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Summary

Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream

Package variables

Included modules

Inherit

Bio::AlignIO

Synopsis

Do not use this module directly. Use it via the Bio::AlignIO class.

Description

This object can transform Bio::SimpleAlign objects to and from
metafasta flat file databases.
The format of a metafasta file is

  >test/1-25
  ABCDEFHIJKLMNOPQRSTUVWXYZ
  &charge
  NBNAANCNJCNNNONNCNNUNNXNZ
  &chemical
  LBSAARCLJCLSMOIMCHHULRXRZ

where the sequence block is followed by one or several meta blocks.
Each meta block starts with the ampersand character '&' in the first
column and is immediately followed by the name of the meta data which
continues until the new line. The meta data follows it. All
characters, except new line, are important in meta data.

Methods

Methods description

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object - returns 0 on end of file
	    or on error
 Args    : NONE

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in fasta format
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object

 Title   : width
 Usage   : $obj->width($newval)
 Function: Get/Set the line width for METAFASTA output
 Returns : value of width
 Args    : newvalue (optional)

Methods code

BEGIN {

 $WIDTH = 60

}

sub _initialize {

  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  my ($width) = $self->_rearrange([qw(WIDTH)], @args);
  $width && $self->width($width);

}

sub next_aln {

    my( $self ) = @_;
    my $seq;
    my $alphabet;
    local $/ = "\n>";

    my $aln =  Bio::SimpleAlign->new();

    while(defined (my $entry = $self->_readline)) {
        chomp($entry);
        if ($entry =~ m/\A\s*\Z/s) { # very first one
            return unless $entry = $self->_readline;
            chomp($entry);
        }
        $entry =~ s/^>//;

        my ($top,$sequence) = split(/\n/,$entry,2);
        defined $sequence && $sequence =~ s/>//g;

        my @metas;
        ($sequence, @metas) = split /\n&/, $sequence;

        my ($id, $start, $end);
        if ( $top =~ /(\S+)\/(\d+)-(\d+)/ ) {
            $id = $1;
            $start = $2;
            $end = $3;
        }
        elsif ($top =~ /(\S+)/) {
            $id = $1;
            $start = 1;
            $end = length($sequence);
        }

        defined $sequence && $sequence =~ s/\s//g; # Remove whitespace

        $seq = Bio::Seq::Meta->new('-seq'        => $sequence,
				   '-display_id' => $id,
				   '-start'      => $start,
				   '-end'        => $end,
				   '-alphabet'   => $self->alphabet,
				   );

        foreach my $meta (@metas) {
            my ($name,$string) = split /\n/, $meta;
            $string =~ s/\n//g;	# Remove newlines, spaces are important
            $seq->named_meta($name, $string);
        }

	$aln->add_seq($seq);
	
	# alignment needs seqs all the same length, pad with gaps
	my $alnlen = $aln->length;
	foreach my $seq ( $aln->each_seq ) {
		if ( $seq->length < $alnlen ) {
			my ($diff) = ($alnlen - $seq->length);
			$seq->seq( $seq->seq() . "-" x $diff);
		}
	}
    }
    return $aln if $aln->num_sequences;
	return;

}

sub write_aln {

    my ($self,@aln) = @_;
    my $width = $self->width;

    foreach my $aln (@aln) {
	if( ! $aln || ! $aln->isa('Bio::Align::AlignI')  ) {
	    $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
	    next;
	}
	foreach my $seq ( $aln->each_seq() ) {
	    my $name = $aln->displayname($seq->get_nse);

	    my $str  = $seq->seq();
            if(length($str) > 0) {
                $str =~ s/(.{1,$width})/$1\n/g;
            } else {
                $str = "\n";
            }
            $self->_print (">",$name,"\n",$str) or return;
            if ($seq->isa('Bio::Seq::MetaI')) {
                foreach my $meta ($seq->meta_names) {
                    my $str = $seq->named_meta($meta);
                    $str =~ s/(.{1,$width})/$1\n/g;
                    $self->_print ("&",$meta,"\n",$str);
                }
            }
	}
    }
    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 1;

}

sub width {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'width'} = $value;
    }
    return $self->{'width'} || $WIDTH;
}

1;

}

General documentation

Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:

  https://redmine.open-bio.org/projects/bioperl/

Email heikki-at-bioperl-dot-org

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _