converter for genscan result;

more doc for converter factory to enumerate all instances so far.

modules/Bio/EnsEMBL/Utils/Converter.pm

@@ -28,6 +28,15 @@ Bio::EnsEMBL::Utils::Converter, a converter factory
     
     Module to converter the business objects between EnsEMBL and any other projects, currently BioPerl.
 
+    What the ready conversions are,
+
+Bio::SeqFeature::Generic <-> Bio::EnsEMBL::SeqFeature, Bio::EnsEMBL::SimpleFeature
+Bio::SeqFeature::FeaturePair <-> Bio::EnsEMBL::SeqFeature, Bio::EnsEMBL::RepeatFeature
+Bio::Search::HSP::GenericHSP -> Bio::EnsEMBL::BaseAlignFeature's submodules
+Bio::Tools::Prediction::Gene -> Bio::EnsEMBL::PredictionTranscript
+Bio::Tools::Prediction::Exon -> Bio::EnsEMBL::Exon
+Bio::Pipeline::Analysis -> Bio::EnsEMBL::Analysis
+
 =head1 FEEDBACK
 
 

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

@@ -105,6 +105,10 @@ sub _guess_module {
         $tail = 'bio_ens_featurePair';
     }elsif($in eq 'Bio::Pipeline::Analysis'){
         $tail = 'bio_ens_analysis';
+    }elsif($in eq 'Bio::Tools::Prediction::Gene'){
+        $tail = 'bio_ens_predictionGene';
+    }elsif($in eq 'Bio::Tools::Prediction::Exon'){
+        $tail = 'bio_ens_predictionExon';
     }else{
         $self->throw("[$in] to [$out], not supported");
     }

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

+# Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon
+#
+# Created and cared for by Juguang Xiao <juguang@tll.org.sg>
+# Created date: 19/3/2003
+# 
+# Copyright Juguang Xiao
+# 
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon
+
+=head1 SYNOPISIS
+
+my $converter = new Bio::EnsEMBL::Utils::Converter(
+    -in => 'Bio::Tools::Prediction::Exon',
+    -out => 'Bio::EnsEMBL::Exon'
+    -contig => $ens_contig
+);
+
+=head1 DESCRIPTION
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@tll.org.sg>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin ...
+
+package Bio::EnsEMBL::Utils::Converter::bio_ens_predictionExon;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Utils::Converter;
+use Bio::EnsEMBL::Exon;
+use Bio::EnsEMBL::Utils::Converter::bio_ens;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
+
+sub _convert_single {
+    my ($self, $input) = @_;
+    
+
+    $input || $self->throw("a input object needed");
+    $self->throw("a Bio::Tools::Prediction::Exon object needed")
+        unless($input->isa("Bio::Tools::Prediction::Exon"));
+
+    $output = Bio::EnsEMBL::Exon->new(
+        -start => $input->start,
+        -end => $input->end,
+        -strand => $input->strand
+    );
+
+    $output->score($input->score);
+    $output->p_value($input->significance);
+
+    $output->phase($input->get_tag_values("phase")); # only first element is used
+    $output->end_phase($input->get_tag_values("end_phase"));
+
+    $output->contig($self->contig);
+
+    return $output;
+}
+
+
+1;

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

+# Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene
+#
+# Created and cared for by Juguang Xiao <juguang@tll.org.sg>
+# Created date: 18/3/2003
+# 
+# Copyright Juguang Xiao
+# 
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::Converter::bio_ens_predictionGene
+
+=head1 SYNOPISIS
+
+
+
+=head1 DESCRIPTION
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+=head2 Reporting Bugs
+
+
+=head1 AUTHOR Juguang Xiao
+
+Juguang Xiao <juguang@tll.org.sg>
+
+=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::Utils::Converter::bio_ens_predictionGene;
+
+use strict;
+use vars qw(@ISA);
+use Bio::EnsEMBL::Utils::Converter;
+use Bio::EnsEMBL::PredictionTranscript;
+use Bio::EnsEMBL::Utils::Converter::bio_ens;
+@ISA = qw(Bio::EnsEMBL::Utils::Converter::bio_ens);
+
+sub _initialize {
+    my ($self, @args) = @_;
+
+    $self->SUPER::_initialize(@args);
+
+    $self->{_predictionExonConverter} = new Bio::EnsEMBL::Utils::Converter(
+        -in => 'Bio::Tools::Prediction::Exon',
+        -out => 'Bio::EnsEMBL::Exon',
+        -contig => $self->contig
+    );
+
+}
+
+sub _convert_single {
+    my ($self, $input) = @_;
+    
+    $self->throw("one argument needed") unless($input and defined($input));
+    $self->throw("a Bio::Tools::Prediction::Gene object needed")
+        unless(ref($input) && $input->isa('Bio::Tools::Prediction::Gene'));
+
+    my $output = Bio::EnsEMBL::PredictionTranscript->new;
+    $output->analysis($self->analysis);
+
+    my @exons = sort {$a->start <=> $b->start} $input->exons;
+
+    # Not sure on the correctivity of phase calculation.
+    my $previous_end_phase = -1;
+    foreach(@exons){
+        my $length = $_->length;
+        my $frame = $_->frame;
+        my $phase = ($previous_end_phase+1) %3;
+        my $end_phase = ($length-$frame)  %1;
+        $previous_end_phase = $end_phase;
+        $_->add_tag_value("phase", $phase);
+        $_->add_tag_value("end_phase", $end_phase);
+    }
+
+    my @ens_exons = @{$self->{_predictionExonConverter}->convert(\@exons)};
+
+    $output->add_Exon($_) foreach(@ens_exons);
+
+    return $output;
+
+}
+
+=head2 contig
+  Title   : contig
+  Usage   : $self->contig
+  Function: get and set for contig
+  Return  : L<Bio::EnsEMBL::RawContig>
+  Args    : L<Bio::EnsEMBL::RawContig>
+=cut
+
+sub contig {
+    my ($self, $arg) = @_;
+    if(defined($arg)){
+        $self->throws("A Bio::EnsEMBL::RawContig object expected.") unless(defined $arg);
+        $self->{_contig} = $arg;
+        # assign it to the sub converter which converts exons
+        $self->{_predictionExonConverter}->contig($arg);
+    }
+    return $self->{_contig};
+}
+1;