bio-ensembl-rest 0.1.0

data/test/test-lookup.rb

@@ -0,0 +1,45 @@
+require_relative 'helper'
+
+class TestLookup < Test::Unit::TestCase
+
+  context 'lookup_id' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      look = Lookup.lookup_id 'ENSG00000157764'
+      assert look.index 'Gene'                # we asked for a gene
+      assert look.index 'core'                # db_type should be this
+      assert look.index 'homo_sapiens'        # we used a human stable ID  
+      assert look.index 'ENSG00000157764'     # exactly this one
+    end
+
+    should 'support the full parameter' do 
+      look_plain = Lookup.lookup_id 'ENSG00000157764'
+      look_full = Lookup.lookup_id 'ENSG00000157764', format: 'full'
+      assert look_full.size > look_plain.size
+    end
+
+    sleep(1)
+
+    should 'return the right object' do 
+      look = JSON.parse Lookup.lookup_id 'ENSG00000157764', format: 'full'
+      assert look['object_type'].casecmp 'gene'
+      assert look['species'].casecmp 'homo_sapiens'
+      assert look['start'] = 140424943
+      assert look['end'] = 140624564
+    end
+
+    should 'support db_type parameter' do 
+      look = JSON.parse Lookup.lookup_id 'ENSG00000157764', db_type: 'core'
+      assert look['db_type'] = 'core'
+    end
+
+    sleep(1)
+
+  end
+
+
+end

data/test/test-mapping.rb

@@ -0,0 +1,105 @@
+require_relative 'helper'
+
+class TestMapping < Test::Unit::TestCase
+
+  context 'test map' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      map = Mapping.map 'NCBI36', 'GRCh37', 'human', 'X:1000000..1000100:1'
+      assert map.index 'NCBI36'            # we asked a map from this
+      assert map.index 'GRCh37'            # to this
+      assert map.index 'X'                 # of a sequence on the X chromosome
+    end
+
+    should 'return work with response: ruby' do 
+      map = Mapping.map 'NCBI36', 'GRCh37', 'human', 'X:1000000..1000100:1', 
+              response: 'ruby'
+      from = map['mappings'][0]['original']         # from here
+      to = map['mappings'][0]['mapped']             # to here
+
+      assert from['assembly'] = 'NCBI36'            # from has to be NCBI36
+      assert from['start'] = 1000000                # its region start here
+      assert from['end'] = 1000100                  # and ends here
+      assert to['assembly'] = 'GRCh37'              # to has to be GRCh37
+      assert to['start'] = 1080000                  # its region starts here
+      assert to['end'] = 1080100                    # and ends here
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test map_from_cdna' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do 
+      map = Mapping.map_from_cdna 'ENST00000288602', '100..300'
+      assert map.index 'chromosome'        # we asked a map on chromosome
+      assert map.index '7'                 # chromosome 7, in fact
+      assert map.index '-1'                # strand -1
+    end
+
+    should 'return the right mapping' do 
+      map = Mapping.map_from_cdna 'ENST00000288602', '100..300',
+              response: 'ruby'
+      from = map['mappings'][0]
+      to = map['mappings'][1]
+      from['seq_region_name'] = '7'
+      from['start'] = 140624366
+      to['end'] = 140624465
+      from['seq_region_name'] = '7'
+      from['start'] = 140549912
+      to['end'] = 140550012 
+    end
+
+    sleep(1)
+
+  end
+
+  context 'test map_from_cds' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end  
+
+    should 'support a basic call and return the correct data' do 
+      map = Mapping.map_from_cds 'ENST00000288602', '1..1000'
+      assert map.index '7'                 # we asked for stuff on chromosome 7
+      assert map.index '-1'                # strand -1
+      assert map.index '140624366'         # one of the mapping starts here
+      assert map.index '140624503'         # and ends here
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test map_from_translation' do
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do 
+      map = Mapping.map_from_translation 'ENSP00000288602', '100..300'
+      assert map.index '7'                 # we asked for stuff on chromosome 7
+      assert map.index '-1'                # strand -1
+      assert map.index '140534409'         # one of the mapping starts here
+      assert map.index '140534615'         # and ends here
+    end
+
+    sleep(1)
+
+  end
+
+
+end

