// ========================================================================== // SeqAn - The Library for Sequence Analysis // ========================================================================== // Copyright (c) 2006-2011, Knut Reinert, FU Berlin // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // * Neither the name of Knut Reinert or the FU Berlin nor the names of // its contributors may be used to endorse or promote products derived // from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH // DAMAGE. // // ========================================================================== // Author: Hannes Hauswedell // ========================================================================== // FASTA-Tests for seqan/stream/read_fasta_fastq.h // ========================================================================== #ifndef TEST_STREAM_TEST_STREAM_READ_GENBANK_H_ #define TEST_STREAM_TEST_STREAM_READ_GENBANK_H_ // Return an GenBank format string with two entries. char const * testHelperReturnGenBankFile() { char const * result = "LOCUS SCU49845 5028 bp DNA PLN 21-JUN-1999\n" "DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p\n" " (AXL2) and Rev7p (REV7) genes, complete cds.\n" "ACCESSION U49845\n" "VERSION U49845.1 GI:1293613\n" "KEYWORDS .\n" "SOURCE Saccharomyces cerevisiae (baker's yeast)\n" " ORGANISM Saccharomyces cerevisiae\n" " Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;\n" " Saccharomycetales; Saccharomycetaceae; Saccharomyces.\n" "REFERENCE 1 (bases 1 to 5028)\n" " AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.\n" " TITLE Cloning and sequence of REV7, a gene whose function is required for\n" " DNA damage-induced mutagenesis in Saccharomyces cerevisiae\n" " JOURNAL Yeast 10 (11), 1503-1509 (1994)\n" " PUBMED 7871890\n" "REFERENCE 2 (bases 1 to 5028)\n" " AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M.\n" " TITLE Selection of axial growth sites in yeast requires Axl2p, a novel\n" " plasma membrane glycoprotein\n" " JOURNAL Genes Dev. 10 (7), 777-793 (1996)\n" " PUBMED 8846915\n" "REFERENCE 3 (bases 1 to 5028)\n" " AUTHORS Roemer,T.\n" " TITLE Direct Submission\n" " JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New\n" " Haven, CT, USA\n" "FEATURES Location/Qualifiers\n" " source 1..5028\n" " /organism=\"Saccharomyces cerevisiae\"\n" " /db_xref=\"taxon:4932\"\n" " /chromosome=\"IX\"\n" " /map=\"9\"\n" " CDS <1..206\n" " /codon_start=3\n" " /product=\"TCP1-beta\"\n" " /protein_id=\"AAA98665.1\"\n" " /db_xref=\"GI:1293614\"\n" " /translation=\"SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA\n" " AEVLLRVDNIIRARPRTANRQHM\"\n" " gene 687..3158\n" " /gene=\"AXL2\"\n" " CDS 687..3158\n" " /gene=\"AXL2\"\n" " /note=\"plasma membrane glycoprotein\"\n" " /codon_start=1\n" " /function=\"required for axial budding pattern of S.\n" " cerevisiae\"\n" " /product=\"Axl2p\"\n" " /protein_id=\"AAA98666.1\"\n" " /db_xref=\"GI:1293615\"\n" " /translation=\"MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF\n" " TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN\n" " VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE\n" " VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE\n" " TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV\n" " YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG\n" " DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ\n" " DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA\n" " NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA\n" " CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN\n" " NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ\n" " SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS\n" " YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK\n" " HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL\n" " VDFSNKSNVNVGQVKDIHGRIPEML\"\n" " gene complement(3300..4037)\n" " /gene=\"REV7\"\n" " CDS complement(3300..4037)\n" " /gene=\"REV7\"\n" " /codon_start=1\n" " /product=\"Rev7p\"\n" " /protein_id=\"AAA98667.1\"\n" " /db_xref=\"GI:1293616\"\n" " /translation=\"MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ\n" " FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD\n" " KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR\n" " RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK\n" " LISGDDKILNGVYSQYEEGESIFGSLF\"\n" "ORIGIN\n" " 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg\n" " 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct\n" " 121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa\n" " 181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg\n" " 241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa\n" " 301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa\n" " 361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat\n" " 421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga\n" " 481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc\n" " 541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga\n" " 601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta\n" " 661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag\n" " 721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa\n" " 781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata\n" " 841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga\n" " 901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac\n" " 961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg\n" " 1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc\n" " 1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa\n" " 1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca\n" " 1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac\n" " 