removed since broken, can be readded later

modules/t/converter.t

-use lib 't';
-use strict;
-
-BEGIN {
-    $| = 1;
-    use Test;
-    plan tests => 37;
-}
-
-END {
-
-}
-
-
-use Bio::EnsEMBL::Utils::Converter;
-
-use Bio::EnsEMBL::Analysis;
-use Bio::EnsEMBL::RawContig;
-use Bio::SeqFeature::Generic;
-use Bio::SeqFeature::FeaturePair;
-
-# Global constants
-
-my $ens_analysis = new Bio::EnsEMBL::Analysis(
-    -dbID => 1,
-    -logic_name => 'test_fake_analysis'
-);
-
-my $ens_contig = new Bio::EnsEMBL::RawContig();
-
-my $seqFeature1 = new Bio::SeqFeature::Generic(
-    -start => 100,
-    -end => 200,
-    -strand => 1,
-    -score => 10
-);
-
-my $seqFeature2 = new Bio::SeqFeature::Generic(
-    -start => 1234,
-    -end => 5678,
-    -strand => -1,
-    -score => 14
-);
-
-my $featurePair1 = new Bio::SeqFeature::FeaturePair(
-    -feature1 => $seqFeature1,
-    -feature2 => $seqFeature2
-);
-
-use Bio::EnsEMBL::Utils::Converter;
-
-&test_SeqFeature;
-&test_FeaturePair;
-&test_hit;
-&test_predictionTranscript;
-&test_gene;
-
-# Test for SeqFeature, 10 OKs
-sub test_SeqFeature{
-    # bio to ens
-    #
-    # testing the analysis conversion firsti
-    my $analysis = $ens_analysis;
-    eval { require Bio::Pipeline::Analysis;};
-
-    unless($@){
-        $analysis = new Bio::Pipeline::Analysis(
-            -logic_name => 'analysis to test converter'
-        ); 
-    }
-    my $converter = new Bio::EnsEMBL::Utils::Converter(
-        -in => 'Bio::SeqFeature::Generic',
-        -out => 'Bio::EnsEMBL::SeqFeature',
-        -analysis => $analysis,
-        -contig => $ens_contig
-    );
-
-    my ($ens_seqFeature1, $ens_seqFeature2) = 
-        @{$converter->convert([$seqFeature1, $seqFeature2])};
-
-    ok ref($ens_seqFeature1), 'Bio::EnsEMBL::SeqFeature';
-    ok ref($ens_seqFeature2), 'Bio::EnsEMBL::SeqFeature';
-    
-    ok ref($ens_seqFeature1->analysis), 'Bio::EnsEMBL::Analysis';
-    
-    ok $seqFeature1->start, $ens_seqFeature1->start;
-    ok $seqFeature1->end, $ens_seqFeature1->end;
-    ok $seqFeature1->strand, $ens_seqFeature1->strand;
-    ok $seqFeature1->score, $ens_seqFeature1->score;
-    ok $seqFeature1->source_tag, $ens_seqFeature1->source_tag;
-    
-    # from ens to bio
-    $converter = new Bio::EnsEMBL::Utils::Converter(
-        -in => 'Bio::EnsEMBL::SeqFeature',
-        -out => 'Bio::SeqFeature::Generic',
-    );
-
-    my ($bio_seqFeature1, $bio_seqFeature2) =
-        @{$converter->convert([$ens_seqFeature1, $ens_seqFeature2])};
-
-    ok ref($bio_seqFeature1), 'Bio::SeqFeature::Generic';
-    ok ref($bio_seqFeature2), 'Bio::SeqFeature::Generic';
-
-    
-    ok $seqFeature1->start, $bio_seqFeature1->start;
-    ok $seqFeature1->end, $bio_seqFeature1->end;
-    ok $seqFeature1->strand, $bio_seqFeature1->strand;
-    ok $seqFeature1->score, $bio_seqFeature1->score;
-    ok $seqFeature1->source_tag, $bio_seqFeature1->source_tag;
-    
-}
-
-
-sub test_FeaturePair{
-    
-    my $converter = new Bio::EnsEMBL::Utils::Converter(
-        -in => 'Bio::SeqFeature::FeaturePair',
-        -out => 'Bio::EnsEMBL::RepeatFeature',
-        -analysis => $ens_analysis,
-    );
-    $converter->contig($ens_contig);
-    my ($ens_repeatFeature1) = @{$converter->convert([$featurePair1])};
-
-    ok ref($ens_repeatFeature1), 'Bio::EnsEMBL::RepeatFeature';
-    
-    ok $ens_repeatFeature1->start, $featurePair1->feature1->start;
-    ok $ens_repeatFeature1->end, $featurePair1->feature1->end;
-    ok $ens_repeatFeature1->strand, $featurePair1->feature1->strand;
-    ok $ens_repeatFeature1->seqname, $featurePair1->feature1->seq_id;
-    ok $ens_repeatFeature1->repeat_consensus->name, $featurePair1->feature2->seq_id;
-    
-    if($featurePair1->feature1->strand == 1){
-        ok $ens_repeatFeature1->hstart, $featurePair1->feature2->start;
-        ok $ens_repeatFeature1->hend, $featurePair1->feature2->end;
-    }else{
-        ok $ens_repeatFeature1->hstart, $featurePair1->feature2->end;
-        ok $ens_repeatFeature1->hend, $featurePair1->feature2->start;
-    }
-        
-}
-
-# 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';
-    
-}
-
-sub test_predictionTranscript{
-    my $converter = new Bio::EnsEMBL::Utils::Converter(
-        -in => 'Bio::Tools::Prediction::Gene',
-        -out => 'Bio::EnsEMBL::PreditionTranscript'
-    );
-    ok 1;
-}
-
-sub test_gene{
-    my $converter = new Bio::EnsEMBL::Utils::Converter(
-        -in => 'Bio::SeqFeature::Gene::GeneStructure',
-        -out => 'Bio::EnsEMBL::Gene'
-    );
-    ok 1;
-}