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Summary

Bio::Coordinate::Utils - Additional methods to create Bio::Coordinate objects

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

    use Bio::Coordinate::Utils;
    # get a Bio::Align::AlignI compliant object, $aln, somehow
    # it could be a Bio::SimpleAlign

    $mapper = Bio::Coordinate::Utils->from_align($aln, 1);

Description

This class is a holder of methods that work on or create
Bio::Coordinate::MapperI- compliant objects. . These methods are not
part of the Bio::Coordinate::MapperI interface and should in general
not be essential to the primary function of sequence objects. If you
are thinking of adding essential functions, it might be better to
create your own sequence class. See Bio::PrimarySeqI,
Bio::PrimarySeq, and Bio::Seq for more.

Methods

Methods description

 Title   : from_align
 Usage   : $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
 Function:
           Create a mapper out of an alignment.
           The mapper will return a value only when both ends of
           the input range find a match.

           Note: This implementation works only on pairwise alignments
           and is not yet well tested!

 Returns : A Bio::Coordinate::MapperI
 Args    : Bio::Align::AlignI object
           Id for the reference sequence, optional

Methods code

sub from_align {

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

   $aln->isa('Bio::Align::AlignI') ||
       $self->throw('Not a Bio::Align::AlignI object but ['. ref($self). ']');

   # default reference sequence to the first sequence
   $ref ||= 1;

   my $collection = Bio::Coordinate::Collection->new(-return_match=>1);

   # this works only for pairs, so split the MSA
   # take the ref
   #foreach remaining seq in aln, do:

   my $cs = $aln->consensus_string(49);
   while ( $cs =~ /([^-]+)/g) {

       # alignment coordinates
       my $start = pos($cs) - length($1) + 1;
       my $end = $start+length($1)-1;

       my $seq1 = $aln->get_seq_by_pos(1);
       my $seq2 = $aln->get_seq_by_pos(2);

       my $match1 = Bio::Location::Simple->new
	   (-seq_id => $seq1->id,
	    -start => $seq1->location_from_column($start)->start,
	    -end => $seq1->location_from_column($end)->start,
	    -strand => $seq1->strand );

       my $match2 = Bio::Location::Simple->new
	   (-seq_id => $seq2->id,
	    -start => $seq2->location_from_column($start)->start,
	    -end => $seq2->location_from_column($end)->start,
	    -strand => $seq2->strand );

       my $pair = Bio::Coordinate::Pair->
	   new(-in => $match1,
	       -out => $match2
	      );

       $collection->add_mapper($pair);
   }

   return @{$collection->each_mapper}[0] if $collection->each_mapper == 1;
   return $collection;

}



1;

}

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
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or the web:

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

Email: heikki@ebi.ac.uk
Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

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