Bio::SeqIO metafasta
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Summary
Bio::SeqIO::metafasta - metafasta sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::Seq::Meta
Bio::Seq::SeqFactory
Bio::Seq::SeqFastaSpeedFactory
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
BEGIN Code
_initialize
No description
Code
next_seqDescriptionCode
write_seqDescriptionCode
widthDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
write_seqcodeprevnextTop
 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
widthcodeprevnextTop
 Title   : width
Usage : $obj->width($newval)
Function: Get/Set the line width for METAFASTA output
Returns : value of width
Args : newvalue (optional)
Methods code
BEGINTop
BEGIN {
 $WIDTH = 60
}
_initializedescriptionprevnextTop
sub _initialize {
  my($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());
  }
}
next_seqdescriptionprevnextTop
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 $seq;
}
write_seqdescriptionprevnextTop
sub write_seq {
   my ($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 $self->_fh;
   return 1;
}
widthdescriptionprevnextTop
sub width {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'width'} = $value;
    }
    return $self->{'width'} || $WIDTH;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Heikki LehvaslaihoTop
Email heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _