Source Code for Module Bio.AlignIO.Interfaces

  1  # Copyright 2008-2010 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  AlignIO support module (not for general use). 
  7   
  8  Unless you are writing a new parser or writer for Bio.AlignIO, you should not 
  9  use this module.  It provides base classes to try and simplify things. 
 10  """ 
 11   
 12  from Bio.Alphabet import single_letter_alphabet 
 13   
 14   
 15 -class AlignmentIterator(object): 
 16      """Base class for building MultipleSeqAlignment iterators. 
 17   
 18      You should write a next() method to return Aligment 
 19      objects.  You may wish to redefine the __init__ 
 20      method as well. 
 21      """ 
 22      #TODO - Should the default be Gapped(single_letter_alphabet) instead? 
 23 -    def __init__(self, handle, seq_count=None, 
 24                   alphabet = single_letter_alphabet): 
 25          """Create an AlignmentIterator object. 
 26   
 27          handle   - input file 
 28          count    - optional, expected number of records per alignment 
 29                     Recommend for fasta file format. 
 30          alphabet - optional, e.g. Bio.Alphabet.generic_protein 
 31   
 32          Note when subclassing: 
 33          - there should be a single non-optional argument, the handle, 
 34            and optional count and alphabet IN THAT ORDER. 
 35          - you do not have to require an alphabet (?). 
 36          - you can add additional optional arguments.""" 
 37          self.handle = handle 
 38          self.records_per_alignment = seq_count 
 39          self.alphabet = alphabet 
 40          ##################################################### 
 41          # You may want to subclass this, for example        # 
 42          # to read through the file to find the first record,# 
 43          # or if additional arguments are required.          # 
 44          ##################################################### 
 45   
 46 -    def next(self): 
 47          """Return the next alignment in the file. 
 48   
 49          This method should be replaced by any derived class to do something 
 50          useful.""" 
 51          raise NotImplementedError("This object should be subclassed") 
 52          ##################################################### 
 53          # You SHOULD subclass this, to split the file up    # 
 54          # into your individual alignments and convert these # 
 55          # into MultipleSeqAlignment objects.                # 
 56          ##################################################### 
 57   
 58 -    def __iter__(self): 
 59          """Iterate over the entries as MultipleSeqAlignment objects. 
 60   
 61          Example usage for (concatenated) PHYLIP files: 
 62   
 63          myFile = open("many.phy","r") 
 64          for alignment in PhylipIterator(myFile): 
 65              print "New alignment:" 
 66              for record in alignment: 
 67                  print record.id 
 68                  print record.seq 
 69          myFile.close()""" 
 70          return iter(self.next, None) 
 71   
 72   
 73 -class AlignmentWriter(object): 
 74      """Base class for building MultipleSeqAlignment writers. 
 75   
 76      You should write a write_alignment() method. 
 77      You may wish to redefine the __init__ method as well""" 
 78   
 79 -    def __init__(self, handle): 
 80          self.handle = handle 
 81   
 82 -    def write_file(self, alignments): 
 83          """Use this to write an entire file containing the given alignments. 
 84   
 85          alignments - A list or iterator returning MultipleSeqAlignment objects 
 86   
 87          In general, this method can only be called once per file. 
 88   
 89          This method should be replaced by any derived class to do something 
 90          useful.  It should return the number of alignments""" 
 91          raise NotImplementedError("This object should be subclassed") 
 92          ##################################################### 
 93          # You SHOULD subclass this, to write the alignment  # 
 94          # objecta to the file handle                        # 
 95          ##################################################### 
 96   
 97 -    def clean(self, text): 
 98          """Use this to avoid getting newlines in the output.""" 
 99          return text.replace("\n", " ").replace("\r", " ").replace("  ", " ") 
100   
101   
102 -class SequentialAlignmentWriter(AlignmentWriter): 
103      """Base class for building MultipleSeqAlignment writers. 
104   
105      This assumes each alignment can be simply appended to the file. 
106      You should write a write_alignment() method. 
107      You may wish to redefine the __init__ method as well""" 
108   
109 -    def __init__(self, handle): 
110          self.handle = handle 
111   
112 -    def write_file(self, alignments): 
113          """Use this to write an entire file containing the given alignments. 
114   
115          alignments - A list or iterator returning MultipleSeqAlignment objects 
116   
117          In general, this method can only be called once per file.""" 
118          self.write_header() 
119          count = 0 
120          for alignment in alignments: 
121              self.write_alignment(alignment) 
122              count += 1 
123          self.write_footer() 
124          return count 
125   
126 -    def write_header(self): 
127          """Use this to write any header. 
128   
129          This method should be replaced by any derived class to do something 
130          useful.""" 
131          pass 
132   
133 -    def write_footer(self): 
134          """Use this to write any footer. 
135   
136          This method should be replaced by any derived class to do something 
137          useful.""" 
138          pass 
139   
140 -    def write_alignment(self, alignment): 
141          """Use this to write a single alignment. 
142   
143          This method should be replaced by any derived class to do something 
144          useful.""" 
145          raise NotImplementedError("This object should be subclassed") 
146          ##################################################### 
147          # You SHOULD subclass this, to write the alignment  # 
148          # objecta to the file handle                        # 
149          ##################################################### 
150