Package Bio :: Package SeqIO :: Module Interfaces
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Source Code for Module Bio.SeqIO.Interfaces

  1  # Copyright 2006-2008 by Peter Cock.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its 
  3  # license.  Please see the LICENSE file that should have been included 
  4  # as part of this package. 
  5  """ 
  6  Bio.SeqIO support module (not for general use). 
  7   
  8  Unless you are writing a new parser or writer for Bio.SeqIO, you should not 
  9  use this module.  It provides base classes to try and simplify things. 
 10  """ 
 11   
 12  from Bio.Alphabet import generic_alphabet 
 13   
14 -class SequenceIterator :
15 """Base class for building SeqRecord iterators. 16 17 You should write a next() method to return SeqRecord 18 objects. You may wish to redefine the __init__ 19 method as well. 20 """
21 - def __init__(self, handle, alphabet=generic_alphabet) :
22 """Create a SequenceIterator object. 23 24 handle - input file 25 alphabet - optional, e.g. Bio.Alphabet.generic_protein 26 27 Note when subclassing: 28 - there should be a single non-optional argument, 29 the handle. 30 - you do not have to require an alphabet. 31 - you can add additional optional arguments.""" 32 self.handle = handle 33 self.alphabet = alphabet
34 ##################################################### 35 # You may want to subclass this, for example # 36 # to read through the file to find the first record,# 37 # or if additional arguments are required. # 38 ##################################################### 39
40 - def next(self) :
41 """Return the next record in the file. 42 43 This method should be replaced by any derived class to do something useful.""" 44 raise NotImplementedError("This object should be subclassed")
45 ##################################################### 46 # You SHOULD subclass this, to split the file up # 47 # into your individual records, and convert these # 48 # into useful objects, e.g. return SeqRecord object # 49 ##################################################### 50
51 - def __iter__(self):
52 """Iterate over the entries as a SeqRecord objects. 53 54 Example usage for Fasta files: 55 56 myFile = open("example.fasta","r") 57 myFastaReader = FastaIterator(myFile) 58 for record in myFastaReader : 59 print record.id 60 print record.seq 61 myFile.close()""" 62 return iter(self.next, None)
63
64 -class InterlacedSequenceIterator(SequenceIterator) :
65 """Base class for any iterator of a non-sequential file type. 66 67 This object is not intended for use directly. 68 69 When writing a parser for any interlaced sequence file where the whole 70 file must be read in order to extract any single record, then you should 71 subclass this object. 72 73 All you need to do is to define your own: 74 (1) __init__ method to parse the file and call self.move_start() 75 (2) __len__ method to return the number of records 76 (3) __getitem__ to return any requested record. 77 78 This class will then provide the iterator methods including next(), but relies 79 on knowing the total number of records and tracking the pending record index in 80 as self._n 81 82 It is up to the subclassed object to decide if it wants to generate a cache of 83 SeqRecords when initialised, or simply use its own lists and dicts and create 84 SeqRecords on request. 85 """ 86
87 - def __init__(self) :
88 """Create the object. 89 90 This method should be replaced by any derived class to do something useful.""" 91 #We assume that your implementation of __init__ will ensure self._n=0 92 self.move_start() 93 raise NotImplementedError("This object method should be subclassed")
94 ##################################################### 95 # You SHOULD subclass this # 96 ##################################################### 97
98 - def __len__(self) :
99 """Return the number of records. 100 101 This method should be replaced by any derived class to do something useful.""" 102 raise NotImplementedError("This object method should be subclassed")
103 ##################################################### 104 # You SHOULD subclass this # 105 ##################################################### 106
107 - def __getitem__(self, i) :
108 """Return the requested record. 109 110 This method should be replaced by any derived class to do something 111 useful. 112 113 It should NOT touch the value of self._n""" 114 raise NotImplementedError("This object method should be subclassed")
115 ##################################################### 116 # You SHOULD subclass this # 117 ##################################################### 118
119 - def move_start(self) :
120 self._n = 0
121
122 - def next(self) :
123 next_record = self._n 124 if next_record < len(self) : 125 self._n = next_record+1 126 return self[next_record] 127 else : 128 #StopIteration 129 return None
130
131 - def __iter__(self):
132 return iter(self.next, None)
133
134 -class SequenceWriter:
