bio 2.0.1 → 2.0.4

data/test/unit/bio/db/embl/test_uniprotkb_P28907.rb

@@ -0,0 +1,325 @@
+# frozen_string_literal: true
+#
+# test/unit/bio/db/embl/test_uniprotkb_P28907.rb - Unit tests for Bio::UniProtKB
+#
+# Copyright:::  Copyright (C) 2022 BioRuby Project <staff@bioruby.org>
+# License::     The Ruby License
+# Contributor:: 2005 Mitsuteru Nakao <n@bioruby.org>
+#               2022 Naohisa Goto <ng@bioruby.org>
+#
+
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+
+# libraries needed for the tests
+require 'test/unit'
+require 'bio/db/embl/uniprotkb'
+
+module Bio
+  class TestUniProtKB_P28907 < Test::Unit::TestCase
+
+    def setup
+      data = File.read(File.join(BioRubyTestDataPath, 
+                                 'uniprot', 'P28907.uniprot'))
+      @obj = Bio::UniProtKB.new(data)
+    end
+
+    def test_id_line
+      assert(@obj.id_line)
+    end
+
+    def test_id_line_entry_name
+      assert_equal('CD38_HUMAN', @obj.id_line('ENTRY_NAME'))
+    end   
+
+    def test_id_line_data_class
+      assert_equal('Reviewed', @obj.id_line('DATA_CLASS'))
+    end
+
+    #def test_id_line_molecule_type
+    #  assert_equal('PRT', @obj.id_line('MOLECULE_TYPE'))
+    #end
+
+    def test_id_line_sequence_length
+      assert_equal(300, @obj.id_line('SEQUENCE_LENGTH'))
+    end
+
+    def test_entry
+      entry = 'CD38_HUMAN'
+      assert_equal(entry, @obj.entry)
+      assert_equal(entry, @obj.entry_name)
+      assert_equal(entry, @obj.entry_id)
+    end
+
+    #def test_molecule
+    #  assert_equal('PRT', @obj.molecule)
+    #  assert_equal('PRT', @obj.molecule_type)
+    #end
+
+    def test_sequence_length
+      seqlen = 300
+      assert_equal(seqlen, @obj.sequence_length)
+      assert_equal(seqlen, @obj.aalen)
+    end
+
+    def test_ac
+      acs = ["P28907", "O00121", "O00122", "Q96HY4"].freeze
+      assert_equal(acs, @obj.ac)
+      assert_equal(acs, @obj.accessions)
+    end
+
+    def test_accession
+      assert_equal('P28907', @obj.accession)
+    end
+
+    def test_dr
+      assert_equal(81, @obj.dr.size)
+      assert_equal(39, @obj.dr['GO'].size)
+      assert_equal([["IPR003193", "ADP-ribosyl_cyclase"],
+                    ["IPR033567", "CD38"]],
+                   @obj.dr['InterPro'])
+    end
+
+    def test_dr_with_key
+      pfam = [{" "              => "1",
+               "Version"        => "Rib_hydrolayse",
+               "Accession"      => "PF02267",
+               "Molecular Type" => nil
+              }].freeze
+      assert_equal(pfam, @obj.dr('Pfam'))
+      embl = [{"Accession"      => "M34461",
+               "Version"        => "AAA68482.1",
+               " "              => "-",
+               "Molecular Type" => "mRNA"},
+              {"Accession"      => "D84276",
+               "Version"        => "BAA18964.1",
+               " "              => "-",
+               "Molecular Type" => "mRNA"},
+              {"Accession"      => "D84277",
+               "Version"        => "BAA18965.1",
+               " "              => "-",
+               "Molecular Type" => "mRNA"},
+              {"Accession"      => "D84284",
+               "Version"        => "BAA18966.1",
+               " "              => "-",
+               "Molecular Type" => "Genomic_DNA"},
+              {"Accession"      => "BC007964",
+               "Version"        => "AAH07964.1",
+               " "              => "-",
+               "Molecular Type" => "mRNA"}].freeze
+      assert_equal(embl, @obj.dr('EMBL'))
+    end
+
+    def test_dr_with_key_empty
+      assert_equal([], @obj.dr('NOT_A_DATABASE'))
+    end
+
+    def test_dt
+      assert(@obj.dt)
+    end
+
+    def test_dt_created
+      assert_equal('01-DEC-1992, integrated into UniProtKB/Swiss-Prot.',
+                   @obj.dt('created'))
+    end
+
+    def test_dt_sequence
+      assert_equal('23-NOV-2004, sequence version 2.', 
+                   @obj.dt('sequence'))
+    end
+
+    def test_dt_annotation
+      assert_equal('03-AUG-2022, entry version 213.', 
+                   @obj.dt('annotation'))
+    end
+
+    def test_de
+      assert(@obj.de)
+    end
+
+    def test_protein_name
+      assert_equal("ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1",
+                   @obj.protein_name)
+    end
+
+    def test_synonyms
+      ary = [
+        "EC 3.2.2.6",
+        "2'-phospho-ADP-ribosyl cyclase",
+        "2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferase",
+        "EC 2.4.99.20",
+        "2'-phospho-cyclic-ADP-ribose transferase",
+        "ADP-ribosyl cyclase 1",
+        "ADPRC 1",
+        "Cyclic ADP-ribose hydrolase 1",
+        "cADPr hydrolase 1",
+        "T10",
+        "CD_antigen=CD38"
+      ].freeze
+      assert_equal(ary, @obj.synonyms)
