view variant_effect_predictor/Bio/EnsEMBL/Compara/ConstrainedElement.pm @ 1:d6778b5d8382 draft default tip

Deleted selected files

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=head1 NAME

Bio::EnsEMBL::Compara::ConstrainedElement - constrained element data produced by Gerp

=head1 SYNOPSIS
  
  use Bio::EnsEMBL::Compara::ConstrainedElement;
  
  my $constrained_element = new Bio::EnsEMBL::Compara::ConstrainedElement(
          -adaptor => $constrained_element_adaptor,
          -method_link_species_set_id => $method_link_species_set_id,
	  -reference_dnafrag_id => $dnafrag_id,
          -score => 56.2,
          -p_value => '1.203e-6',
          -alignment_segments => [ [$dnafrag1_id, $start, $end, $genome_db_id, $dnafrag1_name ], [$dnafrag2_id, ... ], ... ],
      );

GET / SET VALUES
  $constrained_element->adaptor($constrained_element_adaptor);
  $constrained_element->dbID($constrained_element_id);
  $constrained_element->method_link_species_set_id($method_link_species_set_id);
  $constrained_element->score(56.2);
  $constrained_element->p_value('5.62e-9');
  $constrained_element->alignment_segments([ [$dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], ... ]);
  $constrained_element->slice($slice);
  $constrained_element->start($constrained_element_start - $slice_start + 1);
  $constrained_element->end($constrained_element_end - $slice_start + 1);
  $constrained_element->seq_region_start($self->slice->start + $self->{'start'} - 1);
  $constrained_element->seq_region_end($self->slice->start + $self->{'end'} - 1);
  $constrained_element->strand($strand);
  $constrained_element->reference_dnafrag_id($dnafrag_id);

=head1 OBJECT ATTRIBUTES

=over

=item dbID

corresponds to constrained_element.constrained_element_id

=item adaptor

Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object to access DB

=item method_link_species_set_id

corresponds to method_link_species_set.method_link_species_set_id (external ref.)

=item score

corresponds to constrained_element.score

=item p_value

corresponds to constrained_element.p_value

=item slice

corresponds to a Bio::EnsEMBL::Slice 

=item start

corresponds to a constrained_element.dnafrag_start (in slice coordinates)

=item end

corresponds to a constrained_element.dnafrag_end (in slice coordinates)

=item seq_region_start

corresponds to a constrained_element.dnafrag_start (in genomic (absolute) coordinates)

=item seq_region_end

corresponds to a constrained_element.dnafrag_end (in genomic (absolute) coordinates)

=item strand

corresponds to a constrained_element.strand

=item $alignment_segments

listref of listrefs (each of which contain 5 strings (dnafrag.dnafrag_id, constrained_element.dnafrag_start, 
constrained_element.dnafrag_end, constrained_element.strand, genome_db.genome_db_id, dnafrag.dnafrag_name) 
   [ [ $dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], .. ]
Each inner listref contains information about one of the species sequences which make up the constarained 
element block from the alignment. 

=back

=head1 APPENDIX

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

=cut


# Let the code begin...


package Bio::EnsEMBL::Compara::ConstrainedElement;
use strict;

# Object preamble
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning info deprecate verbose);
use Bio::EnsEMBL::Compara::DnaFrag;
use Bio::SimpleAlign;
use Data::Dumper;


=head2 new (CONSTRUCTOR)

  Arg [-dbID] : int $dbID (the database ID for 
		the constrained element block for this object)
  Arg [-ADAPTOR]
              : (opt.) Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor $adaptor
                (the adaptor for connecting to the database)
  Arg [-METHOD_LINK_SPECIES_SET_ID]
              : int $mlss_id (the database internal ID for the $mlss)
  Arg [-SCORE]
              : float $score (the score of this alignment)
  Arg [-ALIGNMENT_SEGMENTS]
              : (opt.) listref of listrefs which each contain 5 values 
		[ [ $dnafrag_id, $dnafrag_start, $dnafrag_end, $genome_db_id, $dnafrag_name ], ... ]
		corresponding to the all the species in the constrained element block.
  Arg [-P_VALUE]
              : (opt.) string $p_value (the p_value of this constrained element)
  Arg [-SLICE]
	     : (opt.) Bio::EnsEMBL::Slice object
  Arg [-START]
	     : (opt.) int ($dnafrag_start - Bio::EnsEMBL::Slice->start + 1).
  Arg [-END]
	     : (opt.) int ($dnafrag_end - Bio::EnsEMBL::Slice->start + 1).
  Arg [-STRAND]
	     : (opt.) int (the strand from the genomic_align).
  Arg [-REFERENCE_DNAFRAG_ID]
	     : (opt.) int $dnafrag_id of the slice or dnafrag 

