bio 2.0.4 → 2.0.6

data/test/unit/bio/db/embl/test_uniprotkb_P03589.rb

@@ -0,0 +1,378 @@
+# frozen_string_literal: true
+#
+# test/unit/bio/db/embl/test_uniprotkb_P03589.rb - Unit tests for Bio::UniProtKB
+#
+# Copyright:::  Copyright (C) 2023 BioRuby Project <staff@bioruby.org>
+# License::     The Ruby License
+# Contributor:: 2005 Mitsuteru Nakao <n@bioruby.org>
+#               2023 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_P03589 < Test::Unit::TestCase
+
+    def setup
+      data = File.read(File.join(BioRubyTestDataPath, 
+                                 'uniprot', 'P03589.uniprot'))
+      @obj = Bio::UniProtKB.new(data)
+    end
+
+    def test_id_line
+      assert(@obj.id_line)
+    end
+
+    def test_id_line_entry_name
+      assert_equal('1A_AMVLE', @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(1126, @obj.id_line('SEQUENCE_LENGTH'))
+    end
+
+    def test_entry
+      entry = '1A_AMVLE'
+      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 = 1126
+      assert_equal(seqlen, @obj.sequence_length)
+      assert_equal(seqlen, @obj.aalen)
+    end
+
+    def test_ac
+      acs = ["P03589"].freeze
+      assert_equal(acs, @obj.ac)
+      assert_equal(acs, @obj.accessions)
+    end
+
+    def test_accession
+      assert_equal('P03589', @obj.accession)
+    end
+
+    def test_dr
+      assert_equal(13, @obj.dr.size)
+      assert_equal(8, @obj.dr['GO'].size)
+      assert_equal([["IPR027351", "(+)RNA_virus_helicase_core_dom"],
+                    ["IPR002588", "Alphavirus-like_MT_dom"],
+                    ["IPR027417", "P-loop_NTPase"]],
+                   @obj.dr['InterPro'])
+    end
+
+    def test_dr_with_key
+      pfam = [{" "              => "1",
+               "Version"        => "Viral_helicase1",
+               "Accession"      => "PF01443",
+               "Molecular Type" => nil
+              },
+              {" "              => "1",
+               "Version"        => "Vmethyltransf",
+               "Accession"      => "PF01660",
+               "Molecular Type" => nil
+              }].freeze
+      assert_equal(pfam, @obj.dr('Pfam'))
+      embl = [{"Accession"      => "L00163",
+               "Version"        => "AAA46289.1",
+               " "              => "-",
+               "Molecular Type" => "Genomic_RNA"
+              }].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('21-JUL-1986, integrated into UniProtKB/Swiss-Prot.',
+                   @obj.dt('created'))
+    end
+
+    def test_dt_sequence
+      assert_equal('21-JUL-1986, sequence version 1.', 
+                   @obj.dt('sequence'))
+    end
+
+    def test_dt_annotation
+      assert_equal('22-FEB-2023, entry version 78.', 
+                   @obj.dt('annotation'))
+    end
+
+    def test_de
+      assert(@obj.de)
+    end
+
+    def test_protein_name
+      assert_equal("Replication protein 1a",
+                   @obj.protein_name)
+    end
+
+    def test_synonyms
+      assert_equal([], @obj.synonyms)
+    end
+
+    def test_protein_name_after_calling_de
+      assert(@obj.de)
+      assert_equal("Replication protein 1a",
+                   @obj.protein_name)
+    end
+
+    def test_gn
+      assert_equal([{:orfs=>["ORF1a"], :synonyms=>[], :name=>"", :loci=>[]}], 
+                   @obj.gn)
+    end
+
+    def test_gn_uniprot_parser
+      assert_equal([{:orfs=>["ORF1a"], :loci=>[], :name=>"", :synonyms=>[]}], 
+                   @obj.instance_eval("gn_uniprot_parser"))
+    end
+
+    def test_gn_old_parser
+      assert_equal([["ORFNames=ORF1a;"]], 
+                   @obj.instance_eval("gn_old_parser"))
+    end
+
+    def test_gene_names
+      assert_equal([""], @obj.gene_names)
+    end
+
+    def test_gene_name
+      assert_equal('', @obj.gene_name)
+    end
+
+    def test_os
+      assert(@obj.os)
+    end
+
+    def test_os_access
+      assert_equal("Alfalfa mosaic virus (strain 425 / isolate Leiden)",
