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Summary

Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects

Package variables

Included modules

Inherit

Exporter

Synopsis

use Bio::Align::Utilities qw(aa_to_dna_aln);
my $dna_aln = aa_to_dna_aln($aaaln,\%dnaseqs);

Description

This module contains utility methods for manipulating sequence
alignments ( Bio::Align::AlignI) objects.
The aa_to_dna_aln utility is essentially the same as the mrtrans
program by Bill Pearson available at
ftp://ftp.virginia.edu/pub/fasta/other/mrtrans.shar. Of course this
is a pure-perl implementation, but just to mention that if anything
seems odd you can check the alignments generated against Bill's
program.

Methods

Methods description

 Title   : aa_to_dna_aln
 Usage   : my $dnaaln = aa_to_dna_aln($aa_aln, \%seqs);
 Function: Will convert an AA alignment to DNA space given the 
           corresponding DNA sequences.  Note that this method expects 
           the DNA sequences to be in frame +1 (GFF frame 0) as it will
           start to project into coordinates starting at the first base of 
           the DNA sequence, if this alignment represents a different 
           frame for the cDNA you will need to edit the DNA sequences
           to remove the 1st or 2nd bases (and revcom if things should be).
 Returns : Bio::Align::AlignI object 
 Args    : 2 arguments, the alignment and a hashref.
           Alignment is a Bio::Align::AlignI of amino acid sequences. 
           The hash reference should have keys which are 
           the display_ids for the aa 
           sequences in the alignment and the values are a 
           Bio::PrimarySeqI object for the corresponding 
           spliced cDNA sequence. 

Methods code

sub aa_to_dna_aln {

    my ($aln,$dnaseqs) = @_;
    unless( defined $aln && 
	    ref($aln) &&
	    $aln->isa('Bio::Align::AlignI') ) { 
	croak('Must provide a valid Bio::Align::AlignI object as the first argument to aa_to_dna_aln, see the documentation for proper usage and the method signature');
    }
    my $alnlen = $aln->length;
    #print "HSP length is $alnlen\n";
    my $dnaalign = new Bio::SimpleAlign;
    foreach my $seq ( $aln->each_seq ) {    
	my $newseq;	    
	my $dnaseq = $dnaseqs->{$seq->display_id} || croak("cannot find ".
							 $seq->display_id);
	foreach my $pos ( 1..$alnlen ) {
	    my $loc = $seq->location_from_column($pos);
	    my $dna = ''; 
	    if( !defined $loc || $loc->location_type ne 'EXACT' ) {
		$dna = '---';
	    } else {
		# To readjust to codon boundaries
		# end needs to be +1 so we can just multiply by CODONSIZE 
		# to get this		    

		my ($start,$end) = ((($loc->start - 1)* CODONSIZE) +1,
				    ($loc->end)* CODONSIZE);
		
		if( $start <=0 || $end > $dnaseq->length() ) {
		    print STDERR "start is ", $loc->start, " end is ", $loc->end, " while dnaseq length is ", $dnaseq->length(), " and start/end projected are $start,$end\n ";
		    warn("codons don't seem to be matching up for $start,$end");
		    $dna = '---';			    
		} else {
		    $dna = $dnaseq->subseq($start,$end);
		}
	    }
	    $newseq .= $dna;
	}
	# funky looking math is to readjust to codon boundaries and deal
	# with fact that sequence start with 1
	my $newdna = new Bio::LocatableSeq(-display_id  => $seq->id(),
					   -start => (($seq->start - 1) * 
						      CODONSIZE) + 1, 
					   -end   => ($seq->end * CODONSIZE),
					   -strand => $seq->strand,
					   -seq   => $newseq);    
	$dnaalign->add_seq($newdna);
    }
    return $dnaalign;
}
1;

}

General documentation

User feedback is an integral part of the evolution of this and other
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  bioperl-bugs@bioperl.org
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Email jason@bioperl.org

Additional contributors names and emails here

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