diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t index 9b1fc58ab002eb7693647e36df90238af9fafc0b..bae422d0c4e01148b7ba076e5505d5ad7f4f22da 100644 --- a/modules/t/dbEntries.t +++ b/modules/t/dbEntries.t @@ -338,24 +338,25 @@ ok($id_total - $id_count == count_rows($db, 'identity_xref')); $multi->restore('core', 'object_xref', 'identity_xref', 'go_xref'); -# new info type checks +# new type checks # fetch_all_by Gene Transcript Translation # transclation info type $translation = $ta->fetch_by_dbID(21737)->translation; -$dbes = $translation->get_all_DBEntries(undef,"DEPENDENT"); +$dbes = $translation->get_all_DBEntries(undef,"MISC"); -ok(@$dbes == 2); # test 44 +ok(@$dbes == 19); # test 44 -$dbes = $translation->get_all_DBLinks(undef,"DEPENDENT"); -ok(@$dbes == 2); -$dbes = $translation->get_all_DBLinks(undef,"SEQUENCE_MATCH"); -ok(@$dbes == 1); +$dbes = $translation->get_all_DBLinks(undef,"MISC"); +ok(@$dbes == 19); + +$dbes = $translation->get_all_DBLinks(undef,"ALT_TRANS"); +ok(@$dbes == 9); -$dbes = $translation->get_all_DBLinks(undef,"INFERRED_PAIR"); +$dbes = $translation->get_all_DBLinks(undef,"ARRAY"); ok(@$dbes == 1); $dbes = $translation->get_all_DBLinks(undef,"RUBBISH"); @@ -363,20 +364,20 @@ ok(@$dbes == 0); -# transcript info type +# transcript external type my $transcript = $ta->fetch_by_dbID(21737); -$dbes = $transcript->get_all_DBEntries(undef,"DEPENDENT"); +$dbes = $transcript->get_all_DBEntries(undef,"MISC"); ok(@$dbes == 0); # test 49 -$dbes = $transcript->get_all_DBLinks(undef,"DEPENDENT"); -ok(@$dbes == 2); +$dbes = $transcript->get_all_DBLinks(undef,"MISC"); +ok(@$dbes == 19); -$dbes = $transcript->get_all_DBLinks(undef,"SEQUENCE_MATCH"); -ok(@$dbes == 1); +$dbes = $transcript->get_all_DBLinks(undef,"ALT_TRANS"); +ok(@$dbes == 9); -$dbes = $transcript->get_all_DBLinks(undef,"INFERRED_PAIR"); +$dbes = $transcript->get_all_DBLinks(undef,"ARRAY"); ok(@$dbes == 1); $dbes = $transcript->get_all_DBLinks(undef,"RUBBISH"); @@ -384,20 +385,20 @@ ok(@$dbes == 0); -# gene info type +# gene external type $gene = $ga->fetch_by_dbID(18272); -$dbes = $gene->get_all_DBEntries(undef,"DEPENDENT"); +$dbes = $gene->get_all_DBEntries(undef,"MISC"); ok(@$dbes == 0); # test 54 -$dbes = $gene->get_all_DBLinks(undef,"DEPENDENT"); -ok(@$dbes == 2); +$dbes = $gene->get_all_DBLinks(undef,"MISC"); +ok(@$dbes == 19); -$dbes = $gene->get_all_DBLinks(undef,"SEQUENCE_MATCH"); -ok(@$dbes == 1); +$dbes = $gene->get_all_DBLinks(undef,"ALT_TRANS"); +ok(@$dbes == 9); -$dbes = $gene->get_all_DBLinks(undef,"INFERRED_PAIR"); +$dbes = $gene->get_all_DBLinks(undef,"ARRAY"); ok(@$dbes == 1); $dbes = $gene->get_all_DBLinks(undef,"RUBBISH"); diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt b/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt index 402e4a811126cefa5f850eef5cabad6de5a5d139..d07f51f513a24c28ffa0320c5c732f2ed39911b6 100644 --- a/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt +++ b/modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt @@ -24,11 +24,11 @@ 6 GO 1 KNOWNXREF 1 0 5 GO MISC 5 HUGO 1 KNOWNXREF 0 1 100 HUGO MISC 11 Interpro 1 XREF 1 0 5 Interpro MISC -10 EntrezGene 1 KNOWNXREF 1 0 10 EntrezGene MISC +10 EntrezGene 1 KNOWNXREF 1 0 10 EntrezGene ARRAY 1400 MarkerSymbol 1 KNOWNXREF 1 0 50 MarkerSymbol MISC 4 MIM 1 KNOWNXREF 1 0 5 MIM MISC 8 PDB 1 KNOWNXREF 1 0 5 PDB MISC -3 protein_id 1 KNOWNXREF 1 0 5 Protein ID MISC +3 protein_id 1 KNOWNXREF 1 0 5 Protein ID ALT_TRANS 9 RefSeq_dna 1 KNOWN 1 0 25 RefSeq DNA MISC 1805 RefSeq_dna_predicted 1 PRED 1 0 15 RefSeq DNA predicted MISC 1810 RefSeq_peptide 1 KNOWN 1 0 26 RefSeq peptide MISC