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Commit 6c8aeef4 authored by Monika Komorowska's avatar Monika Komorowska
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stable_id merge changes

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with 136 additions and 38 deletions
modules/t/archiveStableId.t
+ 0
− 1
View file @ 6c8aeef4
......@@ -154,7 +154,6 @@ ok( ! $asi->is_latest );
$asi = $asi->get_latest_incarnation;
ok( $asi->is_latest and $asi->version == 3 );
#
# 19 associated IDs in archive
#
......
modules/t/exon.t
+ 7
− 4
View file @ 6c8aeef4
......@@ -181,18 +181,18 @@ ok($first_seq->seq() && $first_seq->seq() eq $second_seq->seq());
ok($first_seq->display_id() && $first_seq->display_id() eq $second_seq->display_id());
#
# test the remove method works
#
$multi->save("core", "exon", "exon_stable_id", "supporting_feature",
$multi->save("core", "exon", "supporting_feature",
"dna_align_feature", "protein_align_feature");
my $ex_count = count_rows($db, 'exon');
my $exstable_count = count_rows($db, 'exon_stable_id');
my $supfeat_count = count_rows($db, 'supporting_feature');
$exon = $exonad->fetch_by_stable_id('ENSE00000859937');
# check the created and modified times
my @date_time = localtime( $exon->created_date());
ok( $date_time[3] == 6 && $date_time[4] == 11 && $date_time[5] == 104 );
......@@ -206,7 +206,6 @@ my $supfeat_minus = @{$exon->get_all_supporting_features()};
$exonad->remove($exon);
ok(count_rows($db, 'exon') == $ex_count - 1);
ok(count_rows($db, 'exon_stable_id') == $exstable_count - 1);
ok(count_rows($db, 'supporting_feature') == $supfeat_count - $supfeat_minus);
$multi->restore();
......@@ -291,3 +290,7 @@ ok( $exon->cdna_coding_end($transcript) == 462 );
ok( $exon->coding_region_start($transcript) == 30577779 );
ok( $exon->coding_region_end($transcript) == 30578038 );
#test the get_species_and_object_type method from the Registry
my $registry = 'Bio::EnsEMBL::Registry';
my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('ENSE00000859937');
ok( $species eq 'homo_sapiens' && $object_type eq 'Exon');
modules/t/gene.t
+ 15
− 9
View file @ 6c8aeef4
......@@ -3,7 +3,7 @@ use warnings;
BEGIN { $| = 1;
use Test;
plan tests => 93;
plan tests => 94;
}
use Bio::EnsEMBL::Test::MultiTestDB;
......@@ -284,7 +284,7 @@ my $stable_id = 'ENSG00000171456';
$gene->description($desc);
$gene->stable_id($stable_id);
$multi->hide( "core", "meta_coord", "gene", "transcript", "exon", "exon_transcript", "translation", "gene_stable_id", "transcript_stable_id", "exon_stable_id", "translation_stable_id", "supporting_feature", "dna_align_feature" );
$multi->hide( "core", "meta_coord", "gene", "transcript", "exon", "exon_transcript", "translation", "supporting_feature", "dna_align_feature" );
my $gene_ad = $db->get_GeneAdaptor();
debug( "Storing the gene" );
......@@ -527,10 +527,9 @@ ok( $ok );
# Gene remove test
#
$multi->save( "core", "gene", "gene_stable_id",
"transcript", "transcript_stable_id",
"translation", "translation_stable_id", "protein_feature",
"exon", "exon_stable_id", "exon_transcript", "supporting_feature",
$multi->save( "core", "gene", "transcript",
"translation", "protein_feature",
"exon", "exon_transcript", "supporting_feature",
"object_xref", "ontology_xref", "identity_xref",
"dna_align_feature", "protein_align_feature");
......@@ -540,7 +539,6 @@ my $gene_count = count_rows( $db, "gene" );
my $exon_count = count_rows( $db, "exon" );