data/test/test-ontologies.rb

@@ -0,0 +1,116 @@
+require_relative 'helper'
+
+class TestOntologies < Test::Unit::TestCase
+
+  context 'test ontology_ancestor' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      ont = Ontologies.ontology_ancestor 'GO:0005667'
+      assert ont.index 'GO:0000120'       # GO:000566 should have this ancestor
+      assert ont.index 'GO:0000126'       # and this 
+      assert ont.index 'GO:0000127'       # and this
+      assert ont.index 'GO:0097221'       # and this one, too
+    end
+
+    should 'work both with GO and EFO IDs' do
+      assert_nothing_raised do
+        Ontologies.ontology_ancestor 'GO:0005667' 
+        Ontologies.ontology_ancestor 'EFO:0000493'
+      end
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test ontology_ancestor_chart' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      ont = Ontologies.ontology_ancestor_chart 'GO:0005667'
+      assert ont.index 'GO:0005575'       # GO:0005667 should have this ancestor
+      assert ont.index 'GO:0005622'       # and this 
+      assert ont.index 'GO:0005623'       # and this
+      assert ont.index 'GO:0005654'       # and this one, too
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test ontology_descendants' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      ont = Ontologies.ontology_descendents 'GO:0005667'
+      assert ont.index 'GO:0043234'       # GO:0005667 should have this descendent
+      assert ont.index 'GO:0044451'       # and this 
+      assert ont.index 'GO:0005654'       # and this
+      assert ont.index 'GO:0043231'       # and this one, too
+    end
+
+    should 'support the subset parameter' do 
+      ont1 = Ontologies.ontology_descendents 'GO:0005667', subset: 'goslim_generic'
+      ont2 = Ontologies.ontology_descendents 'GO:0005667'
+      assert ont1.size < ont2.size
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test ontology_id' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      ont = Ontologies.ontology_id 'GO:0005667'
+      assert ont.index 'transcription factor complex'    # what GO:0005667 is
+      assert ont.index 'GO:0000120'                      # a son of him
+      assert ont.index 'GO:0044451'                      # his parent
+    end
+
+    should 'return a ruby object' do 
+      ont = Ontologies.ontology_id 'GO:0005667', response: 'ruby'
+      assert_instance_of Hash, ont
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test ontology_name' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      ont = Ontologies.ontology_name 'transcription factor complex'
+      assert ont.index 'GO:0005667'       # ID of transcription factor complex
+      assert ont.index 'GO:0000120'       # a son of him
+      assert ont.index 'GO:0044451'       # his parent
+    end
+
+    sleep(1)
+
+  end
+
+
+end

data/test/test-sequence.rb

@@ -0,0 +1,110 @@
+require_relative 'helper'
+
+class TestSequence < Test::Unit::TestCase
+
+  context 'sequence_id' do
+    
+    setup do
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      seq = Sequence.sequence_id 'ENSG00000236597'
+      seq2 = Sequence.sequence_id 'ENSG00000228131'
+      assert_equal seq, 'CTAACTGGGGA'
+      assert_equal seq2.size, 18
+    end
+
+    should 'expand the sequence 10 pairs upstream' do
+      seq1 = Sequence.sequence_id 'ENSE00001154485',
+              response: 'text',
+              type: 'genomic'
+      seq2 = Sequence.sequence_id 'ENSE00001154485',
+              response: 'text',
+              type: 'genomic',
+              expand_5prime: 10
+      assert_equal 10 + seq1.size, seq2.size
+      assert_equal seq1, seq2[10..-1]
+    end
+
+    sleep(1)
+
+    should 'return a Bio::Sequence object' do
+      seq = Sequence.sequence_id 'ENSVPAG00000001567',
+              response: 'ruby'
+      assert_instance_of Bio::Sequence, seq
+    end
+
+    should 'raise an error: ID not found' do
+      assert_raises RuntimeError do
+        Sequence.sequence_id 'CCDS5863.1',
+          response: 'fasta',
+          object_type: 'transcript',
+          db_type: 'otherfeatures',
+          type: 'cds',
+          species: 'human'
+        end
+    end
+
+    should 'return multiple sequences' do
+      response = Sequence.sequence_id 'ENSG00000157764',
+                  response: 'fasta', 
+                  multiple_sequences: true,
+                  type: 'protein'
+      assert response.scan(/>\w{15,18}\n/).size > 1
+    end
+
+    sleep(1)
+
+    should 'return masked sequences' do
+      seq1 = Sequence.sequence_id 'ENST00000288602', 
+              mask: 'hard'
+      seq2 = Sequence.sequence_id 'ENST00000288602', 
+              mask: 'soft'
+      assert_equal 'N'*10, seq1[0..9]
+      assert_equal seq2[0..9].downcase, seq2[0..9]
+    end
+
+  end
+
+
+  context 'sequence_region' do
+
+    setup do
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      seq = Sequence.sequence_region 'human', 'X:1000000..1000100:1'
+      assert_equal 'GAAACAGCTACTTGG', seq[0..14]
+      assert_equal seq.size, 101
+    end
+
+    should 'expand the sequence upstream and downstream' do
+      seq = Sequence.sequence_region 'human',
+              'X:1000000..1000100:1',
+              expand_3prime: 50,
+              expand_5prime: 50
+      assert_equal 201, seq.size
+    end
+
+    sleep(1)
+
+    should 'support json response' do
+      seq = Sequence.sequence_region 'human',
+              'X:1000000..1000100:1',  
+              response: 'json'
+      assert_nothing_raised { JSON.parse seq }
+    end
+
+    should 'return a Bio::Sequence object' do
+      seq = Sequence.sequence_region 'human',
+              'X:1000000..1000100:1',
+              response: 'ruby'
+      assert_instance_of Bio::Sequence, seq
+      assert_equal 101, seq.to_s.size
+    end
+
+  end
+
+end

