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Commit 2223def0 authored by Andy Yates's avatar Andy Yates
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switching from ok to is & Test::More

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use strict;
use warnings;
BEGIN {
$| = 1;
use Test;
plan tests => 50;
}
use Test::More;
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Operon;
......@@ -21,6 +17,8 @@ ok(1);
my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
$multi->save('core', 'operon', 'operon_transcript', 'gene', 'transcript');
my $dba = $multi->get_DBAdaptor("core");
debug("Test database instatiated");
......@@ -40,7 +38,7 @@ my $operon = Bio::EnsEMBL::Operon->new( -START => $start,
-STRAND => $strand,
-SLICE => $slice,
-DISPLAY_LABEL => $display_label, -STABLE_ID=>"op1", -ANALYSIS=>$analysis );
ok( $analysis, $operon->analysis(), "Analysis" );
is( $analysis, $operon->analysis());
my $gene_name = "accB";
my $gene_start = 31225346;
......@@ -91,6 +89,7 @@ for my $feature ( $gene2, $transcript2, $exon2 ) {
$feature->slice($slice);
$feature->strand($gene_strand);
}
$gene2->analysis($analysis);
$transcript2->analysis($analysis);
$exon2->phase(0);
......@@ -122,7 +121,7 @@ my $operon_transcript =
$operon_transcript->add_gene($gene);
$operon_transcript->add_gene($gene2);
$operon->add_OperonTranscript($operon_transcript);
ok( $analysis, $operon_transcript->analysis(), "Analysis" );
is( $analysis, $operon_transcript->analysis(), "Analysis" );
my $operon_transcript2 =
Bio::EnsEMBL::OperonTranscript->new( -START => $start,
......@@ -131,7 +130,7 @@ my $operon_transcript2 =
-SLICE => $slice, -STABLE_ID=>"opt2", -ANALYSIS=>$analysis );
$operon_transcript2->add_gene($gene);
$operon->add_OperonTranscript($operon_transcript2);
ok( $analysis, $operon_transcript->analysis(), "Analysis" );
is( $analysis, $operon_transcript->analysis(), "Analysis" );
# store the lot
# store operon
......@@ -140,69 +139,69 @@ ok( defined $operon->dbID() );
# retrieve operon
my $operon2 = $operon_adaptor->fetch_by_dbID( $operon->dbID() );
ok( $operon2->dbID(), $operon->dbID(), "Operon ID" );
ok( $operon2->display_label(), $operon->display_label(), "Operon name" );
ok( $operon2->seq_region_start(), $operon->seq_region_start(), "Operon start" );
ok( $operon2->seq_region_end(), $operon->seq_region_end(), "Operon end" );
ok( $operon2->seq_region_strand(),
is( $operon2->dbID(), $operon->dbID(), "Operon ID" );
is( $operon2->display_label(), $operon->display_label(), "Operon name" );
is( $operon2->seq_region_start(), $operon->seq_region_start(), "Operon start" );
is( $operon2->seq_region_end(), $operon->seq_region_end(), "Operon end" );
is( $operon2->seq_region_strand(),
$operon->seq_region_strand(),
"Operon strand" );
ok( $operon2->analysis(), $operon->analysis(), "Analysis" );
is( $operon2->analysis(), $operon->analysis(), "Analysis" );
my @operon_transcripts = @{ $operon2->get_all_OperonTranscripts() };
# check operon transcript
ok( scalar @operon_transcripts, 2, "Expected number of transcripts" );
is( scalar @operon_transcripts, 2, "Expected number of transcripts" );
my $operon_transcript_r = $operon_transcripts[0];
ok( $operon_transcript_r->dbID(), $operon_transcript->dbID(),
is( $operon_transcript_r->dbID(), $operon_transcript->dbID(),
"Operon transcript ID" );
ok( $operon_transcript_r->seq_region_start(),
is( $operon_transcript_r->seq_region_start(),
$operon_transcript->seq_region_start(),
"Operon transcript start" );
ok( $operon_transcript_r->seq_region_end(),
is( $operon_transcript_r->seq_region_end(),
$operon_transcript->seq_region_end(),
"Operon transcript end" );