+                   @obj.os(0))
+    end
+
+    def test_os_access2
+      assert_equal({"name"=>"(strain 425 / isolate Leiden)",
+                    "os"=>"Alfalfa mosaic virus"}, @obj.os[0])
+    end
+
+    def test_oc
+      assert_equal(["Viruses",
+                    "Riboviria",
+                    "Orthornavirae",
+                    "Kitrinoviricota",
+                    "Alsuviricetes",
+                    "Martellivirales",
+                    "Bromoviridae",
+                    "Alfamovirus"],
+                   @obj.oc)
+    end
+
+    def test_ox
+      assert_equal({"NCBI_TaxID"=>["12322"]}, @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
+      assert_equal(nil, @obj.cc('ALTERNATIVE PRODUCTS'))
+    end
+
+    def test_cc_mass_spectrometry
+      assert_equal(nil, @obj.cc('MASS SPECTROMETRY'))
+    end
+
+
+    def test_kw
+      keywords = ["ATP-binding",
+                  "Helicase",
+                  "Host endoplasmic reticulum",
+                  "Host membrane",
+                  "Hydrolase",
+                  "Membrane",
+                  "Methyltransferase",
+                  "Nucleotide-binding",
+                  "Reference proteome",
+                  "Transferase"]
+      assert_equal(keywords, @obj.kw)
+    end
+
+    def test_ft
+      assert(@obj.ft)
+      ft = {"CHAIN" => [
+              {"From"=>1, "To"=>1126, "diff"=>[],
+               "original"=>["CHAIN", "1", "1126",
+                            [["note", "Replication protein 1a"],
+                             ["id", "PRO_0000083254"]]],
+               "note"=>"Replication protein 1a",
+               "id"=>"PRO_0000083254",
+               "FTId"=>"PRO_0000083254"}],
+            "DOMAIN"=>
+            [{"From"=>90, "To"=>278,"diff"=>[],
+              "original"=>["DOMAIN", "90", "278",
+                           [["note", "Alphavirus-like MT"],
+                            ["evidence",
+                             "ECO:0000255|PROSITE-ProRule:PRU01079"]]],
+              "note"=>"Alphavirus-like MT",
+              "evidence"=>"ECO:0000255|PROSITE-ProRule:PRU01079"},
+             {"From"=>806, "To"=>963, "diff"=>[],
+              "original"=>["DOMAIN", "806", "963",
+                           [["note", "(+)RNA virus helicase ATP-binding"]]],
+              "note"=>"(+)RNA virus helicase ATP-binding"},
+             {"From"=>964, "To"=>1125, "diff"=>[],
+              "original"=>["DOMAIN", "964", "1125",
+                           [["note", "(+)RNA virus helicase C-terminal"]]],
+              "note"=>"(+)RNA virus helicase C-terminal"}],
+            "REGION"=>
+            [{"From"=>69, "To"=>406, "diff"=>[],
+              "original"=>["REGION", "69", "406",
+                           [["note", "Methyltransferase"]]],
+              "note"=>"Methyltransferase"},
+             {"From"=>834, "To"=>1094, "diff"=>[],
+              "original"=>["REGION", "834", "1094",
+                           [["note", "ATP-dependent helicase"]]],
+              "note"=>"ATP-dependent helicase"}],
+            "BINDING"=>
+            [{"From"=>838, "To"=>845, "diff"=>[],
+              "original"=>["BINDING", "838", "845",
+                           [["ligand", "ATP"],
+                            ["ligand_id", "ChEBI:CHEBI:30616"],
+                            ["evidence", "ECO:0000255"]]],
+              "ligand"=>"ATP", "ligand_id"=>"ChEBI:CHEBI:30616",
+              "evidence"=>"ECO:0000255"}]}
+      assert_equal(ft, @obj.ft)
+    end
+
+    def test_sq
+      assert_equal({"CRC64"=>"BF5A8019B47D4CBF", "aalen"=>1126, "MW"=>125828}, 
+                   @obj.sq)
+    end
+
+    def test_sq_crc64
+      assert_equal("BF5A8019B47D4CBF", @obj.sq('CRC64'))
+    end
+
+    def test_sq_mw
+      mw = 125828
+      assert_equal(mw, @obj.sq('mw'))
+      assert_equal(mw, @obj.sq('molecular'))
+      assert_equal(mw, @obj.sq('weight'))
+    end
+
+    def test_sq_len
