Bio::AlignIO metafasta
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Summary
Bio::AlignIO::metafasta - Metafasta MSA Sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::Seq::Meta
Bio::Seq::SeqFactory
Bio::Seq::SeqFastaSpeedFactory
Bio::SimpleAlign
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
BEGIN Code
_initialize
No description
Code
next_alnDescriptionCode
write_alnDescriptionCode
widthDescriptionCode
Methods description
next_alncode    nextTop
 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
write_alncodeprevnextTop
 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
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);
}
next_alndescriptionprevnextTop
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 $aln->num_sequences; return;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($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 $self->_fh;
    return 1;
}
widthdescriptionprevnextTop
sub width {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'width'} = $value;
    }
    return $self->{'width'} || $WIDTH;
}

1;
}
General documentation
SEE ALSOTop
Bio::SeqIO::metafasta
FEEDBACKTop
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 _