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Summary

Bio::AlignIO::mase - mase 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::Align::AlignI objects to and from mase flat
file databases.

Methods

Methods description

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object
 Args    : NONE

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in mase format  ###Not yet implemented!###
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object

Methods code

sub next_aln {

    my $self = shift;
    my $entry;
    my $name;
    my $start;
    my $end;
    my $seq;
    my $add;
    my $count = 0;
    my $seq_residues;

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


    while( $entry = $self->_readline) {
        $entry =~ /^;/ && next;
	if(  $entry =~ /^(\S+)\/(\d+)-(\d+)/ ) {
	    $name = $1;
	    $start = $2;
	    $end = $3;
	} else {
	    $entry =~ s/\s//g;
	    $name = $entry;
	    $end = -1;
	}

	$seq = "";

	while( $entry = $self->_readline) {
	    $entry =~ /^;/ && last;
	    $entry =~ s/[^A-Za-z\.\-]//g;
	    $seq .= $entry;
	}
	if( $end == -1) {
	    $start = 1;

	    $seq_residues = $seq;
	    $seq_residues =~ s/\W//g;
	    $end = length($seq_residues);
	}

	$add = new Bio::LocatableSeq('-seq'=>$seq,
			    '-id'=>$name,
			    '-start'=>$start,
			    '-end'=>$end,
			    );


       $aln->add_seq($add);


#  If $end <= 0, we have either reached the end of
#  file in <> or we have encountered some other error
#
   if ($end <= 0) { undef $aln;}

   }

   return $aln;

}

sub write_aln {

    my ($self,@aln) = @_;

    $self->throw("Sorry: mase-format output, not yet implemented! /n");
}

1;

}

General documentation

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

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email: schattner@alum.mit.edu

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