my $trans_count = count_rows( $db, "transcript" );
my $tl_count = count_rows( $db, "translation" );
my $gstable_count = count_rows($db, "gene_stable_id");
my $tminus = scalar( @{$gene->get_all_Transcripts() } );
my $eminus = scalar( @{$gene->get_all_Exons() } );
......@@ -557,7 +555,6 @@ $ga->remove( $gene );
ok( count_rows( $db, "gene" ) == ( $gene_count - 1 ));
ok( count_rows( $db, "transcript" ) == ($trans_count-$tminus));
ok( count_rows( $db, "exon" ) == ( $exon_count - $eminus ));
ok( count_rows( $db, "gene_stable_id" ) == ($gstable_count -1));
ok(!defined($gene->dbID()));
ok(!defined($gene->adaptor()));
......@@ -688,6 +685,10 @@ $gene = $ga->fetch_by_translation_stable_id('ENSP00000355555');
debug("fetch_by_translation_stable_id");
ok( $gene->dbID == 18275 );
$gene = $ga->fetch_by_exon_stable_id('ENSE00001109603');
debug("fetch_by_exon_stable_id");
ok( $gene->dbID == 18275 );
@genes = @{ $ga->fetch_all_by_external_name('PAL2_HUMAN') };
debug( "fetch_all_by_external_name" );
ok( scalar(@genes) == 1 && $genes[0]->dbID == 18264 );
......@@ -712,7 +713,7 @@ foreach my $t (@{ $gene->get_all_Transcripts }) {
}
$multi->hide( "core", "gene", "transcript", "exon", 'xref', 'object_xref',
"exon_transcript", "translation", "gene_stable_id" );
"exon_transcript", "translation" );
$gene->version(3);
$gene->dbID(undef);
......@@ -786,3 +787,8 @@ ok(@{$utaa->fetch_all_by_gene($new_gene)} == 0);
$new_gene = $ga->fetch_by_dbID(18256);
ok($new_gene->canonical_transcript->dbID == 21716); #test 85
ok($new_gene->canonical_annotation eq 'longest transcript in gene'); #test 86
#test the get_species_and_object_type method from the Registry
my $registry = 'Bio::EnsEMBL::Registry';
my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('ENSG00000355555');
ok( $species eq 'homo_sapiens' && $object_type eq 'Gene');
modules/t/info_testdb.pl
+ 6
− 7
View file @ 6c8aeef4
......@@ -93,7 +93,7 @@ if( $print_contig ) {
if( $print_gene ) {
print "Gene ids and names\n";
$sth = $db->prepare( "select gene_id, stable_id from gene_stable_id" );
$sth = $db->prepare( "select gene_id, stable_id from gene" );
$sth->execute();
$sth->bind_columns( \$id, \$name );
while( $sth->fetch() ) {
......@@ -104,7 +104,7 @@ if( $print_gene ) {
if( $print_transcript ) {
print "Transcript ids and names.\n";
$sth = $db->prepare( "select transcript_id, stable_id from transcript_stable_id" );
$sth = $db->prepare( "select transcript_id, stable_id from transcript" );
$sth->execute();
$sth->bind_columns( \$id, \$name );
while( $sth->fetch() ) {
......@@ -114,7 +114,7 @@ if( $print_transcript ) {
if( $print_translation ) {
print "Translations ids and names\n";
$sth = $db->prepare( "select translation_id, stable_id from translation_stable_id" );
$sth = $db->prepare( "select translation_id, stable_id from translation" );
$sth->execute();
$sth->bind_columns( \$id, \$name );
while( $sth->fetch() ) {
......@@ -125,11 +125,10 @@ if( $print_translation ) {
if( $print_exon ) {
print "Exon information\n";
$sth = $db->prepare( "
select et.transcript_id, e.exon_id, esi.stable_id,
select et.transcript_id, e.exon_id,
e.contig_id, e.contig_start, e.contig_end, e.contig_strand
from exon e, exon_stable_id esi, exon_transcript et
where e.exon_id = esi.exon_id
and e.exon_id = et.exon_id
from exon e, exon_transcript et
where e.exon_id = et.exon_id
order by et.transcript_id, et.rank, e.sticky_rank
" );
$sth->execute();
......
