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Sourcecode: python-biopython version File versions

Interfaces.py

# Copyright 2006-2008 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.
"""
Bio.SeqIO support module (not for general use).

Unless you are writing a new parser or writer for Bio.SeqIO, you should not
use this module.  It provides base classes to try and simplify things.
"""

from Bio.Alphabet import generic_alphabet

00014 class SequenceIterator :
    """Base class for building SeqRecord iterators.

    You should write a next() method to return SeqRecord
    objects.  You may wish to redefine the __init__
    method as well.
    """
00021     def __init__(self, handle, alphabet=generic_alphabet) :
        """Create a SequenceIterator object.

        handle - input file
        alphabet - optional, e.g. Bio.Alphabet.generic_protein

        Note when subclassing:
        - there should be a single non-optional argument,
          the handle.
        - you do not have to require an alphabet.
        - you can add additional optional arguments."""
        self.handle = handle
        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.          #
        #####################################################

00040     def next(self) :
        """Return the next record 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 records, and convert these   #
        # into useful objects, e.g. return SeqRecord object #
        #####################################################

00051     def __iter__(self):
        """Iterate over the entries as a SeqRecord objects.

        Example usage for Fasta files:

        myFile = open("example.fasta","r")
        myFastaReader = FastaIterator(myFile)
        for record in myFastaReader :
            print record.id
            print record.seq
        myFile.close()"""
        return iter(self.next, None)

00064 class InterlacedSequenceIterator(SequenceIterator) :
    """Base class for any iterator of a non-sequential file type.

    This object is not intended for use directly.
    
    When writing a parser for any interlaced sequence file where the whole
    file must be read in order to extract any single record, then you should
    subclass this object.

    All you need to do is to define your own:
    (1) __init__ method to parse the file and call self.move_start()
    (2) __len__ method to return the number of records
    (3) __getitem__ to return any requested record.

    This class will then provide the iterator methods including next(), but relies
    on knowing the total number of records and tracking the pending record index in
    as self._n

    It is up to the subclassed object to decide if it wants to generate a cache of
    SeqRecords when initialised, or simply use its own lists and dicts and create
    SeqRecords on request.
    """

00087     def __init__(self) :
        """Create the object.

        This method should be replaced by any derived class to do something useful."""
        #We assume that your implementation of __init__ will ensure self._n=0
        self.move_start()
        raise NotImplementedError("This object method should be subclassed")
        #####################################################
        # You SHOULD subclass this                          #
        #####################################################

00098     def __len__(self) :
        """Return the number of records.

        This method should be replaced by any derived class to do something useful."""
        raise NotImplementedError("This object method should be subclassed")
        #####################################################
        # You SHOULD subclass this                          #
        #####################################################

00107     def __getitem__(self, i) :
        """Return the requested record.

        This method should be replaced by any derived class to do something
        useful.

        It should NOT touch the value of self._n"""
        raise NotImplementedError("This object method should be subclassed")
        #####################################################
        # You SHOULD subclass this                          #
        #####################################################

    def move_start(self) :
        self._n = 0

00122     def next(self) :
        next_record = self._n
        if next_record < len(self) :
            self._n = next_record+1
            return self[next_record]
        else :
            #StopIteration
            return None
    
00131     def __iter__(self):
        return iter(self.next, None)

00134 class SequenceWriter:
    """This class should be subclassed.

    Interlaced file formats (e.g. Clustal) should subclass directly.

    Sequential file formats (e.g. Fasta, GenBank) should subclass
    the SequentialSequenceWriter class instead.
    """
00142     def __init__(self, handle):
        """Creates the writer object.

        Use the method write_file() to actually record your sequence records."""
        self.handle = handle

00148     def _get_seq_string(self, record):
        """Use this to catch errors like the sequence being None."""
        try :
            #The tostring() method is part of the Seq API, we could instead
            #use str(record.seq) but that would give a string "None" if the
            #sequence was None, and unpredicatable output if an unexpected
            #object was present.
            return record.seq.tostring()
        except AttributeError :
            if record.seq is None :
                #We could silently treat this as an empty sequence, Seq(""),
                #but that would be an implict assumption we should avoid.
                raise TypeError("SeqRecord (id=%s) has None for its sequence." \
                                % record.id)
            else :
                raise TypeError("SeqRecord (id=%s) has an invalid sequence." \
                                % record.id)

00166     def clean(self, text) :
        """Use this to avoid getting newlines in the output."""
        answer = text
        for x in ["\n", "\r"] :
            answer = answer.replace(x, " ")
        return answer.replace("  ", " ")
    
00173     def write_file(self, records) :
        """Use this to write an entire file containing the given records.

        records - A list or iterator returning SeqRecord objects

        Should return the number of records (as an integer).

        This method can only be called once."""
        #Note when implementing this, you should close the file at the end.
        raise NotImplementedError("This object should be subclassed")
        #####################################################
        # You SHOULD subclass this                          #
        #####################################################

00187 class SequentialSequenceWriter(SequenceWriter):
    """This class should be subclassed.

    It is intended for sequential file formats with an (optional)
    header, repeated records, and an (optional) footer.

    In this case (as with interlaced file formats), the user may
    simply call the write_file() method and be done.

    However, they may also call the write_header(), followed
    by multiple calls to write_record() and/or write_records()
    followed finally by write_footer().

    Users must call write_header() and write_footer() even when
    the file format concerned doesn't have a header or footer.
    This is to try and make life as easy as possible when
    switching the output format.
    
    Note that write_header() cannot require any assumptions about
    the number of records.
    """
00208     def __init__(self, handle):
        self.handle = handle
        self._header_written = False
        self._record_written = False
        self._footer_written = False

    def write_header(self) :
        assert not self._header_written, "You have aleady called write_header()"
        assert not self._record_written, "You have aleady called write_record() or write_records()"
        assert not self._footer_written, "You have aleady called write_footer()"
        self._header_written = True
        
    def write_footer(self) :
        assert self._header_written, "You must call write_header() first"
        assert self._record_written, "You have not called write_record() or write_records() yet"
        assert not self._footer_written, "You have aleady called write_footer()"
        self._footer_written = True

00226     def write_record(self, record):
        """Write a single record to the output file.

        record - a SeqRecord object

        Once you have called write_header() you can call write_record()
        and/or write_records() as many times as needed.  Then call
        write_footer() and close()."""
        assert self._header_written, "You must call write_header() first"
        assert not self._footer_written, "You have already called write_footer()"
        self._record_written = True
        raise NotImplementedError("This object should be subclassed")
        #####################################################
        # You SHOULD subclass this                          #
        #####################################################

00242     def write_records(self, records):
        """Write multiple record to the output file.

        records - A list or iterator returning SeqRecord objects

        Once you have called write_header() you can call write_record()
        and/or write_records() as many times as needed.  Then call
        write_footer() and close().

        Returns the number of records written.
        """
        #Default implementation:
        assert self._header_written, "You must call write_header() first"
        assert not self._footer_written, "You have already called write_footer()"
        count = 0
        for record in records :
            self.write_record(record)
            count += 1
        #Mark as true, even if there where no records
        self._record_written = True
        return count

00264     def write_file(self, records) :
        """Use this to write an entire file containing the given records.

        records - A list or iterator returning SeqRecord objects

        This method can only be called once.  Returns the number of records
        written.
        """
        self.write_header()
        count = self.write_records(records)
        self.write_footer()
        return count

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