Modware::Feature

Aligned

   Modware::Feature::Aligned - Parent Class of all Modware::Feature::* classes derived from BLAST alignments.

  do not create a Modware::Feature::Aligned object directly, it is for use by the Modware::Feature object

   THis is an abstract subclass of Modware::Feature and should not be called directly.  It contains
   methods specific to features which are blasted against the genome (ests, mRNAs, Genbank records).

   The main distinction here is that these objects will have TWO bioperl objects associated with them

   1. bioperl           - this represents the entitiy in question.  i.e. and EST is represented by a 
                          Bio::Seq object
   2. bioperl_alignment - this represents the blast hit that maps this feature to the genome.  it is 
                          represented by a Bio::SeqFeature::Generic object and its locations on the reference
                          sequence map to hsps.

   The bioperl object should be used when you want to work with the object itself ( for example, looking
   at the sequence)  whereas the alignment object should be used
   when inspecting the objects location on the genome ( for example to find features that touch it ).

Methods description

 Title    : _blast
 Function : runs a blast, sets new bioperl_alignment
 Returns  : boolean ( true if valid lis is parsed and bioperl_alignment set )
 Args     : -type ( type of seq to blast ie 'DNA Coding Sequence', 'mRNA Sequence' etc. )

 Title    : _get_bioperl
 Note     : creates a bioperl object representing this EST (Bio::Seq)
 Usage    : called internally by lazy evaluated 'bioperl' method 
 Function : creates a bioperl object with a location on the chromosome's bioperl object.
 Returns  : nothing
 Args     : none

 Title    : _get_bioperl_alignment
 Note     : creates a bioperl_alignment object from the database
          : for alignment features such as EST's and mRNA's,
          : this feature is created from where the feature aligns
          : to the chromosome after BLASTING and filtering the hsp's
          : with the LIS algorithm.
          :
          : Bio::SeqFeature::Generic object
          :   tag: hit_id ( ID of chromosome that alignment maps to )
 Usage    : called internally by lazy evaluated 'bioperl_alignment' method 
 Function : creates a bioperl_alignment object ( with location where applicable ) 
 Returns  : nothing
 Args     : none

 Title    : _get_chromosome
 Usage    : $feature->_get_chromosome();
 Function : gets the chromosome object for this feature (called from chromosome)
 Returns  : nothing
 Args     : none

 Title    : _init
 Note     : sets attributes specific to Aligned features
 Usage    : called internally by new
 Function : 
 Returns  : nothing
 Args     : none

 Title    : alignment_type
 Function : returns type of alignment for SUBfeature table
 Returns  : nothing
 Args     : none

 Title    : bioperl_alignment
 Note     : Fetches the bioperl_alignment object associated with this feature ( Bio::SeqFeature::Generic )
          : which has the location of the blast hits on the chromosome
          : This is lazy evaluated
          : each feature type will have its own _get_bioperl_alignment method
          : An non-alignment is represented as an empty Bio::SeqFeature::Generic object
 Usage    : To print the bioperl_alignment name of the bioperl_alignment that this feature belongs to 
          : print $self->bioperl_alignment->bioperl_alignment_name();
 Function : gets/sets the bioperl_alignment attribute of the feature
 Returns  : a Bio::SeqFeatureI implementing object
 Args     : optional: bioperl_alignment object

 Title    : blast
 Function : runs a blast, sets new bioperl_alignment
 Returns  : boolean ( true if valid lis is parsed and bioperl_alignment set )
 Args     : -type ( type of seq to blast ie 'DNA Coding Sequence', 'mRNA Sequence' etc. )

 Title    : end
 Note     : reads end from the hightest coordinate on the chromosome in bioperl_alignment object
 Usage    : print "Start coordinate: " $self->end();
 Function : returns end coordinate of the alignment of this feature in chromosomal coordinates
 Returns  : nothing
 Args     : none

 Title    : insert
 Function : calls SUPER::insert, then a method to update the alignment
 Returns  : nothing
 Args     : none

 Title    : match_type
 Function : returns type of alignment for SUBfeature table
 Returns  : nothing
 Args     : none

 Title    : start
 Note     : reads start from the lowest coordinate on the chromosome in bioperl_alignment object
 Usage    : print "Start coordinate: " $self->start();
 Function : returns start coordinate of the alignment of this feature in chromosomal coordinates
 Returns  : nothing
 Args     : none

 Title    : update
 Function : calls SUPER::update, then a method to update the alignment
 Returns  : nothing
 Args     : none

 Title    : update_alignment
 Function : updates the alignment subfeatures based on bioperl_alignment object
          : 
 Returns  : nothing
 Args     : none

Methods code

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

   $self->throw( "Need to implement _blast method which blasts, parses report into Bio::SearchIO object and sets bioperl_alignment accessor");

   return 1;

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

   $self->throw_not_implemented();

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

   if ( $self->feature_id ) {
      my $bioperl_alignment  = new Bio::SeqFeature::Generic();

      my $chrom_primary_id;

      my $hit_iterator = Chado::Feature->search( name => $self->primary_id().".match");
      
      return undef if $hit_iterator->count() == 0;

      my $hit_feature = new Modware::Feature( -feature_id => $hit_iterator->next()->feature_id() );

        
      my @subfeatures = grep{ $_->type_id->name eq 'match_part' } $hit_feature->subfeatures();

     #
     #  This whole mess is called a 'schwartzian transform' and is a useful
     #  sorting algorithm for calculated values using map and sort.
     #  for more info do a google search
     #
      my @hsps        = map  { $_->[0] }
                        sort { $a->[1] <=> $b->[1] }
                        map  { [$_, [$_->featureloc_feature_id()]->[0]->strand()*[$_->featureloc_feature_id()]->[0]->fmin() ] } 
                        @subfeatures;
       
      foreach my $hsp ( @hsps ) {
         my @locs     = $hsp->featureloc_feature_id();
         my ($location) = grep{ $_->srcfeature_id != $self->feature_id } @locs;;
       
         $chrom_primary_id  = $location->srcfeature_id->dbxref->accession;

         my $strand = $location->strand();
         my $start  = $location->fmin() + 1;
         my $end    = $location->fmax();

         my $hsp = new Bio::SeqFeature::Generic(
              -strand       => $strand,
              -start        => $start,
              -end          => $end
         );

         $bioperl_alignment->add_SeqFeature($hsp, 'EXPAND');
      }

      $bioperl_alignment->add_tag_value( 'hit_id', $chrom_primary_id ) if $chrom_primary_id;

      $self->bioperl_alignment( $bioperl_alignment );
   }

   my ($self) = @_;

   $self->bioperl_alignment();  # need to call to assign feature to chromosome at the moment
                                # will eventually store in feature table but right now
                                # its all in teh subfeature table (as blast hits)


   $self->SUPER::_get_chromosome();

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

   $self->throw_not_implemented();

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

   $self->throw_not_implemented();

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

  #
  # fetches bioperl_alignment from database (_get_bioperl_alignment) if bioperl_alignment is not yet defined
  #  and the user is not attempting to set the bioperl_alignment
  #
   defined $self->{bioperl_alignment} || defined $obj || $self->_get_bioperl_alignment();

   if(scalar @_ > 1) {
      use Data::Dumper;
      print STDERR "Got an alignment".Dumper( $obj ) if DEBUG;
      if ( $obj ) {
         $self->strand( $obj->strand() );
         $self->{bioperl_alignment} = $obj;
         if ( $obj->has_tag('hit_id') ){
            my $chrom = new Modware::Feature ( -primary_id => [$obj->get_tag_values('hit_id')]->[0] );
            print "setting chromosome to ".$chrom->name()."\n" if DEBUG;
            $self->reference_feature( $chrom );

            $self->reference_feature( $self->bioperl_alignment() );
         }
      }
      else {
         $self->{bioperl_alignment} = new Bio::SeqFeature::Generic();
      }
   }
   return $self->{bioperl_alignment};

   my ($self, @args) = @_;
   $self->throw_not_implemented();