modules/t/operon.t
+ 58
− 1
View file @ 6c8aeef4
......@@ -4,7 +4,7 @@ use warnings;
BEGIN {
$| = 1;
use Test;
plan tests => 15;
plan tests => 24;
}
use Bio::EnsEMBL::DBEntry;
use Bio::EnsEMBL::Operon;
......@@ -70,3 +70,60 @@ ok( $operon2->analysis(),
$operon->analysis(),
"Analysis" );
#test the get_species_and_object_type method from the Registry
my $registry = 'Bio::EnsEMBL::Registry';
my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('16152-16153-4840');
ok( $species eq 'homo_sapiens' && $object_type eq 'Operon');
debug ("Operon->list_stable_ids");
my $stable_ids = $operon_adaptor->list_stable_ids();
ok (@{$stable_ids});
$operon = $operon_adaptor->fetch_by_stable_id('16152-16153-4840');
debug( "Operon->fetch_by_stable_id()" );
ok( $operon );
#19
my @operons = @{ $operon_adaptor->fetch_all_versions_by_stable_id('16152-16153-4840') };
debug("fetch_all_versions_by_stable_id");
ok( scalar(@operons) == 1 );
#20
$operon = $operon_adaptor->fetch_by_operon_transcript_stable_id('T16152-16153-4840');
debug( "Operon->fetch_by_operon_transcript_stable_id()" );
ok( $operon );
#21-24
#
# Operon remove test
#
$multi->save( "core", "operon", "operon_transcript",
"object_xref", "ontology_xref", "identity_xref");
$operon = $operon_adaptor->fetch_by_stable_id( "16152-16153-4840" );
my $operon_count = count_rows( $dba, "operon" );
my $operon_trans_count = count_rows( $dba, "operon_transcript" );
my $ots = scalar( @{$operon->get_all_OperonTranscripts() } );
debug( "Operons before ".$operon_count );
debug( "OperonTranscripts before ".$operon_trans_count );
debug( "Operon has ".$ots." transcripts" );
$operon_adaptor->remove( $operon );
ok( count_rows( $dba, "operon" ) == ( $operon_count - 1 ));
ok( count_rows( $dba, "operon_transcript" ) == ($operon_trans_count-$ots));
ok(!defined($operon->dbID()));
ok(!defined($operon->adaptor()));
$multi->restore('core');
modules/t/operon_transcript.t
+ 22
− 2
View file @ 6c8aeef4
......@@ -4,7 +4,7 @@ use warnings;
BEGIN {
$| = 1;
use Test;
plan tests => 46;
plan tests => 50;
}
use Bio::EnsEMBL::Test::MultiTestDB;
use Bio::EnsEMBL::Test::TestUtils;
......@@ -175,7 +175,7 @@ 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" );
$gene_r = $ogenes[1];
ok( $gene_r->dbID(),$gene2->dbID(), "Gene ID" );
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" );
......@@ -208,3 +208,23 @@ $dba->get_OperonAdaptor()->remove($operon);
$dba->get_GeneAdaptor()->remove($gene);
$dba->get_GeneAdaptor()->remove($gene2);
#test the get_species_and_object_type method from the Registry
my $registry = 'Bio::EnsEMBL::Registry';
my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('T16152-16153-4840');
ok( $species eq 'homo_sapiens' && $object_type eq 'OperonTranscript');
#48
my $ota = $dba->get_OperonTranscriptAdaptor();
$operon_transcript = $ota->fetch_by_stable_id('T16152-16153-4840');
debug( "OperonTranscript->fetch_by_stable_id()" );
ok( $operon_transcript );
#49
@operon_transcripts = @{ $ota->fetch_all_versions_by_stable_id('T16152-16153-4840') };
debug("fetch_all_versions_by_stable_id");
ok( scalar(@operon_transcripts) == 1 );
#50
debug ("OperonTranscript->list_stable_ids");
my $stable_ids = $ota->list_stable_ids();
ok (@{$stable_ids});
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+ 1
− 0
View file @ 6c8aeef4
......@@ -22,3 +22,4 @@
64 1 assembly.mapping chromosome:NCBI33#chunk
65 1 assembly.mapping alt_chrom#chromosome:NCBI33
66 1 assembly.mapping alt_chrom|chromosome:NCBI33|contig
67 1 species.production_name homo_sapiens
modules/t/transcript.t
+ 9
− 8
View file @ 6c8aeef4
......@@ -315,15 +315,14 @@ ok(!defined($five_prime));
