Coverage for Bio.AlignIO.Interfaces : 50%

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# Copyright 2008-2013 by Peter Cock. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package.
Unless you are writing a new parser or writer for Bio.AlignIO, you should not use this module. It provides base classes to try and simplify things. """
"""Base class for building MultipleSeqAlignment iterators.
You should write a next() method to return Aligment objects. You may wish to redefine the __init__ method as well. """ #TODO - Should the default be Gapped(single_letter_alphabet) instead? alphabet = single_letter_alphabet): """Create an AlignmentIterator object.
handle - input file count - optional, expected number of records per alignment Recommend for fasta file format. alphabet - optional, e.g. Bio.Alphabet.generic_protein
Note when subclassing: - there should be a single non-optional argument, the handle, and optional count and alphabet IN THAT ORDER. - you do not have to require an alphabet (?). - you can add additional optional arguments.""" self.handle = handle self.records_per_alignment = seq_count self.alphabet = alphabet ##################################################### # You may want to subclass this, for example # # to read through the file to find the first record,# # or if additional arguments are required. # #####################################################
"""Return the next alignment in the file.
This method should be replaced by any derived class to do something useful.""" raise NotImplementedError("This object should be subclassed") ##################################################### # You SHOULD subclass this, to split the file up # # into your individual alignments and convert these # # into MultipleSeqAlignment objects. # #####################################################
"""Python 2 style alias for Python 3 style __next__ method.""" return self.__next__()
"""Iterate over the entries as MultipleSeqAlignment objects.
Example usage for (concatenated) PHYLIP files:
with open("many.phy","r") as myFile: for alignment in PhylipIterator(myFile): print "New alignment:" for record in alignment: print record.id print record.seq """ return iter(self.__next__, None)
"""Base class for building MultipleSeqAlignment writers.
You should write a write_alignment() method. You may wish to redefine the __init__ method as well"""
self.handle = handle
"""Use this to write an entire file containing the given alignments.
alignments - A list or iterator returning MultipleSeqAlignment objects
In general, this method can only be called once per file.
This method should be replaced by any derived class to do something useful. It should return the number of alignments""" raise NotImplementedError("This object should be subclassed") ##################################################### # You SHOULD subclass this, to write the alignment # # objecta to the file handle # #####################################################
"""Use this to avoid getting newlines in the output.""" return text.replace("\n", " ").replace("\r", " ").replace(" ", " ")
"""Base class for building MultipleSeqAlignment writers.
This assumes each alignment can be simply appended to the file. You should write a write_alignment() method. You may wish to redefine the __init__ method as well"""
self.handle = handle
"""Use this to write an entire file containing the given alignments.
alignments - A list or iterator returning MultipleSeqAlignment objects
In general, this method can only be called once per file.""" self.write_header() count = 0 for alignment in alignments: self.write_alignment(alignment) count += 1 self.write_footer() return count
"""Use this to write any header.
This method should be replaced by any derived class to do something useful.""" pass
"""Use this to write any footer.
This method should be replaced by any derived class to do something useful.""" pass
"""Use this to write a single alignment.
This method should be replaced by any derived class to do something useful.""" raise NotImplementedError("This object should be subclassed") ##################################################### # You SHOULD subclass this, to write the alignment # # objecta to the file handle # ##################################################### |