  Example    : my $constrained_element =
                   new Bio::EnsEMBL::Compara::ConstrainedElement(
		       -dbID => $constrained_element_id,
                       -adaptor => $adaptor,
                       -method_link_species_set_id => $method_link_species_set_id,
                       -score => 28.2,
                       -alignment_segments => [ [ $dnafrag_id, $dnafrag_start, $dnafrag_end, $genome_db_id, $dnafrag_name ], .. ], 
									#danfarg_[start|end|id] from constrained_element table
                       -p_value => '5.023e-6',
		       -slice => $slice_obj,
		       -start => ( $dnafrag_start - $slice_obj->start + 1),
		       -end => ( $dnafrag_end - $slice_obj->start + 1),
		       -strand => $strand,
		       -reference_dnafrag_id => $dnafrag_id,
                   );
  Description: Creates a new ConstrainedElement object
  Returntype : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElement
  Exceptions : none
  Caller     : general

=cut

sub new {
  my($class, @args) = @_;
  
  my $self = {};
  bless $self,$class;
    
  my ($adaptor, $dbID, $alignment_segments, 
	$method_link_species_set_id, $score, $p_value, 
	$slice, $start, $end, $strand, $reference_dnafrag_id) = 
    rearrange([qw(
        ADAPTOR DBID ALIGNMENT_SEGMENTS 
  METHOD_LINK_SPECIES_SET_ID SCORE P_VALUE 
  SLICE START END STRAND REFERENCE_DNAFRAG_ID 
	)],
            @args);

  $self->adaptor($adaptor) if (defined ($adaptor));
  $self->dbID($dbID) 
	if (defined ($dbID));
  $self->method_link_species_set_id($method_link_species_set_id)
      if (defined ($method_link_species_set_id));
  $self->alignment_segments($alignment_segments) 
      if (defined ($alignment_segments));
  $self->score($score) if (defined ($score));
  $self->p_value($p_value) if (defined ($p_value));
  $self->slice($slice) if (defined ($slice));
  $self->start($start) if (defined ($start));
  $self->end($end) if (defined ($end));
  $self->strand($strand) if (defined ($strand));
  $self->reference_dnafrag_id($reference_dnafrag_id)
      if (defined($reference_dnafrag_id));
  return $self;
}

sub new_fast {
  my $class = shift;
  my $hashref = shift;

  return bless $hashref, $class;
}

=head2 adaptor

  Arg [1]    : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor
  Example    : my $cons_ele_adaptor = $constrained_element->adaptor();
  Example    : $cons_ele_adaptor->adaptor($cons_ele_adaptor);
  Description: Getter/Setter for the adaptor this object uses for database
               interaction.
  Returntype : Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object
  Exceptions : thrown if $adaptor is not a
               Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object
  Caller     : general

=cut

sub adaptor {
  my ($self, $adaptor) = @_;

  if (defined($adaptor)) {
    throw("$adaptor is not a Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor object")
        unless ($adaptor->isa("Bio::EnsEMBL::Compara::DBSQL::ConstrainedElementAdaptor"));
    $self->{'adaptor'} = $adaptor;
  }

  return $self->{'adaptor'};
}

=head2 dbID

  Arg [1]    : integer $dbID
  Example    : my $dbID = $constrained_element->dbID();
  Example    : $constrained_element->dbID(2);
  Description: Getter/Setter for the attribute dbID 
  Returntype : integer
  Exceptions : returns undef if no ref.dbID
  Caller     : general

=cut

sub dbID {
  my ($self, $dbID) = @_;

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

  return $self->{'dbID'};
}


=head2 p_value 

  Arg [1]    : float $p_value
  Example    : my $p_value = $constrained_element->p_value();
  Example    : $constrained_element->p_value('5.35242e-105');
  Description: Getter/Setter for the attribute p_value
  Returntype : float 
  Exceptions : returns undef if no ref.p_value
  Caller     : general

=cut

sub p_value {
  my ($self, $p_value) = @_;

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

  return $self->{'p_value'};
}


=head2 score

  Arg [1]    : float $score
  Example    : my $score = $constrained_element->score();
  Example    : $constrained_element->score(16.8);
  Description: Getter/Setter for the attribute score 
  Returntype : float
  Exceptions : returns undef if no ref.score
  Caller     : general

=cut

sub score {
  my ($self, $score) = @_;

  if (defined($score)) {
    $self->{'score'} = $score;
  } 
  return $self->{'score'};
}