135 """This class should be subclassed. 136 137 Interlaced file formats (e.g. Clustal) should subclass directly. 138 139 Sequential file formats (e.g. Fasta, GenBank) should subclass 140 the SequentialSequenceWriter class instead. 141 """
142 - def __init__(self, handle):
143 """Creates the writer object. 144 145 Use the method write_file() to actually record your sequence records.""" 146 self.handle = handle
147
148 - def _get_seq_string(self, record):
149 """Use this to catch errors like the sequence being None.""" 150 try : 151 #The tostring() method is part of the Seq API, we could instead 152 #use str(record.seq) but that would give a string "None" if the 153 #sequence was None, and unpredicatable output if an unexpected 154 #object was present. 155 return record.seq.tostring() 156 except AttributeError : 157 if record.seq is None : 158 #We could silently treat this as an empty sequence, Seq(""), 159 #but that would be an implict assumption we should avoid. 160 raise TypeError("SeqRecord (id=%s) has None for its sequence." \ 161 % record.id) 162 else : 163 raise TypeError("SeqRecord (id=%s) has an invalid sequence." \ 164 % record.id)
165
166 - def clean(self, text) :
167 """Use this to avoid getting newlines in the output.""" 168 answer = text 169 for x in ["\n", "\r"] : 170 answer = answer.replace(x, " ") 171 return answer.replace(" ", " ")
172
173 - def write_file(self, records) :
174 """Use this to write an entire file containing the given records. 175 176 records - A list or iterator returning SeqRecord objects 177 178 Should return the number of records (as an integer). 179 180 This method can only be called once.""" 181 #Note when implementing this, you should close the file at the end. 182 raise NotImplementedError("This object should be subclassed")
183 ##################################################### 184 # You SHOULD subclass this # 185 ##################################################### 186
187 -class SequentialSequenceWriter(SequenceWriter):
188 """This class should be subclassed. 189 190 It is intended for sequential file formats with an (optional) 191 header, repeated records, and an (optional) footer. 192 193 In this case (as with interlaced file formats), the user may 194 simply call the write_file() method and be done. 195 196 However, they may also call the write_header(), followed 197 by multiple calls to write_record() and/or write_records() 198 followed finally by write_footer(). 199 200 Users must call write_header() and write_footer() even when 201 the file format concerned doesn't have a header or footer. 202 This is to try and make life as easy as possible when 203 switching the output format. 204 205 Note that write_header() cannot require any assumptions about 206 the number of records. 207 """
208 - def __init__(self, handle):
209 self.handle = handle 210 self._header_written = False 211 self._record_written = False 212 self._footer_written = False
213
214 - def write_header(self) :
215 assert not self._header_written, "You have aleady called write_header()" 216 assert not self._record_written, "You have aleady called write_record() or write_records()" 217 assert not self._footer_written, "You have aleady called write_footer()" 218 self._header_written = True
219 225
226 - def write_record(self, record):
227 """Write a single record to the output file. 228 229 record - a SeqRecord object 230 231 Once you have called write_header() you can call write_record() 232 and/or write_records() as many times as needed. Then call 233 write_footer() and close().""" 234 assert self._header_written, "You must call write_header() first" 235 assert not self._footer_written, "You have already called write_footer()" 236 self._record_written = True 237 raise NotImplementedError("This object should be subclassed")
238 ##################################################### 239 # You SHOULD subclass this # 240 ##################################################### 241
242 - def write_records(self, records):
243 """Write multiple record to the output file. 244 245 records - A list or iterator returning SeqRecord objects 246 247 Once you have called write_header() you can call write_record() 248 and/or write_records() as many times as needed. Then call 249 write_footer() and close(). 250 251 Returns the number of records written. 252 """ 253 #Default implementation: 254 assert self._header_written, "You must call write_header() first" 255 assert not self._footer_written, "You have already called write_footer()" 256 count = 0 257 for record in records : 258 self.write_record(record) 259 count += 1 260 #Mark as true, even if there where no records 261 self._record_written = True 262 return count
263
264 - def write_file(self, records) :
265 """Use this to write an entire file containing the given records. 266 267 records - A list or iterator returning SeqRecord objects 268 269 This method can only be called once. Returns the number of records 270 written. 271 """ 272 self.write_header() 273 count = self.write_records(records) 274 self.write_footer() 275 return count
276