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Sourcecode: python-biopython version File versions


from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Interfaces import SequentialSequenceWriter

#This is a generator function!
def FastaIterator(handle, alphabet = single_letter_alphabet, title2ids = None) :
    """Generator function to iterate over Fasta records (as SeqRecord objects).

    handle - input file
    alphabet - optional alphabet
    title2ids - A function that, when given the title of the FASTA
    file (without the beginning >), will return the id, name and
    description (in that order) for the record.

    If this is not given, then the entire title line will be used
    as the description, and the first word as the id and name.

    Note that use of title2ids matches that of Bio.Fasta.SequenceParser
    but the defaults are slightly different.
    #Skip any text before the first record (e.g. blank lines, comments)
    while True :
        line = handle.readline()
        if line == "" : return #Premature end of file, or just empty?
        if line[0] == ">" :

    while True :
        if line[0]<>">" :
            raise SyntaxError("Records in Fasta files should start with '>' character")
        if title2ids :
            id, name, descr = title2ids(line[1:].rstrip())
        else :
            descr = line[1:].rstrip()
            id   = descr.split()[0]
            name = id
        lines = []
        line = handle.readline()
        while True:
            if not line : break
            if line[0] == ">": break
            #Remove trailing whitespace, and any internal spaces
            lines.append(line.rstrip().replace(" ",""))
            line = handle.readline()
        #Return the record and then continue...
        yield SeqRecord(Seq("".join(lines), alphabet),
                         id = id, name = name, description = descr)

        if not line : return #StopIteration
    assert False, "Should not reach this line"

00055 class FastaWriter(SequentialSequenceWriter):
    """Class to write Fasta format files"""
00057     def __init__(self, handle, wrap=None, record2title=None):
        """Create a Fasta writer.

        handle - Handle to an output file, e.g. as returned
                 by open(filename, "w")
        wrap -   Optional line length used to wrap sequence lines.
                 By default a single long line is used for each sequence.
        record2title - Optional function to return the text to be
                 used for the title line of each record.  By default the
                 a combination of the record.id and record.description
                 is used.  If the record.description starts with the
                 record.id, then just the record.description is used.

        You can either use:

        myWriter = FastaWriter(open(filename,"w"))

        Or, follow the sequential file writer system, for example:

        myWriter = FastaWriter(open(filename,"w"))
        writer.write_header() # does nothing for Fasta files
        Multiple calls to writer.write_record() and/or writer.write_records()
        writer.write_footer() # does nothing for Fasta files
        SequentialSequenceWriter.__init__(self, handle)
        #self.handle = handle
        self.wrap = None
        if wrap :
            if wrap < 1 :
                raise ValueError
        self.wrap = wrap
        self.record2title = record2title

00094     def write_record(self, record):
        """Write a single Fasta record to the file"""
        assert self._header_written
        assert not self._footer_written
        self._record_written = True
        if self.record2title :
        else :
            id = self.clean(record.id)
            description = self.clean(record.description)

            #if description[:len(id)]==id :
            if description and description.split(None,1)[0]==id :
                #The description includes the id at the start
                title = description
            else :
                title = "%s %s" % (id, description)

        assert "\n" not in title
        assert "\r" not in title
        self.handle.write(">%s\n" % title)

        data = record.seq.tostring()
        assert "\n" not in data
        assert "\r" not in data

        if self.wrap :
            for i in range(0, len(data), self.wrap):
                self.handle.write(data[i:i+self.wrap] + "\n")
        else :
            self.handle.write(data + "\n")

if __name__ == "__main__" :
    import os
    from Bio.Alphabet import generic_protein, generic_nucleotide
    #Download the files from here:
    fna_filename = "NC_005213.fna"
    faa_filename = "NC_005213.faa"
    def genbank_name_function(text) :
        text, descr = text.split(None,1)
        id = text.split("|")[3]
        name = id.split(".",1)[0]
        return id, name, descr

    def print_record(record) :
        #See also bug 2057
        print "ID:" + record.id
        print "Name:" + record.name
        print "Descr:" + record.description
        print record.seq
        for feature in record.annotations :
            print '/%s=%s' % (feature, record.annotations[feature])
        if record.dbxrefs :
            print "Database cross references:"
            for x in record.dbxrefs : print " - %s" % x

    if os.path.isfile(fna_filename) :
        print "--------"
        print "FastaIterator (single sequence)"
        iterator = FastaIterator(open(fna_filename, "r"), alphabet=generic_nucleotide, title2ids=genbank_name_function)
        for record in iterator :
        assert count == 1
        print str(record.__class__)

    if os.path.isfile(faa_filename) :
        print "--------"
        print "FastaIterator (multiple sequences)"
        iterator = FastaIterator(open(faa_filename, "r"), alphabet=generic_protein, title2ids=genbank_name_function)
        for record in iterator :
        assert count>0
        print str(record.__class__)

    from cStringIO import StringIO
    print "--------"
    print "FastaIterator (empty input file)"
    #Just to make sure no errors happen
    iterator = FastaIterator(StringIO(""))
    count = 0
    for record in iterator :
        count = count+1
    assert count==0

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