DnaAlignFeatureAdaptor in. Waiting now only for RepeatFeatureAdaptor (James!)....

DnaAlignFeatureAdaptor in. Waiting now only for RepeatFeatureAdaptor (James!). Started to retarget the FeatureAdaptor system to the new FeatureAdaptors. Need the FeatureBlock objects around

modules/Bio/EnsEMBL/DBSQL/DnaAlignFeatureAdaptor.pm

+
+
+#
+# BioPerl module for Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor
+#
+# Cared for by Ewan Birney <birney@ebi.ac.uk>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::DnaAlignFeatureAdaptor - Adaptor for DnaAlignFeatures
+
+=head1 SYNOPSIS
+
+    $pfadp = $dbadaptor->get_DnaAlignFeatureAdaptor();
+
+    my @feature_array = $pfadp->fetch_by_contig_id($contig_numeric_id);
+
+    my @feature_array = $pfadp->fetch_by_assembly_location($start,$end,$chr,'UCSC');
+ 
+    $pfadp->store($contig_numeric_id,@feature_array);
+
+
+=head1 DESCRIPTION
+
+
+This is an adaptor for protein features on DNA sequence. Like other
+feature getting adaptors it has a number of fetch_ functions and a
+store function.
+
+
+=head1 AUTHOR - Ewan Birney
+
+Email birney@ebi.ac.uk
+
+Describe contact details here
+
+=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::DBSQL::DnaAlignFeatureAdaptor;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::RootI
+
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::FeatureFactory;
+
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+# new() can be inherited from Bio::Root::RootI
+
+
+=head2 fetch_by_dbID
+
+ Title   : fetch_by_dbID
+ Function:
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub fetch_by_dbID{
+   my ($self,$id) = @_;
+
+   if( !defined $id ) {
+       $self->throw("fetch_by_dbID must have an id");
+   }
+
+   my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line,p.analysis_id from protein_align_feature p where p.protein_align_feature_id = $id");
+   $sth->execute();
+
+   my ($contig_id,$start,$end,$strand,$hstart,$hend,$hstrand,$hname,$cigar,$analysis_id) = $sth->fetchrow_array();
+
+   if( !defined $contig_id ) {
+       $self->throw("No simple feature with id $id");
+   }
+
+   my $contig = $self->db->get_RawContigAdaptor->fetch_by_dbID($contig_id);
+
+   my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();;
+   $out->start($start);
+   $out->end($end);
+   $out->strand($strand);
+
+   $out->hstart($hstart);
+   $out->hend($hend);
+   $out->hstrand($hstrand);
+   $out->hseqname($hname);
+   $out->cigar($cigar);
+   
+   $out->analysis($self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id));
+
+   $out->seqname($contig->id);
+   $out->attach_seq($contig->seq);
+
+   return $out;
+
+}
+
+=head2 fetch_by_contig_id
+
+ Title   : fetch_by_contig_id
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub fetch_by_contig_id{
+   my ($self,$cid) = @_;
+
+   if( !defined $cid ) {
+       $self->throw("fetch_by_contig_id must have an contig id");
+   }
+
+   my $sth = $self->prepare("select p.contig_id,p.contig_start,p.contig_end,p.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line,p.analysis_id from protein_align_feature p where p.contig_id = $cid");
+   $sth->execute();
+
+   my ($contig_id,$start,$end,$strand,$hstart,$hend,$hstrand,$hname,$cigar,$analysis_id);
+
+   $sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hstrand,\$hname,\$cigar,\$analysis_id);
+
+   my @f;
+   my $contig = $self->db->get_RawContigAdaptor->fetch_by_dbID($cid);
+   my %ana;
+
+   while( $sth->fetch ) {
+       if( !defined $ana{$analysis_id} ) {
+	   $ana{$analysis_id} = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
+       }
+
+
+       my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();;
+       $out->start($start);
+       $out->end($end);
+       $out->strand($strand);
+
+       $out->hstart($hstart);
+       $out->hend($hend);
+       $out->hstrand($hstrand);
+       $out->hseqname($hname);
+       $out->cigar($cigar);
+
+       $out->analysis($ana{$analysis_id});
+       $out->seqname($contig->name);
+       $out->attach_seq($contig->seq);
+       push(@f,$out);
+   }
+   
+   return @f;
+}
+
+
+=head2 fetch_by_assembly_location
+
+ Title   : fetch_by_assembly_location
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub fetch_by_assembly_location{
+   my ($self,$start,$end,$chr,$type) = @_;
+
+   if( !defined $type ) {
+       $self->throw("Assembly location must be start,end,chr,type");
