/test/unit/bio/db/test_fasta.rb
Ruby | 209 lines | 158 code | 41 blank | 10 comment | 0 complexity | 4df092b4726e081b0566648d9b8693fe MD5 | raw file
Possible License(s): GPL-2.0, LGPL-2.1
- #
- # test/unit/bio/db/test_fasta.rb - Unit test for Bio::FastaFormat
- #
- # Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
- # License:: The Ruby License
- #
- # $Id:$
- #
- # loading helper routine for testing bioruby
- require 'pathname'
- load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
- 'bioruby_test_helper.rb')).cleanpath.to_s
- # libraries needed for the tests
- require 'test/unit'
- require 'bio/db/fasta'
- module Bio
- class TestFastaFormatConst < Test::Unit::TestCase
- def test_delimiter
- assert_equal("\n>", Bio::FastaFormat::DELIMITER)
- assert_equal("\n>", Bio::FastaFormat::RS)
- end
- end # class TestFastaFormatConst
- class TestFastaFormatSwissProt < Test::Unit::TestCase
- def setup
- text =<<END
- >gi|1171674|sp|P42267|NDD_BPR69 NUCLEAR DISRUPTION PROTEIN
- MKYMTVTDLNNAGATVIGTIKGGEWFLGTPHKDILSKPGFYFLVSKLDGRPFSNPCVSARFYVGNQRSKQGFSAVLSHIR
- QRRSQLARTIANNNMVYTVFYLPASKMKPLTTGFGKGQLALAFTRNHHSEYQTLEEMNRMLADNFKFVLQAY
- END
- @obj = Bio::FastaFormat.new(text)
- end
- def test_locus
- assert_equal(nil, @obj.locus)
- end
- end
- class TestFastaFormatKeggGenesNT < Test::Unit::TestCase
- def setup
- text =<<END
- >eco:b0001 thrL; thr operon leader peptide (N)
- atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
- ggctga
- END
- @obj = Bio::FastaFormat.new(text)
- end
- def test_naseq_class
- assert_equal(Bio::Sequence::NA, @obj.naseq.class)
- end
- def test_naseq
- seq = 'atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctga'
- assert_equal(seq, @obj.naseq)
- end
- def test_nalen
- assert_equal(66, @obj.nalen)
- end
- end
- class TestFastaFormatKeggGenesAA < Test::Unit::TestCase
- def setup
- text =<<END
- >sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
- MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
- VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
- GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
- KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
- IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
- QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
- >sce:YBR274W CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
- MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
- TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
- GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
- DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
- DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
- EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
- AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
- QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
- CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
- FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
- KTGDPLEWRRLFKKISTICRDIILIPN
- END
- @obj = Bio::FastaFormat.new(text)
- end
- def test_entry_id
- assert_equal('sce:YBR160W', @obj.entry_id)
- end
- def test_acc_version
- assert_equal(nil, @obj.acc_version)
- end
- def test_entry
- data = ">sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG\nVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME\nGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL\nKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC\nIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP\nQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES\n"
- assert_equal(data, @obj.entry)
- end
- def test_definition
- data = "sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]"
- assert_equal(data, @obj.definition)
- end
- def test_data
- data = "\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG\nVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME\nGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL\nKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC\nIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP\nQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES\n"
- assert_equal(data, @obj.data)
- end
- end
- class TestFastaFormat < Test::Unit::TestCase
- def setup
- text =<<END
- >gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]
- MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT
- IALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF
- TLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI
- LFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL
- >gi|55416190|gb|AAV50057.1| NADH dehydrogenase subunit 2 [Dasyurus hallucatus]
- MSPYVLMILTLSLFIGTCLTIFSNHWFTAWMGLEINTLAIIPLMTAPNNPRSTEAATKYFLTQATASMLMMFAIIYNAWS
- TNQWALPQLSDDWISLLMTVALAIKLGLAPFHFWVPEVTQGIPLLTGMILLTWQKIAPTAILFQIAPYLNMKFLVILAIL
- STLVGGWGGLNQTHLRKILAYSSIAHMGWMIIIVQINPTLSIFTLTIYVMATLTTFLTLNLSNSTKIKSLGNLWNKSATA
- TIIIFLTLLSLGGLPPLTGFMPKWLILQELINNGNIITATMMALSALLNLFFYMRLIYASSLTMFPSINNSKMQWYNNSM
- KTTTLIPTATVISSLLLPLTPLFVTLY
- END
- @obj = Bio::FastaFormat.new(text)
- end
- def test_entry
- data = ">gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
- assert_equal(data, @obj.entry)
- end
- def test_entry_id
- assert_equal('gi|55416189', @obj.entry_id)
- end
- def test_definition
- data = "gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]"
- assert_equal(data, @obj.definition)
- end
- def test_data
- data = "\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
- assert_equal(data, @obj.data)
- end
- def test_seq
- seq = 'MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL'
- assert_equal(seq, @obj.seq)
- end
- def test_length
- assert_equal(318, @obj.length)
- end
- def test_aaseq
- seq = "MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL"
- assert_equal(seq, @obj.aaseq)
- end
- def test_aalen
- assert_equal(318, @obj.aalen)
- end
- def test_identifiers
- assert_equal(Bio::FastaDefline, @obj.identifiers.class)
- end
- def test_gi
- assert_equal('55416189', @obj.gi)
- end
- def test_accession
- assert_equal('AAV50056', @obj.accession)
- end
- def test_accessions
- assert_equal(['AAV50056'], @obj.accessions)
- end
- def test_acc_version
- assert_equal('AAV50056.1', @obj.acc_version)
- end
- end # class TestFastaFormat
- class TestFastaDefinition < Test::Unit::TestCase
- def setup
- end
- def test_defline
- end
- end # class TestFastaDefinition
- end