568 self.charbuffer = lines[0] + self.charbuffer
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
569 if not keepends:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
570 line = line.splitlines(False)[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
571 break
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
572 line0withend = lines[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
573 line0withoutend = lines[0].splitlines(False)[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
574 if line0withend != line0withoutend: # We really have a line end
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
575 # Put the rest back together and keep it until the next call
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
576 self.charbuffer = "".join(lines[1:]) + self.charbuffer
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
577 if keepends:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
578 line = line0withend
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
579 else:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
580 line = line0withoutend
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
581 break
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
582 # we didn't get anything or this was our only try
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
583 if not data or size is not None:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
584 if line and not keepends:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
585 line = line.splitlines(False)[0]
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
586 break
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
587 if readsize<8000:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
588 readsize *= 2
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
589 return line
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
590
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
591 def readlines(self, sizehint=None, keepends=True):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
592
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
593 """ Read all lines available on the input stream
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
594 and return them as list of lines.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
595
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
596 Line breaks are implemented using the codec's decoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
597 method and are included in the list entries.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
598
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
599 sizehint, if given, is ignored since there is no efficient
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
600 way to finding the true end-of-line.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
601
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
602 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
603 data = self.read()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
604 return data.splitlines(keepends)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
605
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
606 def reset(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
607
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
608 """ Resets the codec buffers used for keeping state.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
609
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
610 Note that no stream repositioning should take place.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
611 This method is primarily intended to be able to recover
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
612 from decoding errors.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
613
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
614 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
615 self.bytebuffer = ""
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
616 self.charbuffer = u""
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
617 self.linebuffer = None
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
618
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
619 def seek(self, offset, whence=0):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
620 """ Set the input stream's current position.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
621
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
622 Resets the codec buffers used for keeping state.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
623 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
624 self.stream.seek(offset, whence)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
625 self.reset()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
626
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
627 def next(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
628
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
629 """ Return the next decoded line from the input stream."""
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
630 line = self.readline()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
631 if line:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
632 return line
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
633 raise StopIteration
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
634
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
635 def __iter__(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
636 return self
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
637
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
638 def __getattr__(self, name,
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
639 getattr=getattr):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
640
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
641 """ Inherit all other methods from the underlying stream.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
642 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
643 return getattr(self.stream, name)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
644
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
645 def __enter__(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
646 return self
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
647
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
648 def __exit__(self, type, value, tb):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
649 self.stream.close()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
650
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
651 ###
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
652
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
653 class StreamReaderWriter:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
654
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
655 """ StreamReaderWriter instances allow wrapping streams which
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
656 work in both read and write modes.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
657
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
658 The design is such that one can use the factory functions
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
659 returned by the codec.lookup() function to construct the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
660 instance.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
661
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
662 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
663 # Optional attributes set by the file wrappers below
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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parents:
diff changeset
664 encoding = 'unknown'
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
665
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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parents:
diff changeset
666 def __init__(self, stream, Reader, Writer, errors='strict'):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
667
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
668 """ Creates a StreamReaderWriter instance.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
669
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
670 stream must be a Stream-like object.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
671
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
672 Reader, Writer must be factory functions or classes
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
673 providing the StreamReader, StreamWriter interface resp.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
674
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
675 Error handling is done in the same way as defined for the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
676 StreamWriter/Readers.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
677
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
678 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
679 self.stream = stream
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
680 self.reader = Reader(stream, errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
681 self.writer = Writer(stream, errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
682 self.errors = errors
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
683
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
684 def read(self, size=-1):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
685
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
686 return self.reader.read(size)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
687
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
688 def readline(self, size=None):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
689
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
690 return self.reader.readline(size)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
691
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
692 def readlines(self, sizehint=None):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
693
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
694 return self.reader.readlines(sizehint)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
695
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
696 def next(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
697
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
698 """ Return the next decoded line from the input stream."""
