Bio::Align Utilities
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Summary
Bio::Align::Utilities - A collection of utilities regarding converting
and manipulating alignment objects
Package variables
No package variables defined.
Included modules
Bio::Root::Version
Carp
Inherit
Exporter
Synopsis
  use Bio::Align::Utilities qw(:all);
# %dnaseqs is a hash of CDS sequences (spliced)
# Even if the protein alignments are local make sure the start/end # stored in the LocatableSeq objects are to the full length protein. # The CoDing Sequence that is passed in should still be the full # length CDS as the nt alignment will be generated. # my $dna_aln = &aa_to_dna_aln($aa_aln,\%dnaseqs); # generate bootstraps my $replicates = &bootstrap_replicates($aln,$count);
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
BEGIN Code
aa_to_dna_alnDescriptionCode
bootstrap_replicatesDescriptionCode
bootstrap_replicates_codonsDescriptionCode
catDescriptionCode
Methods description
aa_to_dna_alncode    nextTop
 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: Bio::Align::AlignI, Bio::SimpleAlign, Bio::PrimarySeq
bootstrap_replicatescodeprevnextTop
 Title   : bootstrap_replicates
Usage : my $alns = &bootstrap_replicates($aln,100);
Function: Generate a pseudo-replicate of the data by randomly
sampling, with replacement, the columns from an alignment for
the non-parametric bootstrap.
Returns : Arrayref of Bio::SimpleAlign objects
Args : Bio::SimpleAlign object
Number of replicates to generate
bootstrap_replicates_codonscodeprevnextTop
 Title   : bootstrap_replicates_codons
Usage : my $alns = &bootstrap_replicates_codons($aln,100);
Function: Generate a pseudo-replicate of the data by randomly
sampling, with replacement, the columns from a codon alignment for
the non-parametric bootstrap. The alignment is assumed to start on
the first position of a codon.
Returns : Arrayref of Bio::SimpleAlign objects
Args : Bio::SimpleAlign object
Number of replicates to generate
catcodeprevnextTop
 Title     : cat
Usage : $aln123 = cat($aln1, $aln2, $aln3)
Function : Concatenates alignment objects. Sequences are identified by id.
An error will be thrown if the sequence ids are not unique in the
first alignment. If any ids are not present or not unique in any
of the additional alignments then those sequences are omitted from
the concatenated alignment, and a warning is issued. An error will
be thrown if any of the alignments are not flush, since
concatenating such alignments is unlikely to make biological
sense.
Returns : A new Bio::SimpleAlign object
Args : A list of Bio::SimpleAlign objects
Methods code
BEGINTop
BEGIN {
    use constant CODONSIZE => 3;
    $GAP = '-';
    $CODONGAP = $GAP x CODONSIZE;
}
aa_to_dna_alndescriptionprevnextTop
sub aa_to_dna_aln {
    my ($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;
    my $dnaalign = Bio::SimpleAlign->new();
    $aln->map_chars('\.',$GAP);

    foreach my $seq ( $aln->each_seq ) {    
	my $aa_seqstr = $seq->seq();
	my $id = $seq->display_id;
	my $dnaseq = $dnaseqs->{$id} || $aln->throw("cannot find ".
						     $seq->display_id);
	my $start_offset = ($seq->start - 1) * CODONSIZE;

	$dnaseq = $dnaseq->seq();
	my $dnalen = $dnaseqs->{$id}->length;
	my $nt_seqstr;
	my $j = 0;
	for( my $i = 0; $i < $alnlen; $i++ ) {
	    my $char = substr($aa_seqstr,$i + $start_offset,1);	    
	    if ( $char eq $GAP || $j >= $dnalen )  { 
		$nt_seqstr .= $CODONGAP;
	    } else {
		$nt_seqstr .= substr($dnaseq,$j,CODONSIZE);
		$j += CODONSIZE;
	    }
	}
	$nt_seqstr .= $GAP x (($alnlen * 3) - length($nt_seqstr));

