FastaSequence.py

# -*- coding: utf-8 -*-
# copyright  2006 inesc/id
# written by luís pedro coelho
#
# licence: mit licence:
#
#   permission is hereby granted, free of charge, to any person obtaining a copy of
#   this software and associated documentation files (the "software"), to deal in
#   the software without restriction, including without limitation the rights to
#   use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
#   of the software, and to permit persons to whom the software is furnished to do
#   so, subject to the following conditions:
#
#   the above copyright notice and this permission notice shall be included in all
#   copies or substantial portions of the software.
#
#   the software is provided "as is", without warranty of any kind, express or
#   implied, including but not limited to the warranties of merchantability,
#   fitness for a particular purpose and noninfringement. in no event shall the
#   authors or copyright holders be liable for any claim, damages or other
#   liability, whether in an action of contract, tort or otherwise, arising
#   from, out of or in connection with the software or the use or other
#   dealings in the software.

class fasta_sequence:
    """
        fasta sequence with a header

        two members: header and seq
    """
    __slots__ = [ 'seq', 'header']
    def __init__(self, h=None, s=None):
        self.SetHeader(h)
        self.SetSeq(s)
    def SetHeader(self,Header):
        self.header = Header
    def SetSeq(self,Seq):
        self.seq = Seq
    def GetSeq(self):
        return self.seq
    def GetHeader(self):
        return self.header


def fasta_read(input):
    """
        fasta_read(input):

        @param input can be either a file or the name of a file.

        returns a list of fasta_sequence objects with all the sequences in the file.
        comments (lines starting with ';') are ignored.
    """
    if type(input) == str:
        if input.endswith('.gz'):
            import gzip
            input=gzip.gzipfile(input)
        else:
            input=file(input)
    results = []
    header = ''
    seq_items = []
    first = true
    for line in input:
        if line[0] == ';':
            continue # comment
        elif line[0] == '>':
            if not first:
                seq= "".join(seq_items)
                results.append(fasta_sequence(header,seq))
                seq_items = []
            header = line[1:-1] # eat '>' and '\n'
            first = false
        else:
            seq_items.append(line[:-1])
    if len(seq_items) > 0:
        seq = "".join(seq_items)
        results.append(fasta_sequence(header,seq))
    return results


def fasta_write(output,s):
    """
        fasta_write(output, sequence[s])

        @param output either a file (opened for writing) or a filename
        @param sequence it can be either a fasta_sequence or a list of fasta_sequence objects

        writes the sequence(s) into the file in fasta format
    """
    line_width=70
    if type(output) == str:
        if output.endswith('.gz'):
            import gzip
            output=gzip.gzipfile(output,'w')
        else:
            output=file(output,'w')
    if type(s) == list:
        for ss in s:
            fasta_write(output,ss)
    else:
        output.write("> %s\n" % s.header)
        for i in xrange(0,len(s.seq),line_width):
            output.write("%s\n" % s.seq[i:i+line_width])


def rfasta_write(output,seqs):
    """
        restricted fasta

        this format (used by biopropector) is just fasta with the whole sequence on one line.
    """
    if type(output) == str: output=file(output,'w')
    for s in seqs:
        output.write("> %s\n" % s.header)
        output.write("%s\n" % s.seq)