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


   return $self->bioperl_alignment() ? $self->bioperl_alignment() : undef;

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


   $self->SUPER::insert();
   $self->update_alignment() if $self->{'bioperl_alignment'};
   $self->_update_gene_association() if ( exists $self->{gene} );
   $self->_update_cached_sequence();
   $self->_insert_or_update_featureprop( 'translation_start', $self->phase() + 1  ) if $self->cached_sequences->{'Protein'};

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

   return $self->bioperl_alignment() ? $self->bioperl_alignment() : undef;

   my ($self, $obj) = @_;
   if($obj) {
      $self->{match_type} = $obj;
   }
   return $self->{match_type};

   my ($type, @args) = @_;

  #
  #  do not bless it here, assume subclass will bless as a subclass type
  #
   my $self = {};
   bless $self,$type;

   my @arglist = qw(
     BIOPERL SOURCE DESCRIPTION
   );

   my ( 
      $bioperl, $source, $description
    )   = $self->_rearrange( [@arglist], @args );

   $self->source           ( $source          ) if defined $source;
   $self->bioperl          ( $bioperl         ) if defined $bioperl;
   $self->description      ( $description     ) if defined $description;
   $self->qualifiers( [] );
   $self->_init();
   return $self;

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

   return $self->bioperl_alignment() ? $self->bioperl_alignment() : undef;

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

   $self->_update_cached_sequence()  if ( exists $self->{bioperl} );
   
   $self->SUPER::update();
   $self->update_alignment() if $self->{'bioperl_alignment'};
   $self->_update_gene_association() if ( exists $self->{gene} );
   $self->_insert_or_update_featureprop( 'translation_start', $self->phase() + 1  ) if $self->cached_sequences->{'Protein'};

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

  #
  # loop through stored exons (in database)
  # for each one pop an exon off of the exon array and update that 
  # subfeature with that exon's coordinates.
  #
  # after this, if the exon array is empty, the remaining subfeatures need to be deleted
  # if there are exons left, then they all need to be inserted.
  #

   my $hit_iterator = Chado::Feature->search( name => $self->primary_id().".match");
   my $hit_feature;

   my @hsps         = $self->bioperl_alignment();

   if ( @hsps && $hit_iterator->count() == 0 ) {
      $hit_feature = new Modware::Feature( 
         -type              => $self->match_type(),
         -source            => 'dictyBase',
         -reference_feature => $self->reference_feature(),
         -start             => $self->bioperl_alignment(),
         -end               => $self->bioperl_alignment()
      );
      $hit_feature->insert();
      $hit_feature->_database_object()->name( $self->primary_id().".match" );
      $hit_feature->_database_object()->update();
   }
   else {
      $hit_feature = new Modware::Feature( -feature_id => $hit_iterator->next()->feature_id() );
   }
   
   my @subfeatures  = $hit_feature->subfeatures();
   my @stored_hits  = grep{ $_->type_id->name eq 'match_part' } @subfeatures;
   
   if ( scalar @hsps == 0 && $hit_feature ) {
      $hit_feature->_database_object()->delete();
   } elsif (scalar @hsps > 0){
      $hit_feature->{_featureloc} = Chado::Featureloc->find_or_create( feature_id => $hit_feature->feature_id );
      $hit_feature->_featureloc( $self->start() );
      $hit_feature->_featureloc( $self->end() );
      $hit_feature->_featureloc( $self->strand() );
      $hit_feature->_featureloc( $self->reference_feature() );
      $hit_feature->_featureloc();
   } 
   foreach my $stored_hit ( @stored_hits ) {
      $stored_hit->delete();
   }

   foreach my $hsp ( @hsps ) {
      $hit_feature->_insert_subfeature( $hsp, 'match_part' );

   }

General documentation

   Eric Just e-just@northwestern.edu

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

Copyright © 2006, Northwestern University All rights reserved.