	my $newdna = Bio::LocatableSeq->new(-display_id  => $id,
					   -alphabet    => 'dna',
					   -start       => $start_offset+1,
					   -end         => ($seq->end * 
							    CODONSIZE),
					   -strand      => 1,
					   -seq         => $nt_seqstr);    
	$dnaalign->add_seq($newdna);
    }
    return $dnaalign;
}
bootstrap_replicatesdescriptionprevnextTop
sub bootstrap_replicates {
   my ($aln,$count) = @_;
   $count ||= 1;
   my $alen = $aln->length;
   my (@seqs,@nm);
   $aln->set_displayname_flat(1);
   for my $s ( $aln->each_seq ) {
       push @seqs, $s->seq();
       push @nm, $s->id;
   }
   my (@alns,$i);
   while( $count-- > 0 ) {
       my @newseqs;
       for($i =0; $i < $alen; $i++ ) {
	   my $index = int(rand($alen));
	   my $c = 0;
	   for ( @seqs ) {
	       $newseqs[$c++] .= substr($_,$index,1);
	   }
       }
       my $newaln = Bio::SimpleAlign->new();
       my $i = 0;
       for my $s ( @newseqs ) {
       (my $tmp = $s) =~ s{[$Bio::LocatableSeq::GAP_SYMBOLS]+}{}g;
	   $newaln->add_seq( Bio::LocatableSeq->new
			     (-start         => 1,
			      -end           => length($tmp),
			      -display_id    => $nm[$i++],
			      -seq           => $s));
       }
       push @alns, $newaln;
   }
   return\@ alns;
}
bootstrap_replicates_codonsdescriptionprevnextTop
sub bootstrap_replicates_codons {
   my ($aln,$count) = @_;
   $count ||= 1;
   my $alen = $aln->length;
   my $ncodon = int($alen/3);
my (@seqs,@nm); $aln->set_displayname_flat(1); for my $s ( $aln->each_seq ) { push @seqs, $s->seq(); push @nm, $s->id; } my (@alns,$i); while( $count-- > 0 ) { my @newseqs; for($i =0; $i < $ncodon; $i++ ) { my $index = int(rand($ncodon)); my $seqpos = $index * 3; my $c = 0; for ( @seqs ) { $newseqs[$c++] .= substr($_,$seqpos,3); } } my $newaln = Bio::SimpleAlign->new(); my $i = 0; for my $s ( @newseqs ) { (my $tmp = $s) =~ s{[$Bio::LocatableSeq::GAP_SYMBOLS]+}{}g; $newaln->add_seq( Bio::LocatableSeq->new (-start => 1, -end => length($tmp), -display_id => $nm[$i++], -seq => $s)); } push @alns, $newaln; } return\@ alns;
}
catdescriptionprevnextTop
sub cat {
    my ($self, @aln) = @_;
    $self->throw("cat method called with no arguments") unless $self;
    for ($self,@aln) {
	$self->throw($_->id. " not a Bio::Align::AlignI object") unless $_->isa('Bio::Align::AlignI');
	$self->throw($_->id. " is not flush") unless $_->is_flush;
    }
    my $aln = $self->new;
    $aln->id($self->id);
    $aln->annotation($self->annotation);
    my %unique;
  SEQ: foreach my $seq ( $self->each_seq() ) {
        throw("ID: ", $seq->id, " is not unique in initial alignment.") if exists $unique{$seq->id};
        $unique{$seq->id}=1;

        # Can be Bio::LocatableSeq, Bio::Seq::Meta or Bio::Seq::Meta::Array
my $new_seq = $seq->new(-id=> $seq->id, -strand => $seq->strand, -verbose => $self->verbose); $new_seq->seq($seq->seq); $new_seq->start($seq->start); $new_seq->end($seq->end); if ($new_seq->isa('Bio::Seq::MetaI')) { for my $meta_name ($seq->meta_names) { $new_seq->named_submeta($meta_name, $new_seq->start, $new_seq->end, $seq->named_meta($meta_name)); } } for my $cat_aln (@aln) { my @cat_seq=$cat_aln->each_seq_with_id($seq->id); if (@cat_seq==0) { $self->warn($seq->id. " not found in alignment ". $cat_aln->id. ", skipping this sequence."); next SEQ; } if (@cat_seq>1) { $self->warn($seq->id. " found multiple times in alignment ". $cat_aln->id. ", skipping this sequence."); next SEQ; } my $cat_seq=$cat_seq[0]; my $old_end=$new_seq->end; $new_seq->seq($new_seq->seq.$cat_seq->seq); # Not sure if this is a sensible way to deal with end coordinates
$new_seq->end($new_seq->end+$cat_seq->end+1-$cat_seq->start); if ($cat_seq->isa('Bio::Seq::Meta::Array')) { unless ($new_seq->isa('Bio::Seq::Meta::Array')) { my $meta_seq=Bio::Seq::Meta::Array->new; $meta_seq->seq($new_seq->seq); $meta_seq->start($new_seq->start); $meta_seq->end($new_seq->end); if ($new_seq->isa('Bio::Seq::Meta')) { for my $meta_name ($new_seq->meta_names) { $meta_seq->named_submeta($meta_name, $new_seq->start, $old_end, [split(//, $new_seq->named_meta($meta_name))] ); } } $new_seq=$meta_seq; } for my $meta_name ($cat_seq->meta_names) { $new_seq->named_submeta($meta_name, $old_end+1, $new_seq->end, $cat_seq->named_meta($meta_name) ); } } elsif ($cat_seq->isa('Bio::Seq::Meta')) { if ($new_seq->isa('Bio::Seq::Meta::Array')) { for my $meta_name ($cat_seq->meta_names) { $new_seq->named_submeta($meta_name, $old_end+1, $new_seq->end, [split(//,$cat_seq->named_meta($meta_name))] ); } } else { unless ($new_seq->isa('Bio::Seq::Meta')) { my $meta_seq=Bio::Seq::Meta::Array->new; $meta_seq->seq($new_seq->seq); $meta_seq->start($new_seq->start); $meta_seq->end($new_seq->end); $new_seq=$meta_seq; } for my $meta_name ($cat_seq->meta_names) { $new_seq->named_submeta($meta_name, $old_end+1, $new_seq->end, $cat_seq->named_meta($meta_name) ); } } } } $aln->add_seq($new_seq); } my $cons_meta = $self->consensus_meta; my $new_cons_meta; if ($cons_meta) { $new_cons_meta = Bio::Seq::Meta->new(); for my $meta_name ($cons_meta->meta_names) { $new_cons_meta->named_submeta($meta_name, 1, $self->length, $cons_meta->$meta_name); } } my $end=$self->length; for my $cat_aln (@aln) { my $cat_cons_meta=$cat_aln->consensus_meta; if ($cat_cons_meta) { $new_cons_meta = Bio::Seq::Meta->new() if !$new_cons_meta; for my $meta_name ($cat_cons_meta->meta_names) { $new_cons_meta->named_submeta($meta_name, $end+1, $end+$cat_aln->length, $cat_cons_meta->$meta_name); } } $end+=$cat_aln->length; } $aln->consensus_meta($new_cons_meta) if $new_cons_meta; return $aln; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
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.
Reporting BugsTop
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _