Summary

Bio::AlignIO::stockholm - stockholm 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 stockholm flat
file databases.

Methods

Methods description

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

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

Methods code

sub next_aln {

    my $self = shift;
    my $entry;

    my ($start,$end,%align,$name,$seqname,$seq,$count,
	%hash,%c2name, %accession, $no);

    # in stockholm format, every non-blank line that does not start
    # with '#=' is an alignment segment; the '#=' lines are mark up lines.
    # Of particular interest are the '#=GF <name/st-ed> AC <accession>'
    # lines, which give accession numbers for each segment

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

    while( defined($entry = $self->_readline) ) {
        $entry !~ /\w+/ && next;

	if ($entry =~ /^\#\s*STOCKHOLM\s+/) {
	    last;
	}
	else {
	    $self->throw("Not Stockholm format: Expecting\" # STOCKHOLM 1.0\"; Found\" $_\"");
	}
    }
#
#    Next section is same as for selex format
#
    while( defined($entry = $self->_readline) ) {
        $entry =~ /^\#=GS\s+(\S+)\s+AC\s+(\S+)/ && do {
	    $accession{ $1 } = $2;
	    next;
	};
	$entry =~ /^([A-Za-z\.\-]+)$/ && ( $align{$name} .= $1 ) && next; 
	$entry !~ /^([^\#]\S+)\s+([A-Za-z\.\-]+)\s*/ && next;
	
	$name = $1;
	$seq = $2;

	if( ! defined $align{$name}  ) {
	    $count++;
	    $c2name{$count} = $name;
	}
	$align{$name} .= $seq;
    }

    # ok... now we can make the sequences

     foreach $no ( sort { $a <=> $b } keys %c2name ) {
	$name = $c2name{$no};

	if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
	    $seqname = $1;
	    $start = $2;
	    $end = $3;
	} else {
	    $seqname=$name;
	    $start = 1;
	    $end = length($align{$name});
	}
	$seq = new Bio::LocatableSeq('-seq'=>$align{$name},
			    '-id'=>$seqname,
			    '-start'=>$start,
			    '-end'=>$end,
			    '-type'=>'aligned',
				     '-accession_number' => $accession{$name},

			    );

       $aln->add_seq($seq);

   }

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

   return $aln;

}

sub write_aln {

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

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

}

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://bio.perl.org/bioperl-bugs/

Email: schattner@alum.mit.edu

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