[Bioperl-l] parser for BLAT cDNA-genome alignment in Sim4 format

Hong Xu hxu.hong at gmail.com
Thu Jan 11 17:26:34 UTC 2007

Dear all,

I have written a module for parsing BLAT result in Sim4 format. I
borrowed the code from Bio::Tools::Sim4::Results. Hope this code will
be useful to other people.



------------- see code below -------------------------

# BioPerl module for Bio::Tools::Sim4::BlatResults
# Cared for by Hong Xu <hxu.hong at gmail.com>
# Modified from Bio::Tools::Sim4::BlatResults
# that was developed by:
#     Ewan Birney <birney at sanger.ac.uk>
#     and Hilmar Lapp <hlapp at gmx.net>
# Copyright Ewan Birney, Hilmar Lapp, Hong Xu
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Sim4::BlatResults - Results of one BLAT run with Sim4 output


   # to preset the order of EST and genomic file as given on the sim4
   # command line:
   my $sim4 = Bio::Tools::Sim4::BlatResults->new(-file => 'result.sim4',
                                                 -estfirst => 1);
   # to let the order be determined automatically (by length comparison):
   $sim4 = Bio::Tools::Sim4::BlatResults->new( -file => 'sim4.results' );
   # filehandle:
   $sim4 = Bio::Tools::Sim4::BlatResults->new( -fh   => \*INPUT );

   # parse the results
   while(my $exonset = $sim4->next_exonset()) {
       # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Sim4::Exons
       # as sub features
       print "Delimited on sequence ", $exonset->seq_id(),
             "from ", $exonset->start(), " to ", $exonset->end(), "\n";
       foreach my $exon ( $exonset->sub_SeqFeature() ) {
	  # $exon is-a Bio::SeqFeature::FeaturePair
	  print "Exon from ", $exon->start, " to ", $exon->end,
                " on strand ", $exon->strand(), "\n";
          # you can get out what it matched using the est_hit attribute
          my $homol = $exon->est_hit();
          print "Matched to sequence ", $homol->seq_id,
                " at ", $homol->start," to ", $homol->end, "\n";

   # essential if you gave a filename at initialization (otherwise the file
   # stays open)


The sim4 module provides a parser and results object for sim4 output from BLAT.
The sim4 results are specialised types of SeqFeatures, meaning you can add them
to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner.

The sim4 Exon objects are Bio::SeqFeature::FeaturePair inherited objects. The
$esthit = $exon-E<gt>est_hit() is the alignment as a feature on the matching
object (normally, an EST), in which the start/end points are where the hit

To make this module work sensibly you need to run

     blat -out=sim4 genomic.fasta est.fasta exon.sim4

One fiddle here is that there are only two real possibilities to the matching
criteria: either one sequence needs reversing or not. Because of this, it
is impossible to tell whether the match is in the forward or reverse strand
of the genomic DNA. We solve this here by assuming that the genomic DNA is
always forward. As a consequence, the strand attribute of the matching EST is
unknown, and the strand attribute of the genomic DNA (i.e., the Exon object)
will reflect the direction of the hit.


=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 one
of the Bioperl mailing lists.  Your participation is much appreciated.

  bioperl-l at bioperl.org          - General discussion
  http://bio.perl.org/MailList.html             - About the mailing lists

=head2 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via email
or the web:

  bioperl-bugs at bio.perl.org

=head1 AUTHOR - Ewan Birney, Hilmar Lapp, Hong Xu

Email birney at sanger.ac.uk
      hlapp at gmx.net (or hilmar.lapp at pharma.novartis.com)
      hxu.hong at gmail.com

Describe contact details here


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


# Let the code begin...

package Bio::Tools::Sim4::BlatResults;
use vars qw(@ISA);
use strict;

# Object preamble - inherits from Bio::Root::Object

use File::Basename;
use Bio::Root::Root;
use Bio::Tools::AnalysisResult;
use Bio::Tools::Sim4::Exon;

@ISA = qw(Bio::Tools::AnalysisResult);

sub _initialize_state {
    my($self, at args) = @_;

    # call the inherited method first
    my $make = $self->SUPER::_initialize_state(@args);

    my ($est_is_first) = $self->_rearrange([qw(ESTFIRST)], @args);

    $self->{'_est_is_first'} = $est_is_first if(defined($est_is_first));

=head2 analysis_method

 Usage     : $sim4->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
 Returns   : String
 Argument  : n/a


sub analysis_method {
    my ($self, $method) = @_;
    if($method && ($method !~ /blat/i)) {
       $self->throw("method $method not supported in " . ref($self));
    return $self->SUPER::analysis_method($method);

=head2 parse_next_alignment

 Title   : parse_next_alignment
 Usage   : @exons = $sim4_result->parse_next_alignment;
           foreach $exon (@exons) {
               # do something
 Function: Parses the next alignment of the BLAT sim4 result file and returns
           the found exons as an array of Bio::Tools::Sim4::Exon objects. Call
           this method repeatedly until an empty array is returned to get the
           results for all alignments.

           The $exon->seq_id() attribute will be set to the identifier of the
           respective sequence for both sequences. The length is accessible
           via the seqlength() attribute of $exon->query() and

           It automatically determines which of the two sequences has been
           reversed, and adjusts the coordinates for that sequence. It will
           also detect whether the EST sequence(s) were given as first or as
           second file to sim4, unless this has been specified at creation
           time of the object.