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
699 return self.reader.next()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
700
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
701 def __iter__(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
702 return self
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
703
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
704 def write(self, data):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
705
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
706 return self.writer.write(data)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
707
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
708 def writelines(self, list):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
709
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
710 return self.writer.writelines(list)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
711
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
712 def reset(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
713
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
714 self.reader.reset()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
715 self.writer.reset()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
716
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
717 def seek(self, offset, whence=0):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
718 self.stream.seek(offset, whence)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
719 self.reader.reset()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
720 if whence == 0 and offset == 0:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
721 self.writer.reset()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
722
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
723 def __getattr__(self, name,
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
724 getattr=getattr):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
725
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
726 """ Inherit all other methods from the underlying stream.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
727 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
728 return getattr(self.stream, name)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
729
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
730 # these are needed to make "with codecs.open(...)" work properly
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
731
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
732 def __enter__(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
733 return self
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
734
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
735 def __exit__(self, type, value, tb):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
736 self.stream.close()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
737
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
738 ###
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
739
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
740 class StreamRecoder:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
741
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
742 """ StreamRecoder instances provide a frontend - backend
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
743 view of encoding data.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
744
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
745 They use the complete set of APIs returned by the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
746 codecs.lookup() function to implement their task.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
747
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
748 Data written to the stream is first decoded into an
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
749 intermediate format (which is dependent on the given codec
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
750 combination) and then written to the stream using an instance
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
751 of the provided Writer class.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
752
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
753 In the other direction, data is read from the stream using a
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
754 Reader instance and then return encoded data to the caller.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
755
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
756 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
757 # Optional attributes set by the file wrappers below
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
758 data_encoding = 'unknown'
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
759 file_encoding = 'unknown'
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
760
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
761 def __init__(self, stream, encode, decode, Reader, Writer,
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
762 errors='strict'):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
763
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
764 """ Creates a StreamRecoder instance which implements a two-way
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
765 conversion: encode and decode work on the frontend (the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
766 input to .read() and output of .write()) while
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
767 Reader and Writer work on the backend (reading and
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
768 writing to the stream).
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
769
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
770 You can use these objects to do transparent direct
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
771 recodings from e.g. latin-1 to utf-8 and back.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
772
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
773 stream must be a file-like object.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
774
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
775 encode, decode must adhere to the Codec interface, Reader,
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
776 Writer must be factory functions or classes providing the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
777 StreamReader, StreamWriter interface resp.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
778
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
779 encode and decode are needed for the frontend translation,
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
780 Reader and Writer for the backend translation. Unicode is
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
781 used as intermediate encoding.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
782
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
783 Error handling is done in the same way as defined for the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
784 StreamWriter/Readers.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
785
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
786 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
787 self.stream = stream
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
788 self.encode = encode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
789 self.decode = decode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
790 self.reader = Reader(stream, errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
791 self.writer = Writer(stream, errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
792 self.errors = errors
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
793
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
794 def read(self, size=-1):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
795
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
796 data = self.reader.read(size)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
797 data, bytesencoded = self.encode(data, self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
798 return data
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
799
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
800 def readline(self, size=None):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
801
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
802 if size is None:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
803 data = self.reader.readline()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
804 else:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
805 data = self.reader.readline(size)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
806 data, bytesencoded = self.encode(data, self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
807 return data
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
808
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
809 def readlines(self, sizehint=None):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
810
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
811 data = self.reader.read()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
812 data, bytesencoded = self.encode(data, self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
813 return data.splitlines(1)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
814
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
815 def next(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
816
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
817 """ Return the next decoded line from the input stream."""
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
818 data = self.reader.next()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
819 data, bytesencoded = self.encode(data, self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
820 return data
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
821
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
822 def __iter__(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
823 return self
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
824
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
825 def write(self, data):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
826
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
827 data, bytesdecoded = self.decode(data, self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
828 return self.writer.write(data)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
829
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
830 def writelines(self, list):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
831
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
832 data = ''.join(list)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
833 data, bytesdecoded = self.decode(data, self.errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
834 return self.writer.write(data)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
835
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
836 def reset(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
837
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
838 self.reader.reset()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
839 self.writer.reset()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
840
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
841 def __getattr__(self, name,
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
842 getattr=getattr):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
843
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
844 """ Inherit all other methods from the underlying stream.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
845 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
846 return getattr(self.stream, name)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
847
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
848 def __enter__(self):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
849 return self
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
850
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
851 def __exit__(self, type, value, tb):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
