# Copyright 2006-2017,2020 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 removed module 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. """ import warnings from typing import Callable, Optional, Tuple from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from .Interfaces import _clean from .Interfaces import _get_seq_string from .Interfaces import SequenceIterator from .Interfaces import SequenceWriter from .Interfaces import _TextIOSource def SimpleFastaParser(handle): """Iterate over Fasta records as string tuples. Arguments: - handle - input stream opened in text mode 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) for line in handle: if line[0] == ">": title = line[1:].rstrip() break 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. Arguments: - handle - input stream opened in text mode 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? " f"Got: '{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. " f"Have '>{title}' and '{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 " f"two-line-per-record FASTA format. Have title line '{line}'" ) else: assert line[0] != ">", "line[0] == '>' ; this should be impossible!" class FastaIterator(SequenceIterator): """Parser for Fasta files.""" def __init__( self, source: _TextIOSource, alphabet: None = None, ) -> None: """Iterate over Fasta records as SeqRecord objects. Arguments: - source - input stream opened in text mode, or a path to a file - alphabet - optional alphabet, not used. Leave as None. 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 If you want to modify the records before writing, for example to change the ID of each record, you can use a generator function as follows: >>> def modify_records(records): ... for record in records: ... record.id = record.id.upper() ... yield record ... >>> with open('Fasta/dups.fasta') as handle: ... for record in modify_records(FastaIterator(handle)): ... print(record.id) ... ALPHA BETA GAMMA ALPHA DELTA """ if alphabet is not None: raise ValueError("The alphabet argument is no longer supported") super().__init__(source, mode="t", fmt="Fasta") def parse(self, handle): """Start parsing the file, and return a SeqRecord generator.""" records = self.iterate(handle) return records def iterate(self, handle): """Parse the file and generate SeqRecord objects.""" 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), id=first_word, name=first_word, description=title ) class FastaTwoLineIterator(SequenceIterator): """Parser for Fasta files with exactly two lines per record.""" def __init__(self, source): """Iterate over two-line Fasta records (as SeqRecord objects). Arguments: - source - input stream opened in text mode, or a path to a file 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. """ super().__init__(source, mode="t", fmt="FASTA") def parse(self, handle): """Start parsing the file, and return a SeqRecord generator.""" records = self.iterate(handle) return records def iterate(self, handle): """Parse the file and generate SeqRecord objects.""" 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), id=first_word, name=first_word, description=title ) class FastaWriter(SequenceWriter): """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, target, wrap=60, record2title=None): """Create a Fasta writer (OBSOLETE). Arguments: - target - Output stream opened in text mode, or a path to a file. - 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() """ super().__init__(target) 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.""" 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 = f"{id} {description}" else: title = id assert "\n" not in title assert "\r" not in title self.handle.write(f">{title}\n") data = _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. Please use the ``as_fasta_2line`` function instead, or the top level ``Bio.SeqIO.write()`` function instead using ``format="fasta"``. """ 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().__init__(handle, wrap=None, record2title=record2title) def as_fasta(record): """Turn a SeqRecord into a FASTA formatted 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 = f"{id} {description}" else: title = id assert "\n" not in title assert "\r" not in title lines = [f">{title}\n"] 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 formatted 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 = f"{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 f">{title}\n{data}\n" if __name__ == "__main__": from Bio._utils import run_doctest run_doctest(verbose=0)