# Copyright 2006-2017 by Peter Cock. All rights reserved. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause 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.File import as_handle from Bio.Alphabet import single_letter_alphabet from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.SeqIO.Interfaces import SequentialSequenceWriter from Bio.SeqIO.Interfaces import _clean, _get_seq_string def SimpleFastaParser(handle): """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) # This matches the previous implementation where .readline() was used for line in handle: if line[0] == ">": title = line[1:].rstrip() break elif isinstance(line[0], int): # Same exception as for FASTQ files raise ValueError("Is this handle in binary mode not text mode?") else: # no break encountered - probably an empty file return # Main logic # Note, 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) lines = [] for line in handle: if line[0] == ">": yield title, "".join(lines).replace(" ", "").replace("\r", "") lines = [] title = line[1:].rstrip() continue lines.append(line.rstrip()) yield title, "".join(lines).replace(" ", "").replace("\r", "") def FastaTwoLineParser(handle): """Iterate over no-wrapping Fasta records as string tuples. Functionally the same as SimpleFastaParser but with a strict interpretation of the FASTA format as exactly two lines per record, the greater-than-sign identifier with description, and the sequence with no line wrapping. Any line wrapping will raise an exception, as will excess blank lines (other than the special case of a zero-length sequence as the second line of a record). Examples -------- This file uses two lines per FASTA record: >>> with open("Fasta/aster_no_wrap.pro") as handle: ... for title, seq in FastaTwoLineParser(handle): ... print("%s = %s..." % (title, seq[:3])) ... gi|3298468|dbj|BAA31520.1| SAMIPF = GGH... This equivalent file uses line wrapping: >>> with open("Fasta/aster.pro") as handle: ... for title, seq in FastaTwoLineParser(handle): ... print("%s = %s..." % (title, seq[:3])) ... Traceback (most recent call last): ... ValueError: Expected FASTA record starting with '>' character. Perhaps this file is using FASTA line wrapping? Got: 'MTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI' """ idx = -1 # for empty file for idx, line in enumerate(handle): if idx % 2 == 0: # title line if line[0] != ">": raise ValueError( "Expected FASTA record starting with '>' character. " "Perhaps this file is using FASTA line wrapping? " "Got: '{}'".format(line) ) title = line[1:].rstrip() else: # sequence line if line[0] == ">": raise ValueError( "Two '>' FASTA lines in a row. Missing sequence line " "if this is strict two-line-per-record FASTA format. " "Have '>{}' and '{}'".format(title, line) ) yield title, line.strip() if idx == -1: pass # empty file elif idx % 2 == 0: # on a title line raise ValueError( "Missing sequence line at end of file if this is strict " "two-line-per-record FASTA format. Have title line '{}'".format(line) ) else: assert line[0] != ">", "line[0] == '>' ; this should be impossible!" def FastaIterator(handle, alphabet=single_letter_alphabet, title2ids=None): """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 """ with as_handle(handle, "rU") as handle: 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, ) def FastaTwoLineIterator(handle, alphabet=single_letter_alphabet): """Iterate over two-line Fasta records (as SeqRecord objects). Arguments: - handle - input file - alphabet - optional alphabet This uses a strict interpretation of the FASTA as requiring exactly two lines per record (no line wrapping). Only the default title to ID/name/description parsing offered by the relaxed FASTA parser is offered. """ with as_handle(handle, "rU") as handle: for title, sequence in FastaTwoLineParser(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 (OBSOLETE). Please use the ``as_fasta`` function instead, or the top level ``Bio.SeqIO.write()`` function instead using ``format="fasta"``. """ def __init__(self, handle, wrap=60, record2title=None): """Create a Fasta writer (OBSOLETE). 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") class FastaTwoLineWriter(FastaWriter): """Class to write 2-line per record Fasta format files (OBSOLETE). This means we write the sequence information without line wrapping, and will always write a blank line for an empty sequence. """ def __init__(self, handle, record2title=None): """Create a 2-line per record Fasta writer (OBSOLETE). Arguments: - handle - Handle to an output file, e.g. as returned by open(filename, "w") - 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() """ super(FastaTwoLineWriter, self).__init__( handle, wrap=None, record2title=record2title ) def as_fasta(record): """Turn a SeqRecord into a FASTA formated string. This is used internally by the SeqRecord's .format("fasta") method and by the SeqIO.write(..., ..., "fasta") function. """ id = _clean(record.id) description = _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 lines = [">%s\n" % title] data = _get_seq_string(record) # Catches sequence being None assert "\n" not in data assert "\r" not in data for i in range(0, len(data), 60): lines.append(data[i : i + 60] + "\n") return "".join(lines) def as_fasta_2line(record): """Turn a SeqRecord into a two-line FASTA formated string. This is used internally by the SeqRecord's .format("fasta-2line") method and by the SeqIO.write(..., ..., "fasta-2line") function. """ id = _clean(record.id) description = _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 data = _get_seq_string(record) # Catches sequence being None assert "\n" not in data assert "\r" not in data return ">%s\n%s\n" % (title, data) if __name__ == "__main__": from Bio._utils import run_doctest run_doctest(verbose=0)