converter from GenericHSP to BaseAlignFeature's submodules, for blast report

GenericHPS::algorithm tells what program of blastall is used, and in response of this, the code try to find the specific alignment feature in EnsEMBL.

modules/Bio/EnsEMBL/Utils/Converter/bio_ens_hit.pm

+
+=head1
+
+Sequence alignment hits were previously stored within the core database as 
+ungapped alignments. This imposed 2 major constraints on alignments:
+
+a) alignments for a single hit record would require multiple rows in the 
+database, and
+b) it was not possible to accurately retrieve the exact original alignment.
+
+Therefore, in the new branch sequence alignments are now stored as ungapped 
+alignments in the cigar line format (where CIGAR stands for Concise 
+Idiosyncratic Gapped Alignment Report).
+
+In the cigar line format alignments are sotred as follows:
+
+M: Match
+D: Deletino
+I: Insertion
+
+An example of an alignment for a hypthetical protein match is shown below: 
+
+
+Query:   42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
+            PG    P    G     GP   R      PLGP
+Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...
+            
+protein_align_feature table as the following cigar line: 
+
+7M4D12M2I2MD7M 
+
+
+=cut
+
+package Bio::EnsEMBL::Utils::Converter::bio_ens_hit;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Utils::Converter::bio_ens;
+use Bio::EnsEMBL::DnaDnaAlignFeature;
+use Bio::EnsEMBL::DnaPepAlignFeature;
+use Bio::EnsEMBL::PepDnaAlignFeature;
+
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
+
+sub _initialize {
+    my ($self, @args) = @_;
+    $self->SUPER::_initialize(@args);
+
+    # After super initialized, analysis and contig are ready.
+    my $bio_ens_seqFeature_converter = new Bio::EnsEMBL::Utils::Converter(
+        -in => 'Bio::SeqFeature::Generic',
+        -out => 'Bio::EnsEMBL::SeqFeature',
+        -analysis => $self->analysis,
+        -contig => $self->contig
+    );
+    $self->_bio_ens_seqFeature_converter($bio_ens_seqFeature_converter);
+
+}
+
+sub _convert_single {
+    my ($self, $input) = @_;
+    
+    my $in = $self->in;
+    my $out = $self->out;
+    
+    if($in =~ /Bio::Search::Hit::GenericHit/){
+        return $self->_convert_single_hit($input);
+    }elsif($in =~ /Bio::Search::HSP::GenericHSP/){
+        return $self->_convert_single_hsp($input);
+    }else{
+        $self->throw("[$in]->[$out], not implemented");
+    }
+}
+
+sub _convert_single_hit {
+
+
+}
+
+sub _convert_single_hsp {
+    my ($self, $hsp) = @_;
+
+    unless(ref($hsp) && $hsp->isa('Bio::Search::HSP::GenericHSP')){
+        $self->throw("a GenericHSP object needed");
+    }
+
+    my $bio_ens_seqFeature_converter = $self->_bio_ens_seqFeature_converter;
+    my $ens_feature1 = $bio_ens_seqFeature_converter->_convert_single(
+        $hsp->feature1);
+    my $ens_feature2 = $bio_ens_seqFeature_converter->_convert_single(
+        $hsp->feature2);
+
+    $ens_feature1->p_value($hsp->evalue);
+    $ens_feature1->score($hsp->score);
+    $ens_feature1->percent_id($hsp->percent_identity);
+    $ens_feature2->p_value($hsp->evalue);
+    $ens_feature2->score($hsp->score);
+    $ens_feature2->percent_id($hsp->percent_identity);
+    
+    my $cigar_string = $hsp->cigar_string;
+    my @args = (
+        -feature1 => $ens_feature1,
+        -feature2 => $ens_feature2,
+        -cigar_string => $cigar_string
+    );
+
+    my $contig = $self->contig;
+    # choose the AlignFeature based on the blast program
+    my $program = $hsp->algorithm;
+
+    $self->throw("HSP does not have algorithm value") unless(defined($program));
+    my $align_feature;
+    
+    if($program =~ /blastn/i){
+        $align_feature = new Bio::EnsEMBL::DnaDnaAlignFeature(@args);
+        $align_feature->attach_seq($contig);
+    }elsif($program =~ /blastx/i){
+        $align_feature = new Bio::EnsEMBL::DnaPepAlignFeature(@args);
+        $align_feature->attach_seq($contig);
+    }else{
+        $self->throw("$program is not supported yet");
+    }
+    
+    return $align_feature;
+}
+
+# an internal getter/setter for a converter used for seq feature conversion.
+
+sub _bio_ens_seqFeature_converter {
+    my ($self, $arg) = @_;
+    if(defined $arg){
+        $self->{_bio_ens_seqFeature_converter} = $arg;
+    }
+    return $self->{_bio_ens_seqFeature_converter};
+}
+
+1;

modules/t/converter.t

@@ -4,11 +4,9 @@ use strict;
 BEGIN {
     $| = 1;
     use Test;
-    plan tests => 22;
+    plan tests => 36;
 }
 
-use Bio::EnsEMBL::Utils::Converter;
-
 END {
 
 }
@@ -49,6 +47,8 @@ my $featurePair1 = new Bio::SeqFeature::FeaturePair(
     -feature2 => $seqFeature2
 );
 
+use Bio::EnsEMBL::Utils::Converter;
+
 &test_SeqFeature;
 &test_FeaturePair;
 &test_hit;
@@ -125,9 +125,48 @@ sub test_FeaturePair{
         
 }
 
-
+# 14 OKs
 sub test_hit {
+    my $converter = new Bio::EnsEMBL::Utils::Converter(
+        -in => 'Bio::Search::HSP::GenericHSP',
+        -out => 'Bio::EnsEMBL::BaseAlignFeature',
+        -analysis => $ens_analysis,
+        -contig => $ens_contig
+    );
+
+    use Bio::SearchIO;
+    my $searchio = new Bio::SearchIO(
+        -format => 'blast',
+        -file => 't/converter.blast'
+    );
 
+    my @hsps = ();
+    while(my $result = $searchio->next_result){
+        while(my $hit = $result->next_hit){
+            while(my $hsp = $hit->next_hsp){
+                push @hsps, $hsp;
+            }
+        }
+    }
 
+    my @align_features = @{$converter->convert(\@hsps)};
+    my $align_feature = shift @align_features;
+    ok $align_feature->isa('Bio::EnsEMBL::BaseAlignFeature');
+    ok $align_feature->start, 1;
+    ok $align_feature->end, 504;
+    ok $align_feature->strand, 0;
+    ok $align_feature->hstart, 21;
+    ok $align_feature->hend, 1532;
+    ok $align_feature->cigar_string, '504M';
+
+    $align_feature = shift @align_features;
+    ok $align_feature->isa('Bio::EnsEMBL::BaseAlignFeature');
+    ok $align_feature->start, 64;
+    ok $align_feature->end, 324;
+    ok $align_feature->strand, 0;
+    ok $align_feature->hstart, 182;
+    ok $align_feature->hend, 844;
+    ok $align_feature->cigar_string, '29M18I22M11I20MD33M4I22M3I25M5I21MI33MD14M';
+    
 }