data/test/test-taxonomy.rb

@@ -0,0 +1,58 @@
+  require_relative 'helper'
+
+class TestTaxonomy < Test::Unit::TestCase
+
+  context 'test taxonomy_id' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      tax = Taxonomy.taxonomy_id '9606'
+      assert tax.index 'Homo sapiens'           # the species with ID 9606
+      assert tax.index 'Neandertal'             # one if his sons
+      assert tax.index '63221'                  # neandertal has this ID
+    end
+
+    should 'work both with name and NBCI taxon id' do
+      assert_nothing_raised do 
+        Taxonomy.taxonomy_id 'Homo sapiens'
+        Taxonomy.taxonomy_id '9606'
+      end
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test taxonomy_classification' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do
+      tax = Taxonomy.taxonomy_classification 'Homo'
+      assert tax.index '9605'           # the ID of Homo
+      assert tax.index 'Homo sapiens'   # one of his children
+      assert tax.index '9606'           # has this ID
+      assert tax.index 'man'            # and this common name
+    end
+
+    should 'work both with name and NBCI taxon id' do
+      assert_nothing_raised do 
+        Taxonomy.taxonomy_classification 'Homo sapiens'
+        Taxonomy.taxonomy_classification '9606'
+      end
+    end
+
+    sleep(1)
+
+  end
+
+
+
+
+end

data/test/test-variation.rb

@@ -0,0 +1,62 @@
+require_relative 'helper'
+
+class TestVariation < Test::Unit::TestCase
+
+  context 'test vep_id' do 
+
+    setup do 
+      EnsemblRest.connect_db
+    end
+
+    should 'support a basic call and return the correct data' do 
+      var = Variation.vep_id 'COSM476', 'human'
+      assert var.index '7'           # variation we asked for is on chromosome 7
+      assert var.index '140453136'   # and starts here
+    end
+
+    should 'return the correct data' do 
+      data = JSON.parse Variation.vep_id 'COSM476', 'human'
+      var = data['data'].first
+      assert var['name'] == 'COSM476'
+      assert var['is_somatic'] == 1
+      assert var['location']['start'] = 140453136
+      assert var['location']['end'] = 140453136
+    end
+
+    should 'support rs ID' do
+      var = Variation.vep_id 'rs116035550', 'human'
+      assert var.index '11'           # variation we asked for is on chromosome 11
+      assert var.index '212464'       # and starts here
+    end
+
+    sleep(1)
+
+  end
+
+
+  context 'test vep_region' do 
+
+    setup do 
+      EnsemblRest.connect_db
+      require 'rexml/document'
+    end
+
+    should 'support a basic call and return the correct data' do 
+      var = Variation.vep_region 'C', '9:22125503-22125502:1', 'human' 
+      assert var.index '9'           # variation we asked for is on chromosome 7
+      assert var.index '2125503'     # starts here
+      assert var.index '22125502'    # and ends here
+    end
+
+    should 'return an xml object' do 
+      var = Variation.vep_region 'C', '9:22125503-22125502:1', 'human',
+              response: 'xml'
+      assert_nothing_raised { REXML::Document.new var }
+    end
+
+    sleep(1)
+
+  end
+
+
+end