FastaIO.py

# Copyright 2006-2015 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.
#
# This module is for reading and writing FASTA format files as SeqRecord
# objects.  The code is partly inspired  by earlier Biopython modules,
# Bio.Fasta.* and the now deprecated Bio.SeqIO.FASTA

"""Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.

You are expected to use this module via the Bio.SeqIO functions."""

from __future__ import print_function

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


def SimpleFastaParser(handle):
    """Generator function to iterate over Fasta records (as string tuples).

    For each record a tuple of two strings is returned, the FASTA title
    line (without the leading '>' character), and the sequence (with any
    whitespace removed). The title line is not divided up into an
    identifier (the first word) and comment or description.

    >>> with open("Fasta/dups.fasta") as handle:
    ...     for values in SimpleFastaParser(handle):
    ...         print(values)
    ...
    ('alpha', 'ACGTA')
    ('beta', 'CGTC')
    ('gamma', 'CCGCC')
    ('alpha (again - this is a duplicate entry to test the indexing code)', 'ACGTA')
    ('delta', 'CGCGC')

    """
    # 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] == ">":
            break

    while True:
        if line[0] != ">":
            raise ValueError(
                "Records in Fasta files should start with '>' character")
        title = line[1:].rstrip()
        lines = []
        line = handle.readline()
        while True:
            if not line:
                break
            if line[0] == ">":
                break
            lines.append(line.rstrip())
            line = handle.readline()

        # Remove trailing whitespace, and any internal spaces
        # (and any embedded \r which are possible in mangled files
        # when not opened in universal read lines mode)
        yield title, "".join(lines).replace(" ", "").replace("\r", "")

        if not line:
            return  # StopIteration

    assert False, "Should not reach this line"


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

    Arguments:

     - 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 as a tuple of strings.
       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.

    By default this will act like calling Bio.SeqIO.parse(handle, "fasta")
    with no custom handling of the title lines:

    >>> with open("Fasta/dups.fasta") as handle:
    ...     for record in FastaIterator(handle):
    ...         print(record.id)
    ...
    alpha
    beta
    gamma
    alpha
    delta

    However, you can supply a title2ids function to alter this:

    >>> def take_upper(title):
    ...     return title.split(None, 1)[0].upper(), "", title
    >>> with open("Fasta/dups.fasta") as handle:
    ...     for record in FastaIterator(handle, title2ids=take_upper):
    ...         print(record.id)
    ...
    ALPHA
    BETA
    GAMMA
    ALPHA
    DELTA

    """
    if title2ids:
        for title, sequence in SimpleFastaParser(handle):
            id, name, descr = title2ids(title)
            yield SeqRecord(Seq(sequence, alphabet),
                            id=id, name=name, description=descr)
    else:
        for title, sequence in SimpleFastaParser(handle):
            try:
                first_word = title.split(None, 1)[0]
            except IndexError:
                assert not title, repr(title)
                # Should we use SeqRecord default for no ID?
                first_word = ""
            yield SeqRecord(Seq(sequence, alphabet),
                            id=first_word, name=first_word, description=title)


class FastaWriter(SequentialSequenceWriter):
    """Class to write Fasta format files."""
    def __init__(self, handle, wrap=60, record2title=None):
        """Create a Fasta writer.

        Arguments:

         - handle - Handle to an output file, e.g. as returned
           by open(filename, "w")
         - wrap -   Optional line length used to wrap sequence lines.
           Defaults to wrapping the sequence at 60 characters
           Use zero (or None) for no wrapping, giving a single
           long line for the sequence.
         - record2title - Optional function to return the text to be
           used for the title line of each record.  By default
           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::

            handle = open(filename, "w")
            writer = FastaWriter(handle)
            writer.write_file(myRecords)
            handle.close()

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

            handle = open(filename, "w")
            writer = FastaWriter(handle)
            writer.write_header() # does nothing for Fasta files
            ...
            Multiple writer.write_record() and/or writer.write_records() calls
            ...
            writer.write_footer() # does nothing for Fasta files
            handle.close()

        """
        SequentialSequenceWriter.__init__(self, handle)
        self.wrap = None
        if wrap:
            if wrap < 1:
                raise ValueError
        self.wrap = wrap
        self.record2title = record2title

    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:
            title = self.clean(self.record2title(record))
        else:
            id = self.clean(record.id)
            description = self.clean(record.description)
            if description and description.split(None, 1)[0] == id:
                # The description includes the id at the start
                title = description
            elif description:
                title = "%s %s" % (id, description)
            else:
                title = id

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

        data = self._get_seq_string(record)  # Catches sequence being None

        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__":
    from Bio._utils import run_doctest
    run_doctest(verbose=0)