=head2 method_link_species_set_id

  Arg [1]    : integer $method_link_species_set_id
  Example    : $method_link_species_set_id = $constrained_element->method_link_species_set_id;
  Example    : $constrained_element->method_link_species_set_id(3);
  Description: Getter/Setter for the attribute method_link_species_set_id.
  Returntype : integer
  Exceptions : returns undef if no ref.method_link_species_set_id
  Caller     : object::methodname

=cut

sub method_link_species_set_id {
  my ($self, $method_link_species_set_id) = @_;

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

  return $self->{'method_link_species_set_id'};
}

=head2 alignment_segments
 
  Arg [1]    : listref $alignment_segments [ [ $dnafrag_id, $start, $end, $genome_db_id, $dnafrag_name ], .. ]
  Example    : my $alignment_segments = $constrained_element->alignment_segments();
               $constrained_element->alignment_segments($alignment_segments);
  Description: Getter/Setter for the attribute alignment_segments 
  Returntype : listref  
  Exceptions : returns undef if no ref.alignment_segments
  Caller     : general

=cut

sub alignment_segments {
  my ($self, $alignment_segments) = @_;

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

  return $self->{'alignment_segments'};
}


=head2 slice

  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Example    : $slice = $constrained_element->slice;
  Example    : $constrained_element->slice($slice);
  Description: Getter/Setter for the attribute slice.
  Returntype : Bio::EnsEMBL::Slice object
  Exceptions : returns undef if no ref.slice
  Caller     : object::methodname

=cut

sub slice {
  my ($self, $slice) = @_;

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

  return $self->{'slice'};
}

=head2 start

  Arg [1]    : (optional) int $start
  Example    : $start = $constrained_element->start;
  Example    : $constrained_element->start($start);
  Description: Getter/Setter for the attribute start.
  Returntype : int
  Exceptions : returns undef if no ref.start
  Caller     : object::methodname

=cut

sub start {
  my ($self, $start) = @_;

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

  return $self->{'start'};
}

=head2 end

  Arg [1]    : (optional) int $end
  Example    : $end = $constrained_element->end;
  Example    : $constrained_element->end($end);
  Description: Getter/Setter for the attribute end relative to the begining of the slice.
  Returntype : int
  Exceptions : returns undef if no ref.end
  Caller     : object::methodname

=cut

sub end {
  my ($self, $end) = @_;

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

  return $self->{'end'};
}


=head2 seq_region_start

  Arg [1]    : (optional) int $seq_region_start
  Example    : $seq_region_start = $constrained_element->seq_region_start;
  Example    : $constrained_element->seq_region_start($seq_region_start);
  Description: Getter/Setter for the attribute start relative to the begining of the dnafrag (genomic coords).
  Returntype : int
  Exceptions : returns undef if no ref.seq_region_start
  Caller     : object::methodname

=cut
sub seq_region_start {
	my ($self, $seq_region_start) = @_;
	
	if(defined($seq_region_start)) {
		$self->{'seq_region_start'} = $seq_region_start;
	} else {
		$self->{'seq_region_start'} = $self->slice->start + $self->{'start'} - 1;
	}
	return $self->{'seq_region_start'};
}


=head2 seq_region_end

  Arg [1]    : (optional) int $seq_region_end
  Example    : $seq_region_end = $constrained_element->seq_region_end
  Example    : $constrained_element->seq_region_end($seq_region_end);
  Description: Getter/Setter for the attribute end relative to the begining of the dnafrag (genomic coords).
  Returntype : int
  Exceptions : returns undef if no ref.seq_region_end
  Caller     : object::methodname

=cut
sub seq_region_end {
	my ($self, $seq_region_end) = @_;
	
	if(defined($seq_region_end)) {
		$self->{'seq_region_end'} = $seq_region_end;
	} else {
		$self->{'seq_region_end'} = $self->slice->start + $self->{'end'} - 1;
	}
	return $self->{'seq_region_end'};
}



=head2 strand

  Arg [1]    : (optional) int $stand$
  Example    : $end = $constrained_element->strand;
  Example    : $constrained_element->end($strand);
  Description: Getter/Setter for the attribute genomic_align strand.
  Returntype : int
  Exceptions : returns undef if no ref.strand
  Caller     : object::methodname

=cut

sub strand {
  my ($self, $strand) = @_;

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

  return $self->{'strand'};
}

=head2 reference_dnafrag_id

  Arg [1]    : (optional) int $reference_dnafrag_id
  Example    : $dnafrag_id = $constrained_element->reference_dnafrag_id;
  Example    : $constrained_element->reference_dnafrag_id($dnafrag_id);
  Description: Getter/Setter for the attribute end.
  Returntype : int
  Exceptions : returns undef if no ref.reference_dnafrag_id 
  Caller     : object::methodname

=cut

sub reference_dnafrag_id {
  my ($self, $reference_dnafrag_id) = @_;

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

  return $self->{'reference_dnafrag_id'};
}

=head2 get_SimpleAlign

  Arg [1]    : Optional flags for formatting displayed MSA  
  Example    : my $out = Bio::AlignIO->newFh(-fh=>\*STDOUT, -format=> "clustalw");
	       my $cons = $ce_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $slice);
               foreach my $constrained_element(@{ $cons }) {
			my $simple_align = $constrained_element->get_SimpleAlign("uc");
			print $out $simple_align;
	       }
  Description: Rebuilds the constrained element alignment
  Returntype : Bio::SimpleAlign object
  Exceptions : throw if you can not get a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object from the constrained element
  Caller     : object::methodname

=cut

sub get_SimpleAlign {
	my ($self, @flags) = @_;

	my $mlss_adaptor = $self->adaptor->db->get_MethodLinkSpeciesSet;

	my $cons_eles_mlss = $mlss_adaptor->fetch_by_dbID($self->method_link_species_set_id());

	if (defined($cons_eles_mlss)) {
		throw("$cons_eles_mlss is not a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object")
		unless ($cons_eles_mlss->isa("Bio::EnsEMBL::Compara::MethodLinkSpeciesSet"));
	} else {
		throw("unable to get a Bio::EnsEMBL::Compara::MethodLinkSpeciesSet object from this constrained element");
	}

	my $msa_mlss_id = $cons_eles_mlss->get_tagvalue("msa_mlss_id"); # The mlss_id of the alignments from which the constrained elements were generated

	my $msa_mlss = $mlss_adaptor->fetch_by_dbID( $msa_mlss_id );
	
	# setting the flags
	my $skip_empty_GenomicAligns = 1;
	my $uc = 0;
	my $translated = 0;

	for my $flag ( @flags ) {
		$uc = 1 if ($flag =~ /^uc$/i);
		$translated = 1 if ($flag =~ /^translated$/i);
	}		

	my $genomic_align_block_adaptor = $self->adaptor->db->get_GenomicAlignBlock;
	$self->start(1) if $self->start <= 0;
	my $gabs = $genomic_align_block_adaptor->fetch_all_by_MethodLinkSpeciesSet_Slice(
		$msa_mlss, $self->slice->sub_Slice($self->start, $self->end, $self->slice->strand));

	my $sa = Bio::SimpleAlign->new();

	warn "should be only one genomic_align_block associated with each constrained element\n" if @$gabs > 1;

	my $this_genomic_align_block = $gabs->[0];
	my $bio07 = 0; 
	if(!$sa->can('add_seq')) {
		$bio07 = 1; 
	}
	my $reference_genomic_align = $this_genomic_align_block->reference_genomic_align();

	my $restricted_gab = $this_genomic_align_block->restrict_between_reference_positions(
		($self->slice->start + $self->start - 1),
		($self->slice->start + $self->end - 1),
		$reference_genomic_align,
		$skip_empty_GenomicAligns);
	print "dbID: ", $this_genomic_align_block->dbID, ". "; 
	foreach my $genomic_align( @{ $restricted_gab->get_all_GenomicAligns } ) {
		my $alignSeq = $genomic_align->aligned_sequence;
		my $loc_seq = Bio::LocatableSeq->new(
			-SEQ    => $uc ? uc $alignSeq : lc $alignSeq,
			-START  => $genomic_align->dnafrag_start,
			-END    => $genomic_align->dnafrag_end,
			-ID     => $genomic_align->dnafrag->genome_db->name . "/" . $genomic_align->dnafrag->name,
			-STRAND => $genomic_align->dnafrag_strand);

		if($bio07) { 
			$sa->addSeq($loc_seq); 
		}else{ 
			$sa->add_seq($loc_seq); 
		}				
	}
	return $sa;
}

=head2 summary_as_hash

  Example       : $constrained_summary = $constrained_element->summary_as_hash();
  Description   : Retrieves a textual summary of this ConstrainedElement object.
	              Sadly not descended from Feature, so certain attributes must be explicitly requested
  Returns       : hashref of descriptive strings

=cut

sub summary_as_hash {
  my $self = shift;
  my $summary_ref;
  $summary_ref->{'ID'} = $self->dbID;
  $summary_ref->{'start'} = $self->seq_region_start;
  $summary_ref->{'end'} = $self->seq_region_end;
  $summary_ref->{'strand'} = $self->strand;
  $summary_ref->{'seq_region_name'} = $self->slice->seq_region_name;
  $summary_ref->{'score'} = $self->score;
  return $summary_ref;
}

1;