my $tl_count = count_rows($db, "translation");
my $ex_tr_count = count_rows($db, "exon_transcript");
my $tr_count = count_rows($db, "transcript");
my $trstable_count = count_rows($db, "transcript_stable_id");
my $ex_tr_minus = @{$tr->get_all_Exons()};
$multi->save("core", "transcript", "transcript_stable_id", "translation",
"translation_stable_id", "protein_feature", "exon",
"exon_stable_id", "exon_transcript", "object_xref",
$multi->save("core", "transcript", "translation",
"protein_feature", "exon",
"exon_transcript", "object_xref",
"supporting_feature", "dna_align_feature","protein_align_feature",
"ontology_xref", "identity_xref");
......@@ -335,7 +334,6 @@ ok(!defined($tr->adaptor()));
ok( count_rows( $db, "transcript") == ($tr_count - 1));
ok( count_rows( $db, "translation") == ($tl_count - 1));
ok( count_rows( $db, "exon_transcript") == ($ex_tr_count - $ex_tr_minus));
ok( count_rows( $db, "transcript_stable_id") == ($trstable_count - 1));
#
# test _rna_edit for transcripts
......@@ -477,8 +475,7 @@ $tr->adaptor(undef);
}
$multi->hide('core', 'transcript', 'transcript_attrib', 'translation',
'exon_transcript', 'exon', 'exon_stable_id',
'transcript_stable_id', 'translation_stable_id');
'exon_transcript', 'exon');
my $attrib1 = Bio::EnsEMBL::Attribute->new
......@@ -545,7 +542,7 @@ $g = $db->get_GeneAdaptor->fetch_by_transcript_id($tr->dbID);
$tr->get_all_Exons;
$multi->hide( "core", "gene", "transcript", "exon", 'xref', 'object_xref',
"exon_transcript", "translation", "transcript_stable_id" );
"exon_transcript", "translation" );
$tr->version(3);
$tr->dbID(undef);
......@@ -716,3 +713,7 @@ sub print_coords {
}
}
#test the get_species_and_object_type method from the Registry
my $registry = 'Bio::EnsEMBL::Registry';
my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('ENST00000355555');
ok( $species eq 'homo_sapiens' && $object_type eq 'Transcript');
modules/t/translation.t
+ 18
− 6
View file @ 6c8aeef4
......@@ -8,7 +8,7 @@ use Bio::EnsEMBL::Exon;
BEGIN {
$| = 1;
use Test;
plan tests => 40;
plan tests => 41;
}
my $loaded = 0;
......@@ -154,12 +154,11 @@ ok(length($seq) == $translation->length());
# test remove method
#
$multi->save('core', 'translation', 'translation_stable_id',
$multi->save('core', 'translation',
'protein_feature', 'object_xref', 'identity_xref',
'ontology_xref');
my $tl_count = count_rows($db, 'translation');
my $tlstable_count = count_rows($db, 'translation_stable_id');
my $pfeat_count = count_rows($db, 'protein_feature');
......@@ -171,7 +170,6 @@ ok(!defined($translation->dbID));
ok(!defined($translation->adaptor()));
ok(count_rows($db, 'translation') == $tl_count - 1);
ok(count_rows($db, 'translation_stable_id') == $tlstable_count - 1);
ok(count_rows($db, 'protein_feature') == $pfeat_count - $pfeat_minus);
#
......@@ -259,8 +257,7 @@ $tl->adaptor(undef);
$tl->dbID(undef);
$multi->hide('core', 'transcript', 'translation_attrib', 'translation',
'translation_stable_id');
$multi->hide('core', 'transcript', 'translation_attrib', 'translation');
# add a couple of attributes to the translation
......@@ -295,3 +292,18 @@ ok( $tl->cdna_end() == 1690 );
ok( $tl->genomic_start() == 30572315 );
ok( $tl->genomic_end() == 30578038 );
#test the get_species_and_object_type method from the Registry
my $registry = 'Bio::EnsEMBL::Registry';
my ( $species, $object_type, $db_type ) = $registry->get_species_and_object_type('ENSP00000201961');
ok( $species eq 'homo_sapiens' && $object_type eq 'Translation');
#41
my @alt_tls = @{
$ta->fetch_all_alternative_by_Transcript(
$tr)
};
ok(!scalar(@alt_tls))
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