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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);

    # Build a set of mappers which will map, for each sequence,
    # that sequence position in the alignment (exon position to alignment 
    # position) 
    my @mappers = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln);

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

 Title   : from_seq_to_alignmentpos
 Usage   : $mapper = Bio::Coordinate::Utils->from_seq_to_alignmentpos($aln, 1);
 Function:
           Create a mapper out of an alignment.
           The mapper will map the position of a sequence into that position
           in the alignment.

           Will work on alignments of >= 2 sequences 
 Returns : An array of Bio::Coordinate::MapperI
 Args    : Bio::Align::AlignI object

Methods code

sub from_align {

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

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

   # 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:
   $aln->map_chars('\.','-');
   my $cs = $aln->gap_line;
   my $seq1 = $aln->get_seq_by_pos(1);
   my $seq2 = $aln->get_seq_by_pos(2);   
   while ( $cs =~ /([^\-]+)/g) {
       # alignment coordinates
       my $lenmatch = length($1);
       my $start = pos($cs) - $lenmatch +1;
       my $end   = $start + $lenmatch -1;
       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
	    );
       unless( $pair->test ) {
	   $self->warn(join("",
			    "pair align did not pass test ($start..$end):\n",
			    "\tm1=",$match1->to_FTstring(), " len=",
			    $match1->length, 
			    " m2=", $match2->to_FTstring()," len=", 
			    $match2->length,"\n"));
       }
       $collection->add_mapper($pair);
   }
   return ($collection->each_mapper)[0] if $collection->mapper_count == 1;
   return $collection;

}

sub from_seq_to_alignmentpos {

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

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

    # default reference sequence to the first sequence
    my @mappers;
    $aln->map_chars('\.','-');
    for my $seq ( $aln->each_seq ) { 
	my $collection = Bio::Coordinate::Collection->new(-return_match=>1);
	my $cs = $seq->seq();
	# do we change this over to use index and substr for speed?
	while ( $cs =~ /([^\-]+)/g) {
	    # alignment coordinates
	    my $lenmatch = length($1);
	    my $start = pos($cs) - $lenmatch +1;
	    my $end   = $start + $lenmatch -1;

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

	    my $match2 = Bio::Location::Simple->new
		(-seq_id => 'alignment',
		 -start  => $start,
		 -end    => $end,
		 -strand => 0 );

	    my $pair = Bio::Coordinate::Pair->new
		(-in  => $match1,
		 -out => $match2
		 );
	    unless ( $pair->test ) {
		$self->warn(join("",
				 "pair align did not pass test ($start..$end):\n",
				 "\tm1=",$match1->to_FTstring(), " len=",
				 $match1->length, 
				 " m2=", $match2->to_FTstring()," len=", 
				 $match2->length,"\n"));
	    }
	    $collection->add_mapper($pair);
	}
	if( $collection->mapper_count == 1) {
	    push @mappers, ($collection->each_mapper)[0];
	} else { 
	    push @mappers, $collection;
	}
    }
    return @mappers;
}


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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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.

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/

Email: heikki-at-bioperl-dot-org
Jason Stajich jason at bioperl.org

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