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#
# 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_first_name
assert_equal('sce:YBR160W', @obj.first_name)
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_overrun
data =<<END
>gi|55416190|gb|AAV50057.1| NADH dehydrogenase subunit 2 [Dasyurus hallucatus]
MSPYVLMILTLSLFIGTCLTIFSNHWFTAWMGLEINTLAIIPLMTAPNNPRSTEAATKYFLTQATASMLMMFAIIYNAWS
TNQWALPQLSDDWISLLMTVALAIKLGLAPFHFWVPEVTQGIPLLTGMILLTWQKIAPTAILFQIAPYLNMKFLVILAIL
STLVGGWGGLNQTHLRKILAYSSIAHMGWMIIIVQINPTLSIFTLTIYVMATLTTFLTLNLSNSTKIKSLGNLWNKSATA
TIIIFLTLLSLGGLPPLTGFMPKWLILQELINNGNIITATMMALSALLNLFFYMRLIYASSLTMFPSINNSKMQWYNNSM
KTTTLIPTATVISSLLLPLTPLFVTLY
END
assert_equal(data, @obj.entry_overrun)
end
class DummyFactory
def query(str)
@query_str = str
"DummyFactoryResult#{str.length}"
end
attr_reader :query_str
end #class DummyFactory
def test_query
data =<<END
>gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]
MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT
IALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF
TLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI
LFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL
END
factory = DummyFactory.new
assert_equal("DummyFactoryResult401", @obj.query(factory))
assert_equal(data, factory.query_str)
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
def test_first_name
assert_equal('gi|55416189|gb|AAV50056.1|', @obj.first_name)
end
end # class TestFastaFormat
class TestFastaFirstName < Test::Unit::TestCase
def test_first_name1
data = ">abc def\nATGC"
assert_equal 'abc', Bio::FastaFormat.new(data).first_name
end
def test_first_name_multi_identifier
data = ">gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c] #=> 'gi|398365175|ref|NP_009718.3|\nATGCTG"
assert_equal 'gi|398365175|ref|NP_009718.3|', Bio::FastaFormat.new(data).first_name
end
def test_first_name_single_worded_defintion
data = ">abc\nATGC"
assert_equal 'abc', Bio::FastaFormat.new(data).first_name
end
def test_no_definition
data = ">\nATGC"
assert_equal '', Bio::FastaFormat.new(data).first_name
end
def test_tabbed_defintion
data = ">gabc\tdef\nATGC"
assert_equal 'gabc', Bio::FastaFormat.new(data).first_name
end
def test_space_before_first_name
data = "> gabcds\tdef\nATGC"
assert_equal 'gabcds', Bio::FastaFormat.new(data).first_name
end
end
end
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