class TestEnsemblREST

Public Instance Methods

test_archive() click to toggle source
# File lib/test.rb, line 32
def test_archive
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Archive::id_get('ENSG00000157764')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Archive::id_post(["ENSG00000157764", "ENSG00000248378"])}
end
test_genetree() click to toggle source
# File lib/test.rb, line 44
def test_genetree
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree('ENSGT00390000003602')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree_member_id('ENSG00000157764')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genetree_member_symbol('BRCA2')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::genomic_alignment_region('X:1000000..1000100:1')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::homology_ensemblgene('ENSG00000157764')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Comparative::homology_symbol('BRCA2')}
end
test_info() click to toggle source
# File lib/test.rb, line 53
def test_info
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::analysis}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::assembly_info}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::assembly_stats('X')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::biotypes}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::compara_methods}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::compara_species_sets('EPO')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::comparas}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::data}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::external_dbs}
        assert(EnsemblREST::Info::ping)
        assert_instance_of(String, EnsemblREST::Info::rest)
        assert_instance_of(Fixnum, EnsemblREST::Info::software)
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Info::species}
end
test_lookup() click to toggle source
# File lib/test.rb, line 69
def test_lookup
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::id('ENSG00000157764')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::symbol('BRCA2')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::id_post(["ENSG00000157764", "ENSG00000248378"])}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Lookup::symbol_post(["BRCA2", "BRAF"])}
end
test_map() click to toggle source
# File lib/test.rb, line 37
def test_map
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::cdna("ENST00000288602", "100..300")}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::cds('ENST00000288602', '1..1000')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::map('X:1000000..1000100:1', 'GRCh37', 'GRCh38')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Map::translation('ENSP00000288602', '100..300')}
end
test_onto() click to toggle source
# File lib/test.rb, line 76
def test_onto
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::ancestors('GO:0005667')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::ancestors_chart('GO:0005667')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::descendants('GO:0005667')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::id('GO:0005667')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Ontology::name("transcription factor complex")}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::classification('9606')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::id('9606')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Taxonomy::name('Homo%25')}
end
test_overlap() click to toggle source
# File lib/test.rb, line 87
def test_overlap
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::id('ENSG00000157764', 'gene')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::region('7:140424943-140624564', ['gene', 'transcript', 'cds', 'exon'])}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Overlap::translation('ENSP00000288602')}
end
test_regulation() click to toggle source
# File lib/test.rb, line 93
def test_regulation
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Regulation::id('ENSR00001348195')}
end
test_sequence() click to toggle source
# File lib/test.rb, line 97
def test_sequence
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::id("ENSP00000288602")}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::region("X:1000000..1000100:1", 'human')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::id_post(["ENSG00000157764", "ENSG00000248378"])}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Sequence::region_post(["X:1000000..1000100:1", "ABBA01004489.1:1..100"])}
end
test_variation() click to toggle source
# File lib/test.rb, line 104
def test_variation
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Variation::id("rs116035550")}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Variation::post(["rs116035550", "COSM476"])}
end
test_variationga4gh() click to toggle source
# File lib/test.rb, line 109
def test_variationga4gh
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gacallSet}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gavariants(17191024, 17671934, '22', [70])}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::GA4GH::gavariantset}
end
test_vep() click to toggle source
# File lib/test.rb, line 115
def test_vep
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::hgvs_get('AGT:c.803T>C')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::id_get('COSM476')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::region_get('C', '9:22125503-22125502:1')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::id_post(["rs116035550", "COSM476" ])}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::VEP::region_post(["21  26960070  rs116645811 G A . . .", "21  26965148  rs1135638 G A . . ." ])}
end
test_xref() click to toggle source
# File lib/test.rb, line 123
def test_xref
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::external('BRCA2')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::id('ENSG00000157764')}
        assert_nothing_raised(EnsemblREST::InvalidResponse, NoMethodError) {EnsemblREST::Xref::name('BRCA2')}
end