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Graham McVicker authored32c5c651
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dbEntries.t 8.03 KiB
use lib 't';
use strict;
use warnings;
BEGIN { $| = 1;
use Test;
plan tests => 42;
}
use MultiTestDB;
use TestUtils qw ( debug test_getter_setter count_rows );
use Bio::EnsEMBL::DBEntry;
# switch on the debug prints
our $verbose = 0;
debug( "Startup test" );
#
# 1 Test started
#
ok(1);
my $multi = MultiTestDB->new();
my $db = $multi->get_DBAdaptor( "core" );
debug( "Test database instatiated" );
#
# 2 Database instatiated
#
ok( $db );
# some retrievals
my $dbEntryAdaptor = $db->get_DBEntryAdaptor();
my $sth = $db->prepare( 'select count(*) from object_xref where ensembl_object_type = "Translation"' );
$sth->execute();
my ( $xref_count ) = $sth->fetchrow_array();
my $db_entry_count = 0;
my $goxref_count = 0;
my $ident_count = 0;
$sth->finish();
my $ga = $db->get_GeneAdaptor();
my $all_gene_ids = $ga->list_dbIDs();
for my $gene_id ( @$all_gene_ids ) {
my $gene = $ga->fetch_by_dbID( $gene_id );
for my $tr ( @{$gene->get_all_Transcripts()} ) {
my $tl = $tr->translation();
my $dbentries = $dbEntryAdaptor->fetch_all_by_Translation( $tl );
$db_entry_count += scalar( @{$dbentries});
$goxref_count += grep { $_->isa( "Bio::EnsEMBL::GoXref" )} @$dbentries;
$ident_count += grep {$_->isa( "Bio::EnsEMBL::IdentityXref" )} @$dbentries;
}
}
debug( "Found $xref_count xrefs and $db_entry_count dblinks." );
debug( " $goxref_count GoXrefs, $ident_count identityXrefs." );
#
# 3 as many dblinks as entries in object_xref#
ok( $db_entry_count == $xref_count );
#
# 4,5 correct number of GoXrefs and IdentityXrefs
#
ok( $goxref_count == 48 );
ok( $ident_count == 32 );
# try storing and retrieval
my $xref = Bio::EnsEMBL::DBEntry->new
(
-primary_id => "1",
-dbname => "SWISSPROT",
-release => "1",
-display_id => "Ens related thing"
);
my %goxref = %$xref;
my %identxref = %$xref;
my $goref = Bio::EnsEMBL::GoXref->new
(
-primary_id => "1",
-dbname => "GO",
-release => "1",
-display_id => "Ens related GO"
);
$goref->add_linkage_type( "IC" );
my $ident_xref = Bio::EnsEMBL::IdentityXref->new
(
-primary_id => "1",
-dbname => "SPTREMBL",
-release => "1",
-display_id => "Ens related Ident"
);
$ident_xref->query_identity( 100 );
$ident_xref->target_identity( 95 );
$multi->hide( "core", "object_xref", "xref", "identity_xref", "go_xref" );
my $gene = $ga->fetch_by_dbID( $all_gene_ids->[0] );
my $tr = $gene->get_all_Transcripts()->[0];
my $tl = $tr->translation();
$dbEntryAdaptor->store( $xref, $gene, "Gene" );
$dbEntryAdaptor->store( $xref, $tr, "Transcript" );
$dbEntryAdaptor->store( $goref, $tl, "Translation" );
$dbEntryAdaptor->store( $ident_xref, $tl, "Translation" );
$dbEntryAdaptor->store( $ident_xref, $tr, "Transcript" );
my ( $oxr_count, $go_count );
$oxr_count = count_rows($db, 'object_xref');
#
# 6 right number of object xrefs in db
#
debug( "object_xref_count = $oxr_count" );
ok( $oxr_count == 5 );
$xref_count = count_rows($db, 'xref');
$sth->finish();
#
# 7 number of xrefs right
#
debug( "Number of xrefs = $xref_count" );
ok( $xref_count == 3 );
#
# 8 number of go entries right
#
$go_count = count_rows($db, 'go_xref');
debug( "Number of go_xrefs = $go_count" );
ok( $go_count == 1 );
#
# 9 identity xrefs right
#
$ident_count = count_rows($db, 'identity_xref');