ok( $operon_transcript_r->seq_region_strand(),
is( $operon_transcript_r->seq_region_strand(),
$operon_transcript->seq_region_strand(),
"Operon transcript strand" );
ok( $operon_transcript->analysis(), $operon_transcript_r->analysis(), "Analysis" );
is( $operon_transcript->analysis(), $operon_transcript_r->analysis(), "Analysis" );
# check genes
my @ogenes = @{ $operon_transcript_r->get_all_Genes() };
ok( scalar @ogenes, 2, "Expected number of genes" );
is( scalar @ogenes, 2, "Expected number of genes" );
my $gene_r = $ogenes[0];
ok( $gene_r->dbID(), $gene->dbID(), "Gene ID" );
ok( $gene_r->seq_region_start(), $gene->seq_region_start(), "Gene start" );
ok( $gene_r->seq_region_end(), $gene->seq_region_end(), "Gene end" );
ok( $gene_r->seq_region_strand(), $gene->seq_region_strand(), "Gene strand" );
is( $gene_r->dbID(), $gene->dbID(), "Gene ID" );
is( $gene_r->seq_region_start(), $gene->seq_region_start(), "Gene start" );
is( $gene_r->seq_region_end(), $gene->seq_region_end(), "Gene end" );
is( $gene_r->seq_region_strand(), $gene->seq_region_strand(), "Gene strand" );
$gene_r = $ogenes[1];
ok( $gene_r->dbID(), $gene2->dbID(), "Gene ID" );
ok( $gene_r->seq_region_start(), $gene2->seq_region_start(), "Gene start" );
ok( $gene_r->seq_region_end(), $gene2->seq_region_end(), "Gene end" );
ok( $gene_r->seq_region_strand(), $gene2->seq_region_strand(), "Gene strand" );
is( $gene_r->dbID(), $gene2->dbID(), "Gene ID" );
is( $gene_r->seq_region_start(), $gene2->seq_region_start(), "Gene start" );
is( $gene_r->seq_region_end(), $gene2->seq_region_end(), "Gene end" );
is( $gene_r->seq_region_strand(), $gene2->seq_region_strand(), "Gene strand" );
my $operon_transcript_r2 = $operon_transcripts[1];
ok( $operon_transcript_r2->dbID(),
is( $operon_transcript_r2->dbID(),
$operon_transcript2->dbID(),
"Operon transcript ID" );
ok( $operon_transcript_r2->seq_region_start(),
is( $operon_transcript_r2->seq_region_start(),
$operon_transcript2->seq_region_start(),
"Operon transcript start" );
ok( $operon_transcript_r2->seq_region_end(),
is( $operon_transcript_r2->seq_region_end(),
$operon_transcript2->seq_region_end(),
"Operon transcript end" );
ok( $operon_transcript_r2->seq_region_strand(),
is( $operon_transcript_r2->seq_region_strand(),
$operon_transcript2->seq_region_strand(),
"Operon transcript strand" );
ok( $operon_transcript2->analysis(), $operon_transcript_r2->analysis(), "Analysis" );
is( $operon_transcript2->analysis(), $operon_transcript_r2->analysis(), "Analysis" );
# check genes
@ogenes = @{ $operon_transcript_r2->get_all_Genes() };
ok( scalar @ogenes, 1, "Expected number of genes" );
is( scalar @ogenes, 1, "Expected number of genes" );
$gene_r = $ogenes[0];
ok( $gene_r->dbID(), $gene->dbID(), "Gene ID" );
ok( $gene_r->seq_region_start(), $gene->seq_region_start(), "Gene start" );
ok( $gene_r->seq_region_end(), $gene->seq_region_end(), "Gene end" );
ok( $gene_r->seq_region_strand(), $gene->seq_region_strand(), "Gene strand" );
is( $gene_r->dbID(), $gene->dbID(), "Gene ID" );
is( $gene_r->seq_region_start(), $gene->seq_region_start(), "Gene start" );
is( $gene_r->seq_region_end(), $gene->seq_region_end(), "Gene end" );
is( $gene_r->seq_region_strand(), $gene->seq_region_strand(), "Gene strand" );
$dba->get_OperonAdaptor()->remove($operon);
$dba->get_GeneAdaptor()->remove($gene);
......@@ -228,3 +227,7 @@ ok( scalar(@operon_transcripts) == 1 );
debug ("OperonTranscript->list_stable_ids");
my $stable_ids = $ota->list_stable_ids();
ok (@{$stable_ids});
$multi->restore('core');
done_testing();
\ No newline at end of file
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