ENSPROD-55: adding test module for genome container

modules/t/genomeContainer.t

+use strict;
+use warnings;
+
+use Bio::EnsEMBL::DBSQL::GenomeContainer;
+use Bio::EnsEMBL::Test::TestUtils;
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::Test::MultiTestDB;
+
+
+our $verbose = 0;
+
+use Test::More;
+
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
+
+
+#
+# Test constructor
+#
+
+my $db = $multi->get_DBAdaptor("patch");
+debug("Test database instatiated");
+ok($db);
+my $sql_helper = $db->dbc->sql_helper;
+my $genome = $db->get_adaptor('GenomeContainer');
+
+ok($genome && $genome->isa('Bio::EnsEMBL::DBSQL::GenomeContainer'));
+
+# 
+# Test version()
+#
+
+my $sql = "SELECT DISTINCT version FROM coord_system
+        WHERE attrib like '%default_version%'
+          AND version is not null";
+my $version = $sql_helper->execute_single_result(-SQL => $sql);
+is($genome->get_version(), $version, "Genome version is correct");
+
+$sql = "SELECT meta_value FROM meta
+         WHERE meta_key = 'assembly.accession'";
+my $accession = $sql_helper->execute_single_result(-SQL => $sql);
+is($genome->get_accession(), $accession, "Genome accession is correct");
+
+
+#
+# Test feature counts
+#
+
+$sql = "select sum(value) from seq_region_attrib sa, attrib_type at, seq_region s
+        where at.attrib_type_id = sa.attrib_type_id
+        and s.seq_region_id = sa.seq_region_id
+        and code = ?";
+my $coding_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['coding_cnt']);
+is($coding_count, $genome->get_coding_count, "Coding count is correct");
+
+my $lnoncoding_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['lnoncoding_cnt']);
+is($lnoncoding_count, $genome->get_lnoncoding_count, "Long non coding count is correct");
+
+my $snoncoding_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['snoncoding_cnt']);
+is($snoncoding_count, $genome->get_snoncoding_count, "Short non coding count is correct");
+
+my $pseudogene_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['pseudogene_cnt']);
+is($pseudogene_count, $genome->get_pseudogene_count, "Pseudogene count is correct");
+
+my $alt_coding_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['coding_acnt']);
+is($alt_coding_count, $genome->get_alt_coding_count, "Coding count on alternate sequences is correct");
+
+my $alt_lnoncoding_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['lnoncoding_acnt']);
+is($alt_lnoncoding_count, $genome->get_alt_lnoncoding_count, "Long non coding count on alternate sequences is correct");
+
+my $alt_snoncoding_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['snoncoding_acnt']);
+is($alt_snoncoding_count, $genome->get_alt_snoncoding_count, "Short non coding count on alternate sequences is correct");
+
+my $snp_count = $sql_helper->execute_single_result(-SQL => $sql, -PARAMS => ['SNPcount'], -NO_ERROR => 1);
+is($snp_count, $genome->get_snp_count, "SNP count is correct");
+
+is_rows($genome->get_prediction_count, $db, "prediction_transcript");
+is_rows($genome->get_prediction_count('genscan'), $db, "prediction_transcript", "where analysis_id = ?", [8440]);
+
+#
+# Test genome length
+#
+
+$sql = "SELECT sum(length) FROM seq_region sr, seq_region_attrib sra, attrib_type at, coord_system cs
+        WHERE sr.seq_region_id = sra.seq_region_id
+          AND sra.attrib_type_id = at.attrib_type_id
+          AND sr.coord_system_id = cs.coord_system_id 
+          AND at.code = 'toplevel' 
+          AND cs.name != 'lrg' 
+          AND sr.seq_region_id NOT IN 
+            (SELECT DISTINCT seq_region_id FROM assembly_exception ae WHERE ae.exc_type != 'par' )";
+my $ref_length = $sql_helper->execute_single_result(-SQL => $sql); 
+is($ref_length, $genome->get_ref_length, "Reference length is correct");
+
+$sql = "SELECT sum(length(sequence)) FROM dna";
+my $total_length = $sql_helper->execute_single_result(-SQL => $sql);    
+is($total_length, $genome->get_total_length, "Reference length is correct");
+
+
+
+done_testing();