 Example :
 Returns : An array of Bio::Tools::Sim4::Exon objects
 Args    :


sub parse_next_alignment {
   my ($self) = @_;
   my @exons = ();
   my %seq1props = ();
   my %seq2props = ();
   # we refer to the properties of each seq by reference
   my ($estseq, $genomseq, $to_reverse);
   my $started = 0;
   my $hit_direction = 1;

   while(defined($_ = $self->_readline())) {

     # bascially, each sim4 'hit' starts with seq1...
     /^seq1/ && do {
       if($started) {
	     $started = 1;

	     # seqname and length of seq 1
	     /^seq1\s+=\s+(\S+)\,\s+(\d+)/ ||
	       $self->throw("Sim4 parsing error on seq1 [$_] line. Sorry!");
	     $seq1props{'seqname'} = $1;
	     $seq1props{'length'} = $2;
     /^seq2/ && do {
       /^seq2\s+=\s+(\S+)\,\s+(\d+)/ ||
	       $self->throw("Sim4 parsing error on seq2 [$_] line. Sorry!");
	     $seq2props{'seqname'} = $1;
	     $seq2props{'length'} = $2;
     /^\(complement\)/ && do {
	     $hit_direction = -1;

     # this matches
     # start-end (start-end) pctid%
     if(/(\d+)-(\d+)\s+\((\d+)-(\d+)\)\s+(\d+)%/) {
 	     $seq1props{'start'} = $1;
 	     $seq1props{'end'} = $2;
 	     $seq2props{'start'} = $3;
 	     $seq2props{'end'} = $4;
	     my $pctid   = $5;
	     if(! defined($estseq)) {
	       # for the first time here: need to set the references referring
	       # to seq1 and seq2
	       if(! exists($self->{'_est_is_first'})) {
		       # detect which one is the EST by looking at the lengths,
		       # and assume that this holds throughout the entire result
		       # file (i.e., when this method is called for the next
		       # alignment, this will not be checked again)
		       if($seq1props{'length'} > $seq2props{'length'}) {
		         $self->{'_est_is_first'} = 0;
		       } else {
		         $self->{'_est_is_first'} = 1;
	       if($self->{'_est_is_first'}) {
		       $estseq = \%seq1props;
		       $genomseq = \%seq2props;
	       } else {
		       $estseq = \%seq2props;
		       $genomseq = \%seq1props;
	     if($hit_direction == -1) {
	       # we have to reverse the coordinates of one of both seqs
	       my $tmp = $to_reverse->{'start'};
	       $to_reverse->{'start'} =
		     $to_reverse->{'length'} - $to_reverse->{'end'} + 1;
	       $to_reverse->{'end'} = $to_reverse->{'length'} - $tmp + 1;
	     # create and initialize the exon object
	     my $exon = Bio::Tools::Sim4::Exon->new(
					    '-start' => $genomseq->{'start'},
					    '-end'   => $genomseq->{'end'},
					    '-strand' => $hit_direction);
	     # feature1 is supposed to be initialized to a Similarity object,
       # but we provide a safety net
	     if($exon->feature1()->can('seqlength')) {
	     } else {
	     # create and initialize the feature wrapping the 'hit' (the EST)
	     my $fea2 = Bio::SeqFeature::Similarity->new(
                    '-start' => $estseq->{'start'},
					          '-end'   => $estseq->{'end'},
					          '-strand' => 0,
					          '-primary' => "aligning_EST");
	     # store
	     # general properties
	     # push onto array
	     push(@exons, $exon);
	     next; # back to while loop
   return @exons;

=head2 next_exonset

 Title   : next_exonset
 Usage   : $exonset = $sim4_result->parse_next_exonset;
           print "Exons start at ", $exonset->start(),
                 "and end at ", $exonset->end(), "\n";
           foreach $exon ($exonset->sub_SeqFeature()) {
               # do something
 Function: Parses the next alignment of the Sim4 result file and returns the
           set of exons as a container of features. The container is itself
           a Bio::SeqFeature::Generic object, with the Bio::Tools::Sim4::Exon
           objects as sub features. Start, end, and strand of the container
           will represent the total region covered by the exons of this set.

           See the documentation of parse_next_alignment() for further
           reference about parsing and how the information is stored.

 Example :
 Returns : An Bio::SeqFeature::Generic object holding Bio::Tools::Sim4::Exon
           objects as sub features.
 Args    :


sub next_exonset {
    my $self = shift;
    my $exonset;

    # get the next array of exons
    my @exons = $self->parse_next_alignment();
    return if($#exons < 0);
    # create the container of exons as a feature object itself, with the
    # data of the first exon for initialization
    $exonset = Bio::SeqFeature::Generic->new('-start' => $exons[0]->start(),
					     '-end' => $exons[0]->end(),
					     '-strand' => $exons[0]->strand(),
					     '-primary' => "ExonSet");
    # now add all exons as sub features, with enabling EXPANsion of the region
    # covered in total
    foreach my $exon (@exons) {
	$exonset->add_sub_SeqFeature($exon, 'EXPAND');
    return $exonset;

=head2 next_feature

 Title   : next_feature
 Usage   : while($exonset = $sim4->next_feature()) {
                  # do something
 Function: Does the same as L<next_exonset()>. See there for documentation of
           the functionality. Call this method repeatedly until FALSE is

           The returned object is actually a SeqFeatureI implementing object.
           This method is required for classes implementing the
           SeqAnalysisParserI interface, and is merely an alias for
           next_exonset() at present.

 Example :
 Returns : A Bio::SeqFeature::Generic object.
 Args    :


sub next_feature {
    my ($self, at args) = @_;
    # even though next_exonset doesn't expect any args (and this method
    # does neither), we pass on args in order to be prepared if this changes
    # ever
    return $self->next_exonset(@args);


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