Summary

Bio::SeqIO::metafasta - metafasta sequence input/output stream

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

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

  use Bio::SeqIO;

  # read the metafasta file
  $io = Bio::SeqIO->new(-file => "test.metafasta",
                        -format => "metafasta" );

  $seq = $io->next_seq;

Description

This object can transform Bio::Seq::Meta objects to and from metafasta
flat file databases.
For sequence part the code is an exact copy of Bio::SeqIO::fasta
module. The only added bits deal with meta data IO.
The format of a metafasta file is

  >test
  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_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq object
 Args    : NONE

 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : array of 1 to n Bio::PrimarySeqI objects

 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);
  unless ( defined $self->sequence_factory ) {
      $self->sequence_factory(Bio::Seq::SeqFastaSpeedFactory->new());
  }

}

sub next_seq {

	my( $self ) = @_;
	my $seq;
	my $alphabet;
	local $/ = "\n>";
	return unless 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 ($id,$fulldesc);
	if( $top =~ /^\s*(\S+)\s*(.*)/ ) {
		($id,$fulldesc) = ($1,$2);
	}

	if (defined $id && $id eq '') {$id=$fulldesc;} # FIX incase no space 
	                                               # between > and name \AE
	defined $sequence && $sequence =~ s/\s//g;	  # Remove whitespace

	# for empty sequences we need to know the mol.type
	$alphabet = $self->alphabet();
	if(defined $sequence && length($sequence) == 0) {
		if(! defined($alphabet)) {
			# let's default to dna
			$alphabet = "dna";
		}
	} else {
		# we don't need it really, so disable
		$alphabet = undef;
	}

	$seq = $self->sequence_factory->create(
						-seq         => $sequence,
						-id          => $id,
					   # Ewan's note - I don't think this healthy
					   # but obviously to taste.
					   #-primary_id  => $id,
					   -desc        => $fulldesc,
					   -alphabet    => $alphabet,
					   -direct      => 1,
													  );

	$seq = $seq->primary_seq;
	bless $seq, 'Bio::Seq::Meta';

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

	# if there wasn't one before, set the guessed type
	unless ( defined $alphabet ) {
		$self->alphabet($seq->alphabet());
	}
	return $seq;

}

sub write_seq {

   my ($self,@seq) = @_;
   my $width = $self->width;
   foreach my $seq (@seq) {
       $self->throw("Did not provide a valid Bio::PrimarySeqI object") 
	   unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');

       my $str = $seq->seq;
       my $top = $seq->display_id();
       if ($seq->can('desc') and my $desc = $seq->desc()) {
	   $desc =~ s/\n//g;
	   $top .= " $desc";
       }
       if(length($str) > 0) {
	   $str =~ s/(.{1,$width})/$1\n/g;
       } else {
	   $str = "\n";
       }
       $self->_print (">",$top,"\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;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

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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:

  http://bugzilla.open-bio.org/

Email heikki-at-bioperl-dot-org

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