+   }
+
+   if( $start !~ /^\d/ || $end !~ /^\d/ ) {
+       $self->throw("start/end must be numbers not $start,$end (have you typed the location in the right way around - start,end,chromosome,type");
+   }
+
+   my $mapper = $self->db->get_AssemblyMapperAdaptor->fetch_by_type($type);
+   $mapper->register_region($start,$end,$chr);
+
+   my @cids = $mapper->list_contig_ids($start,$end,$chr);
+
+   # build the SQL
+
+   my $cid_list = join(',',@cids);
+   my $sth = $self->prepare("select s.contig_id,s.contig_start,s.contig_end,s.contig_strand,p.hit_start,p.hit_end,p.hit_strand,p.hit_name,p.cigar_line,a.gff_source,a.gff_feature from protein_align_feature p where p.contig_id in ($cid_list)");
+   $sth->execute();
+
+
+   my ($contig_id,$start,$end,$strand,$hstart,$hend,$hstrand,$hname,$cigar,$analysis_id);
+
+   $sth->bind_columns(undef,\$contig_id,\$start,\$end,\$strand,\$hstart,\$hend,\$hname,\$cigar,\$analysis_id);
+
+
+   my @f;
+   my %ana;
+
+   while( $sth->fetch ) {
+       # we whether this is sensible to use or not
+       my @coord_list = $mapper->map_coordinates($start,$end,$strand,$contig_id,"rawcontig");
+       
+       # coord list > 1 - means does not cleanly map. At the moment, skip
+       if( scalar(@coord_list) > 1 ) {
+	   next;
+       }
+
+       if( !defined $ana{$analysis_id} ) {
+	   $ana{$analysis_id} = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
+       }
+
+       # ok, ready to build a sequence feature: do we want this relative or not?
+
+       my $out = Bio::EnsEMBL::FeatureFactory->new_feature_pair();;
+       $out->start($coord_list[0]->start);
+       $out->end($coord_list[0]->end);
+       $out->strand($coord_list[0]->strand);
+       $out->seqname($coord_list[0]->seqname);
+
+       $out->hstart($hstart);
+       $out->hend($hend);
+       $out->hstrand($hstrand);
+       $out->hseqname($hname);
+       $out->cigar($cigar);
+
+       $out->analysis($ana{$analysis_id});
+       
+       push(@f,$out);
+   }
+
+   return @f;
+
+}
+
+=head2 store
+
+ Title   : store
+ Usage   :
+ Function:
+ Example :
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub store{
+   my ($self,$contig_id,@sf) = @_;
+
+   if( scalar(@sf) == 0 ) {
+       $self->throw("Must call store with contig_id then sequence features");
+   }
+
+   if( $contig_id !~ /^\d+$/ ) {
+       $self->throw("Contig_id must be a number, not [$contig_id]");
+   }
+
+   my $sth = $self->prepare("insert into protein_align_feature (contig_id,contig_start,contig_end,contig_strand,hit_start,hit_end,hit_strand,hit_name,cigar_line,analysis_id,score) values (?,?,?,?,?,?,?,?,?,?,?)");
+
+   foreach my $sf ( @sf ) {
+       if( !ref $sf || !$sf->isa("Bio::EnsEMBL::FeaturePair") ) {
+	   $self->throw("Simple feature must be an Ensembl DnaAlignFeature, not a [$sf]");
+       }
+
+       if( !defined $sf->analysis ) {
+	   $self->throw("Cannot store sequence features without analysis");
+       }
+       if( !defined $sf->analysis->dbID ) {
+	   # maybe we should throw here. Shouldn't we always have an analysis from the database?
+	   $self->throw("I think we should always have an analysis object which has originated from the database. No dbID, not putting in!");
+       }
+
+       $sth->execute($contig_id,$sf->start,$sf->end,$sf->strand,$sf->hstart,$sf->hend,$sf->hstrand,$sf->hseqname,$sf->cigar,$sf->analysis->dbID,$sf->score);
+   }
+
+
+}
+
+
+
+1;
+
+

modules/Bio/EnsEMBL/DBSQL/FeatureAdaptor.pm

@@ -195,6 +195,12 @@ sub write {
 sub store {
     my ($self,$contig,@features) = @_;
 
+
+    my ($p,$f,$l) = caller;
+    $self->warn("$f:$l FeatureAdaptor store being phased out. It is better to use the new FeatureAdaptors directly (more type safe)");
+
+
+
     # Check for contig
     $self->throw("$contig is not a Bio::EnsEMBL::DB::ContigI") 
         unless (defined($contig) && $contig->isa("Bio::EnsEMBL::DB::ContigI"));
@@ -228,6 +234,13 @@ sub store {
 	    $analysisid = $feature->analysis->adaptor->store($feature->analysis);
 	}
 
+	#
+	# Retarget to new adaptor scheme
+	# 
+
+	$self->throw("Ewan needs to retarget this to the new feature adaptors once the buisness objects for the features come in");
+
+
 	# What kinda feature we're dealing with?
 	if($feature->isa('Bio::EnsEMBL::RepeatI')) {
 	    $self->_store_Repeat($contig_internal_id,$analysisid,$feature);