# the identity (query/target)values are not normalized ...
debug( "Number of identity_xrefs = $ident_count" );
ok( $ident_count == 2 );
$multi->restore();
#
# 10-12 Test that external synonyms and go evidence tags are retrieved
#
my $ta = $db->get_TranscriptAdaptor();
my $translation = $ta->fetch_by_dbID(21737)->translation;
#pull out an xref that should 2 external synonyms
my $xrefs = $dbEntryAdaptor->fetch_all_by_Translation($translation);
($xref) = grep {$_->dbID == 315} @$xrefs;
my @syns = grep {$_ eq 'syn1' || $_ eq 'syn2'} @{$xref->get_all_synonyms};
ok(@syns == 2);
#and also 2 evidence tags
if($xref && $xref->isa('Bio::EnsEMBL::GoXref')) {
my @evtags =
grep {$_ eq 'IEA' || $_ eq 'IC'} @{$xref->get_all_linkage_types()};
ok(@evtags == 2);
} else {
ok(0);
}
$translation = $ta->fetch_by_dbID(21723)->translation;
$xrefs = $dbEntryAdaptor->fetch_all_by_Translation($translation);
($xref) = grep {$_->dbID == 257} @$xrefs;
if($xref && $xref->isa('Bio::EnsEMBL::GoXref')) {
my ($evtag) = @{$xref->get_all_linkage_types()};
ok($evtag eq 'IC');
} else {
ok(0);
}
#test the idxref mapping code a bit
my $id_xref = Bio::EnsEMBL::IdentityXref->new
(-QUERY_IDENTITY => 80.4,
-TARGET_IDENTITY => 90.1, -SCORE => 100,
-EVALUE => 1,
-CIGAR_LINE => '10M5D10M5I10M',
-QUERY_START => 1,
-QUERY_END => 35,
-TRANSLATION_START => 10,
-TRANSLATION_END => 45,
-ADAPTOR => $dbEntryAdaptor);
my $mapper = $id_xref->get_mapper();
ok($mapper && ref($mapper) && $mapper->isa('Bio::EnsEMBL::Mapper'));
my @coords = $mapper->map_coordinates('external_id', 10, 100, 1, 'external');
ok(@coords == 5);
ok($coords[0]->isa('Bio::EnsEMBL::Mapper::Coordinate'));
ok($coords[0]->start() == 19);
ok($coords[0]->end() == 19);
ok($coords[1]->isa('Bio::EnsEMBL::Mapper::Coordinate'));
ok($coords[1]->start == 25);
ok($coords[1]->end == 34);
ok($coords[2]->isa('Bio::EnsEMBL::Mapper::Gap'));
ok($coords[2]->length == 5);
ok($coords[3]->isa('Bio::EnsEMBL::Mapper::Coordinate'));
ok($coords[3]->start == 35);
ok($coords[3]->end == 44);
ok($coords[4]->isa('Bio::EnsEMBL::Mapper::Gap'));
ok($coords[4]->length == 65);
my $feature = Bio::EnsEMBL::Feature->new
(-START => 10,
-END => 100,
-STRAND => 1,
-SEQNAME => 'SwisProtSeq');
@coords = $id_xref->map_feature($feature);
ok(@coords == 5);
ok($coords[0]->isa('Bio::EnsEMBL::Mapper::Coordinate') &&
$coords[0]->start() == 19 &&
$coords[0]->end() == 19);
my $features = $id_xref->transform_feature($feature);
ok(@$features == 3);
ok($features->[0]->start == 19 &&
$features->[0]->end == 19 &&
$features->[1]->start == 25 &&
$features->[1]->end == 34 &&
$features->[2]->start == 35 &&
$features->[2]->end == 44);
#
# test DBEntryAdaptor::fetch_by_db_accession and
# DBEntryAdaptor::fetch_by_dbID
#
$xref = $dbEntryAdaptor->fetch_by_dbID(152202);
ok($xref->dbID == 152202);
ok($xref->display_id() eq 'C20orf125');
ok($xref->dbname() eq 'HUGO');
ok($xref->primary_id() eq '16118');
$xref = $dbEntryAdaptor->fetch_by_db_accession('Interpro', 'IPR000010');
ok($xref->dbID == 999999);
ok($xref->description eq 'Test interpro desc2');
$multi->hide('core', 'xref');
#make sure this still works when interpro entries missing in xref table
$xref = $dbEntryAdaptor->fetch_by_db_accession('Interpro', 'IPR000010');
ok($xref);
ok($xref->primary_id() eq 'IPR000010');
$multi->restore('core', 'xref');
$multi->save('core', 'object_xref', 'identity_xref', 'go_xref');
#
# test the removal of dbentry associations
#
$translation = $ta->fetch_by_dbID(21723)->translation;
my $dbes = $translation->get_all_DBEntries();
my $all_count = @$dbes;
$go_count = grep {$_->isa('Bio::EnsEMBL::GoXref')} @$dbes;
my $id_count = grep {$_->isa('Bio::EnsEMBL::IdentityXref')} @$dbes;
my $all_total = count_rows($db, 'object_xref');
my $go_total = count_rows($db, 'go_xref');
my $id_total = count_rows($db, 'identity_xref');
print_dbEntries($dbes);
foreach my $dbe (@$dbes) {
$dbEntryAdaptor->remove_from_object($dbe, $translation, 'Translation');
}
# make sure the appropriate rows were deleted
ok($all_total - $all_count == count_rows($db, 'object_xref'));
ok($go_total - $go_count == count_rows($db, 'go_xref'));
ok($id_total - $id_count == count_rows($db, 'identity_xref'));
$multi->restore('core', 'object_xref', 'identity_xref', 'go_xref');
sub print_dbEntries {
my $dbes = shift;
foreach my $dbe (@$dbes) {
if($dbe->isa('Bio::EnsEMBL::IdentityXref')) {
debug("IDXref");
} elsif($dbe->isa('Bio::EnsEMBL::GoXref')) {
debug("GOXref");
} elsif($dbe->isa('Bio::EnsEMBL::DBEntry')) {
debug("DBEntry");
} else {
debug("UNKNOWN dbentry type");
}
debug(" ".$dbe->dbname()."-".$dbe->display_id()."\n");
}
debug(scalar(@$dbes). " total");
}