+      length = 1126
+      assert_equal(length, @obj.sq('len'))
+      assert_equal(length, @obj.sq('length'))
+      assert_equal(length, @obj.sq('AA'))
+    end
+
+    def test_seq
+      seq ="MNADAQSTDASLSMREPLSHASIQEMLRRVVEKQAADDTTAIGKVFSEAGRAYAQDALPS" +
+           "DKGEVLKISFSLDATQQNILRANFPGRRTVFSNSSSSSHCFAAAHRLLETDFVYRCFGNT" +
+           "VDSIIDLGGNFVSHMKVKRHNVHCCCPILDARDGARLTERILSLKSYVRKHPEIVGEADY" +
+           "CMDTFQKCSRRADYAFAIHSTSDLDVGELACSLDQKGVMKFICTMMVDADMLIHNEGEIP" +
+           "NFNVRWEIDRKKDLIHFDFIDEPNLGYSHRFSLLKHYLTYNAVDLGHAAYRIERKQDFGG" +
+           "VMVIDLTYSLGFVPKMPHSNGRSCAWYNRVKGQMVVHTVNEGYYHHSYQTAVRRKVLVDK" +
+           "KVLTRVTEVAFRQFRPNADAHSAIQSIATMLSSSTNHTIIGGVTLISGKPLSPDDYIPVA" +
+           "TTIYYRVKKLYNAIPEMLSLLDKGERLSTDAVLKGSEGPMWYSGPTFLSALDKVNVPGDF" +
+           "VAKALLSLPKRDLKSLFSRSATSHSERTPVRDESPIRCTDGVFYPIRMLLKCLGSDKFES" +
+           "VTITDPRSNTETTVDLYQSFQKKIETVFSFILGKIDGPSPLISDPVYFQSLEDVYYAEWH" +
+           "QGNAIDASNYARTLLDDIRKQKEESLKAKAKEVEDAQKLNRAILQVHAYLEAHPDGGKIE" +
+           "GLGLSSQFIAKIPELAIPTPKPLPEFEKNAETGEILRINPHSDAILEAIDYLKSTSANSI" +
+           "ITLNKLGDHCQWTTKGLDVVWAGDDKRRAFIPKKNTWVGPTARSYPLAKYERAMSKDGYV" +
+           "TLRWDGEVLDANCVRSLSQYEIVFVDQSCVFASAEAIIPSLEKALGLEAHFSVTIVDGVA" +
+           "GCGKTTNIKQIARSSGRDVDLILTSNRSSADELKETIDCSPLTKLHYIRTCDSYLMSASA" +
+           "VKAQRLIFDECFLQHAGLVYAAATLAGCSEVIGFGDTEQIPFVSRNPSFVFRHHKLTGKV" +
+           "ERKLITWRSPADATYCLEKYFYKNKKPVKTNSRVLRSIEVVPINSPVSVERNTNALYLCH" +
+           "TQAEKAVLKAQTHLKGCDNIFTTHEAQGKTFDNVYFCRLTRTSTSLATGRDPINGPCNGL" +
+           "VALSRHKKTFKYFTIAHDSDDVIYNACRDAGNTDDSILARSYNHNF"
+      seq.freeze
+      assert_equal(seq, @obj.seq)
+      assert_equal(seq, @obj.aaseq)
+    end
+
+    def test_oh
+      oh = [
+        {"NCBI_TaxID"=>"4045", "HostName"=>"Apium graveolens (Celery)"},
+        {"NCBI_TaxID"=>"83862",
+         "HostName"=>"Astragalus glycyphyllos (Wild liquorice)"},
+        {"NCBI_TaxID"=>"4072",
+         "HostName"=>"Capsicum annuum (Capsicum pepper)"},
+        {"NCBI_TaxID"=>"41386", "HostName"=>"Caryopteris incana"},
+        {"NCBI_TaxID"=>"3827",
+         "HostName"=>"Cicer arietinum (Chickpea) (Garbanzo)"},
+        {"NCBI_TaxID"=>"3847",
+         "HostName"=>"Glycine max (Soybean) (Glycine hispida)"},
+        {"NCBI_TaxID"=>"35936",
+         "HostName"=>"Lablab purpureus (Hyacinth bean) (Dolichos lablab)"},
+        {"NCBI_TaxID"=>"4236",
+         "HostName"=>"Lactuca sativa (Garden lettuce)"},
+        {"NCBI_TaxID"=>"3864",
+         "HostName"=>"Lens culinaris (Lentil) (Cicer lens)"},
+        {"NCBI_TaxID"=>"3869", "HostName"=>"Lupinus"},
+        {"NCBI_TaxID"=>"145753",
+         "HostName"=>"Malva parviflora (Little mallow) (Cheeseweed mallow)"},
+        {"NCBI_TaxID"=>"3879",
+         "HostName"=>"Medicago sativa (Alfalfa)"},
+        {"NCBI_TaxID"=>"4097",
+         "HostName"=>"Nicotiana tabacum (Common tobacco)"},
+        {"NCBI_TaxID"=>"3885",
+         "HostName"=>"Phaseolus vulgaris (Kidney bean) (French bean)"},
+        {"NCBI_TaxID"=>"23113", "HostName"=>"Philadelphus"},
+        {"NCBI_TaxID"=>"3888", "HostName"=>"Pisum sativum (Garden pea)"},
+        {"NCBI_TaxID"=>"4081",
+         "HostName"=>
+         "Solanum lycopersicum (Tomato) (Lycopersicon esculentum)"},
+        {"NCBI_TaxID"=>"4113", "HostName"=>"Solanum tuberosum (Potato)"},
+        {"NCBI_TaxID"=>"157662", "HostName"=>"Teramnus repens"},
+        {"NCBI_TaxID"=>"60916",
+         "HostName"=>"Trifolium incarnatum (Crimson clover)"},
+        {"NCBI_TaxID"=>"85293",
+         "HostName"=>"Viburnum opulus (High-bush cranberry)"},
+        {"NCBI_TaxID"=>"3916",
+         "HostName"=>
+         "Vigna radiata var. radiata (Mung bean) (Phaseolus aureus)"},
+        {"NCBI_TaxID"=>"3917", "HostName"=>"Vigna unguiculata (Cowpea)"}
+      ]
+      assert_equal(oh, @obj.oh)
+    end
+
+  end # class TestUniProtKB
+end # module Bio
+