# Copyright 2006-2009 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 Bio.Alphabet import single_letter_alphabet from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio.SeqIO.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 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. 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] == ">": break while True: if line[0]!=">": raise ValueError("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 #(and any embedded \r which are possible in mangled files #when not opened in universal read lines mode) lines.append(line.rstrip().replace(" ","").replace("\r","")) 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" class FastaWriter(SequentialSequenceWriter): """Class to write Fasta format files.""" def __init__(self, handle, wrap=60, 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. 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 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")) writer.write_file(myRecords) 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 writer.close() """ SequentialSequenceWriter.__init__(self, handle) #self.handle = 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[:len(id)]==id: 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__": print("Running quick self test") import os from Bio.Alphabet import generic_protein, generic_nucleotide #Download the files from here: #ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans 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 #http://bugzilla.open-bio.org/show_bug.cgi?id=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) count=0 for record in iterator: count=count+1 print_record(record) 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) count=0 for record in iterator: count=count+1 print_record(record) break assert count>0 print(str(record.__class__)) from io 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 print("Done")