Raw content of Bio::Align::Utilities # $Id: Utilities.pm,v 1.8 2002/11/11 18:39:19 jason Exp $ # # BioPerl module for Bio::Align::Utilities # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects =head1 SYNOPSIS use Bio::Align::Utilities qw(aa_to_dna_aln); my $dna_aln = aa_to_dna_aln($aaaln,\%dnaseqs); =head1 DESCRIPTION This module contains utility methods for manipulating sequence alignments ( L<Bio::Align::AlignI>) objects. The B<aa_to_dna_aln> utility is essentially the same as the B<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. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut #' keep my emacs happy # Let the code begin... package Bio::Align::Utilities; use vars qw(@ISA @EXPORT @EXPORT_OK); use strict; use Carp; require Exporter; @ISA = qw(Exporter); @EXPORT = qw(); @EXPORT_OK = qw(aa_to_dna_aln); use constant CODONSIZE => 3; =head2 aa_to_dna_aln 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. See also: L<Bio::Align::AlignI>, L<Bio::SimpleAlign>, L<Bio::PrimarySeq> =cut 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;