852 self.stream.close()
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
853
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
854 ### Shortcuts
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
855
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
856 def open(filename, mode='rb', encoding=None, errors='strict', buffering=1):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
857
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
858 """ Open an encoded file using the given mode and return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
859 a wrapped version providing transparent encoding/decoding.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
860
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
861 Note: The wrapped version will only accept the object format
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
862 defined by the codecs, i.e. Unicode objects for most builtin
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
863 codecs. Output is also codec dependent and will usually be
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
864 Unicode as well.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
865
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
866 Files are always opened in binary mode, even if no binary mode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
867 was specified. This is done to avoid data loss due to encodings
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
868 using 8-bit values. The default file mode is 'rb' meaning to
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
869 open the file in binary read mode.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
870
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
871 encoding specifies the encoding which is to be used for the
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
872 file.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
873
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
874 errors may be given to define the error handling. It defaults
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
875 to 'strict' which causes ValueErrors to be raised in case an
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
876 encoding error occurs.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
877
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
878 buffering has the same meaning as for the builtin open() API.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
879 It defaults to line buffered.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
880
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
881 The returned wrapped file object provides an extra attribute
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
882 .encoding which allows querying the used encoding. This
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
883 attribute is only available if an encoding was specified as
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
884 parameter.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
885
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
886 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
887 if encoding is not None:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
888 if 'U' in mode:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
889 # No automatic conversion of '\n' is done on reading and writing
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
890 mode = mode.strip().replace('U', '')
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
891 if mode[:1] not in set('rwa'):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
892 mode = 'r' + mode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
893 if 'b' not in mode:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
894 # Force opening of the file in binary mode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
895 mode = mode + 'b'
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
896 file = __builtin__.open(filename, mode, buffering)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
897 if encoding is None:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
898 return file
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
899 info = lookup(encoding)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
900 srw = StreamReaderWriter(file, info.streamreader, info.streamwriter, errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
901 # Add attributes to simplify introspection
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
902 srw.encoding = encoding
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
903 return srw
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
904
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
905 def EncodedFile(file, data_encoding, file_encoding=None, errors='strict'):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
906
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
907 """ Return a wrapped version of file which provides transparent
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
908 encoding translation.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
909
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
910 Strings written to the wrapped file are interpreted according
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
911 to the given data_encoding and then written to the original
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
912 file as string using file_encoding. The intermediate encoding
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
913 will usually be Unicode but depends on the specified codecs.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
914
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
915 Strings are read from the file using file_encoding and then
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
916 passed back to the caller as string using data_encoding.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
917
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
918 If file_encoding is not given, it defaults to data_encoding.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
919
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
920 errors may be given to define the error handling. It defaults
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
921 to 'strict' which causes ValueErrors to be raised in case an
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
922 encoding error occurs.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
923
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
924 The returned wrapped file object provides two extra attributes
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
925 .data_encoding and .file_encoding which reflect the given
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
926 parameters of the same name. The attributes can be used for
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
927 introspection by Python programs.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
928
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
929 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
930 if file_encoding is None:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
931 file_encoding = data_encoding
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
932 data_info = lookup(data_encoding)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
933 file_info = lookup(file_encoding)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
934 sr = StreamRecoder(file, data_info.encode, data_info.decode,
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
935 file_info.streamreader, file_info.streamwriter, errors)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
936 # Add attributes to simplify introspection
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
937 sr.data_encoding = data_encoding
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
938 sr.file_encoding = file_encoding
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
939 return sr
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
940
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
941 ### Helpers for codec lookup
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
942
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
943 def getencoder(encoding):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
944
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
945 """ Lookup up the codec for the given encoding and return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
946 its encoder function.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
947
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
948 Raises a LookupError in case the encoding cannot be found.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
949
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
950 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
951 return lookup(encoding).encode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
952
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
953 def getdecoder(encoding):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
954
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
955 """ Lookup up the codec for the given encoding and return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
956 its decoder function.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
957
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
958 Raises a LookupError in case the encoding cannot be found.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
959
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
960 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
961 return lookup(encoding).decode
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
962
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
963 def getincrementalencoder(encoding):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
964
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
965 """ Lookup up the codec for the given encoding and return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
966 its IncrementalEncoder class or factory function.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
967
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
968 Raises a LookupError in case the encoding cannot be found
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
969 or the codecs doesn't provide an incremental encoder.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
970
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
971 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
972 encoder = lookup(encoding).incrementalencoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
973 if encoder is None:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
974 raise LookupError(encoding)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
975 return encoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
976
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
977 def getincrementaldecoder(encoding):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
978
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
979 """ Lookup up the codec for the given encoding and return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
980 its IncrementalDecoder class or factory function.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
981
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
982 Raises a LookupError in case the encoding cannot be found
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
983 or the codecs doesn't provide an incremental decoder.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
984
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
985 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
986 decoder = lookup(encoding).incrementaldecoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
987 if decoder is None:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
988 raise LookupError(encoding)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
989 return decoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
990
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
991 def getreader(encoding):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
992
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
993 """ Lookup up the codec for the given encoding and return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
994 its StreamReader class or factory function.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
995
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
996 Raises a LookupError in case the encoding cannot be found.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
997
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
998 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
999 return lookup(encoding).streamreader
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1000
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1001 def getwriter(encoding):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1002
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1003 """ Lookup up the codec for the given encoding and return
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1004 its StreamWriter class or factory function.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1005
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1006 Raises a LookupError in case the encoding cannot be found.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1007
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1008 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1009 return lookup(encoding).streamwriter
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1010
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1011 def iterencode(iterator, encoding, errors='strict', **kwargs):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1012 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1013 Encoding iterator.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1014
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1015 Encodes the input strings from the iterator using a IncrementalEncoder.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1016
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1017 errors and kwargs are passed through to the IncrementalEncoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1018 constructor.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1019 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1020 encoder = getincrementalencoder(encoding)(errors, **kwargs)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1021 for input in iterator:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1022 output = encoder.encode(input)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1023 if output:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1024 yield output
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1025 output = encoder.encode("", True)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1026 if output:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1027 yield output
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1028
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1029 def iterdecode(iterator, encoding, errors='strict', **kwargs):
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1030 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1031 Decoding iterator.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1032
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1033 Decodes the input strings from the iterator using a IncrementalDecoder.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1034
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1035 errors and kwargs are passed through to the IncrementalDecoder
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1036 constructor.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1037 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1038 decoder = getincrementaldecoder(encoding)(errors, **kwargs)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1039 for input in iterator:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1040 output = decoder.decode(input)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1041 if output:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1042 yield output
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1043 output = decoder.decode("", True)
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1044 if output:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1045 yield output
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yating-l
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1046
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1047 ### Helpers for charmap-based codecs
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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1048
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1049 def make_identity_dict(rng):
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1050
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1051 """ make_identity_dict(rng) -> dict
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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1052
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1053 Return a dictionary where elements of the rng sequence are
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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1054 mapped to themselves.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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diff changeset
1055
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yating-l
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1056 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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1057 res = {}
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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1058 for i in rng:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1059 res[i]=i
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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1060 return res
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1061
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yating-l
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1062 def make_encoding_map(decoding_map):
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yating-l
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diff changeset
1063
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yating-l
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1064 """ Creates an encoding map from a decoding map.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1065
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yating-l
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diff changeset
1066 If a target mapping in the decoding map occurs multiple
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1067 times, then that target is mapped to None (undefined mapping),
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
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1068 causing an exception when encountered by the charmap codec
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
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1069 during translation.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1070
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yating-l
parents:
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1071 One example where this happens is cp875.py which decodes
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1072 multiple character to \\u001a.
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1073
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yating-l
parents:
diff changeset
1074 """
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1075 m = {}
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1076 for k,v in decoding_map.items():
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1077 if not v in m:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1078 m[v] = k
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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1079 else:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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1080 m[v] = None
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1081 return m
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1082
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yating-l
parents:
diff changeset
1083 ### error handlers
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1084
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yating-l
parents:
diff changeset
1085 try:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1086 strict_errors = lookup_error("strict")
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yating-l
parents:
diff changeset
1087 ignore_errors = lookup_error("ignore")
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yating-l
parents:
diff changeset
1088 replace_errors = lookup_error("replace")
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
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1089 xmlcharrefreplace_errors = lookup_error("xmlcharrefreplace")
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yating-l
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1090 backslashreplace_errors = lookup_error("backslashreplace")
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yating-l
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1091 except LookupError:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
diff changeset
1092 # In --disable-unicode builds, these error handler are missing
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1093 strict_errors = None
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yating-l
parents:
diff changeset
1094 ignore_errors = None
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1095 replace_errors = None
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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diff changeset
1096 xmlcharrefreplace_errors = None
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yating-l
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1097 backslashreplace_errors = None
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diff changeset
1098
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yating-l
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1099 # Tell modulefinder that using codecs probably needs the encodings
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yating-l
parents:
diff changeset
1100 # package
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
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1101 _false = 0
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yating-l
parents:
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1102 if _false:
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
yating-l
parents:
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1103 import encodings
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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1104
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yating-l
parents:
diff changeset
1105 ### Tests
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yating-l
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diff changeset
1106
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yating-l
parents:
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1107 if __name__ == '__main__':
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1108
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yating-l
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1109 # Make stdout translate Latin-1 output into UTF-8 output
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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1110 sys.stdout = EncodedFile(sys.stdout, 'latin-1', 'utf-8')
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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1111
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1112 # Have stdin translate Latin-1 input into UTF-8 input
7d1a9a91b989 planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty
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1113 sys.stdin = EncodedFile(sys.stdin, 'utf-8', 'latin-1')