+    end
+
+    def test_protein_name_after_calling_de
+      assert(@obj.de)
+      assert_equal("ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1",
+                   @obj.protein_name)
+    end
+
+    def test_synonyms_after_calling_de
+      assert(@obj.de)
+      assert_equal(11, @obj.synonyms.size)
+    end
+
+    def test_gn
+      assert_equal([{:orfs=>[], :synonyms=>[], :name=>"CD38", :loci=>[]}], 
+                   @obj.gn)
+    end
+
+    def test_gn_uniprot_parser
+      assert_equal([{:orfs=>[], :loci=>[], :name=>"CD38", :synonyms=>[]}], 
+                   @obj.instance_eval("gn_uniprot_parser"))
+    end
+
+    def test_gn_old_parser
+      assert_equal([["Name=CD38;"]], 
+                   @obj.instance_eval("gn_old_parser"))
+    end
+
+    def test_gene_names
+      assert_equal(["CD38"], @obj.gene_names)
+    end
+
+    def test_gene_name
+      assert_equal('CD38', @obj.gene_name)
+    end
+
+    def test_os
+      assert(@obj.os)
+    end
+
+    def test_os_access
+      assert_equal("Homo sapiens (Human)", @obj.os(0))
+    end
+
+    def test_os_access2
+      assert_equal({"name"=>"(Human)", "os"=>"Homo sapiens"}, @obj.os[0])
+    end
+
+    def test_oc
+      assert_equal(["Eukaryota", "Metazoa", "Chordata", "Craniata",
+                    "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria",
+                    "Euarchontoglires", "Primates",
+                    "Haplorrhini", "Catarrhini", "Hominidae", "Homo"],
+                   @obj.oc)
+    end
+
+    def test_ox
+      assert_equal({"NCBI_TaxID"=>["9606"]}, @obj.ox)
+    end
+
+    def test_ref # Bio::UniProtKB#ref
+      assert_equal(Array, @obj.ref.class)
+    end
+
+    def test_cc
+      assert_equal(Hash, @obj.cc.class)
+    end
+   
+    def test_cc_database
+      assert_equal(nil, @obj.cc('DATABASE'))
+    end
+
+    def test_cc_alternative_products
+      ap = { "Event"=>["Alternative splicing"],
+             "Named isoforms"=>"2",
+             "Comment"=>"",
+             "Variants"=>
+             [{"Name"=>"1",
+               "Synonyms"=>[],
+               "IsoId"=>["P28907-1"],
+               "Sequence"=>["Displayed"]},
+              {"Name"=>"2",
+               "Synonyms"=>[],
+               "IsoId"=>["P28907-2"],
+               "Sequence"=>["VSP_000707", "VSP_000708"]}]}
+      assert_equal(ap, @obj.cc('ALTERNATIVE PRODUCTS'))
+    end
+
+    def test_cc_mass_spectrometry
+      assert_equal(nil, @obj.cc('MASS SPECTROMETRY'))
+    end
+
+
+    def test_kw
+      keywords = ["3D-structure", "Alternative splicing",
+                  "Diabetes mellitus", "Disulfide bond",
+                  "Glycoprotein", "Hydrolase", "Membrane",
+                  "NAD", "NADP", "Receptor", "Reference proteome",
+                  "Signal-anchor", "Transferase", "Transmembrane",
+                  "Transmembrane helix"]
+      assert_equal(keywords, @obj.kw)
+    end
+    
+    def test_ft
+      assert(@obj.ft)
+      name = 'TOPO_DOM'
+      data = [{"From"=>1,
+               "To"=>21,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "1",
+                "21",
+                [["note", "Cytoplasmic"],
+                 ["evidence", "ECO:0000255"]]],
+               "note"=>"Cytoplasmic",
+               "evidence"=>"ECO:0000255"},
+              {"From"=>43,
+               "To"=>300,
+               "diff"=>[],
+               "original"=>
+               ["TOPO_DOM",
+                "43",
+                "300",
+                [["note", "Extracellular"],
+                 ["evidence", "ECO:0000255"]]],
+               "note"=>"Extracellular",
+               "evidence"=>"ECO:0000255"}].freeze
+
+      assert_equal(data, @obj.ft[name])
+    end
+
+    def test_sq
+      assert_equal({"CRC64"=>"47BBE38C3DE3E6AA", "aalen"=>300, "MW"=>34328}, 
+                   @obj.sq)
+    end
+
+    def test_sq_crc64
+      assert_equal("47BBE38C3DE3E6AA", @obj.sq('CRC64'))
+    end
+
+    def test_sq_mw
+      mw = 34328
+      assert_equal(mw, @obj.sq('mw'))
+      assert_equal(mw, @obj.sq('molecular'))
+      assert_equal(mw, @obj.sq('weight'))
+    end
+
+    def test_sq_len
+      length = 300
+      assert_equal(length, @obj.sq('len'))
+      assert_equal(length, @obj.sq('length'))
+      assert_equal(length, @obj.sq('AA'))
+    end
+
+    def test_seq
+      seq = "MANCEFSPVSGDKPCCRLSRRAQLCLGVSILVLILVVVLAVVVPRWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCNITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFNTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLNGSRSKIFDKNSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI"
+      assert_equal(seq, @obj.seq)
+      assert_equal(seq, @obj.aaseq)
+    end
+
+  end # class TestUniProtKB
+end # module Bio
+