1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa\n" " 1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag\n" " 1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct\n" " 1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac\n" " 1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa\n" " 1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc\n" " 1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata\n" " 1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca\n" " 1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc\n" " 1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc\n" " 1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca\n" " 1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc\n" " 1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg\n" " 2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt\n" " 2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc\n" " 2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg\n" " 2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca\n" " 2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata\n" " 2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg\n" " 2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga\n" " 2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt\n" " 2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat\n" " 2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt\n" " 2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc\n" " 2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag\n" " 2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta\n" " 2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa\n" " 2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact\n" " 2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt\n" " 3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa\n" " 3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag\n" " 3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct\n" " 3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt\n" " 3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact\n" " 3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa\n" " 3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg\n" " 3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt\n" " 3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc\n" " 3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca\n" " 3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc\n" " 3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc\n" " 3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat\n" " 3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa\n" " 3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga\n" " 3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat\n" " 3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc\n" " 4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc\n" " 4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa\n" " 4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg\n" " 4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc\n" " 4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt\n" " 4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg\n" " 4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg\n" " 4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt\n" " 4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt\n" " 4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat\n" " 4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc\n" " 4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct\n" " 4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta\n" " 4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac\n" " 4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct\n" " 4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct\n" " 4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc\n" "//\n" "LOCUS AB031069 2487 bp mRNA PRI 27-MAY-2000\n" "DEFINITION Homo sapiens PCCX1 mRNA for protein containing CXXC domain 1,\n" " complete cds.\n" "ACCESSION AB031069\n" "VERSION AB031069.1 GI:8100074\n" "KEYWORDS .\n" "SOURCE Homo sapiens embryo male lung fibroblast cell_line:HuS-L12 cDNA to\n" " mRNA.\n" " ORGANISM Homo sapiens\n" " Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;\n" " Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.\n" "REFERENCE 1 (sites)\n" " AUTHORS Fujino,T., Hasegawa,M., Shibata,S., Kishimoto,T., Imai,Si. and\n" " Takano,T.\n" " TITLE PCCX1, a novel DNA-binding protein with PHD finger and CXXC domain,\n" " is regulated by proteolysis\n" " JOURNAL Biochem. Biophys. Res. Commun. 271 (2), 305-310 (2000)\n" " MEDLINE 20261256\n" "REFERENCE 2 (bases 1 to 2487)\n" " AUTHORS Fujino,T., Hasegawa,M., Shibata,S., Kishimoto,T., Imai,S. and\n" " Takano,T.\n" " TITLE Direct Submission\n" " JOURNAL Submitted (15-AUG-1999) to the DDBJ/EMBL/GenBank databases.\n" " Tadahiro Fujino, Keio University School of Medicine, Department of\n" " Microbiology; Shinanomachi 35, Shinjuku-ku, Tokyo 160-8582, Japan\n" " (E-mail:fujino@microb.med.keio.ac.jp,\n" " Tel:+81-3-3353-1211(ex.62692), Fax:+81-3-5360-1508)\n" "FEATURES Location/Qualifiers\n" " source 1..2487\n" " /organism=\"Homo sapiens\"\n" " /db_xref=\"taxon:9606\"\n" " /sex=\"male\"\n" " /cell_line=\"HuS-L12\"\n" " /cell_type=\"lung fibroblast\"\n" " /dev_stage=\"embryo\"\n" " gene 229..2199\n" " /gene=\"PCCX1\"\n" " CDS 229..2199\n" " /gene=\"PCCX1\"\n" " /note=\"a nuclear protein carrying a PHD finger and a CXXC\n" " domain\"\n" " /codon_start=1\n" " /product=\"protein containing CXXC domain 1\"\n" " /protein_id=\"BAA96307.1\"\n" " /db_xref=\"GI:8100075\"\n" " /translation=\"MEGDGSDPEPPDAGEDSKSENGENAPIYCICRKPDINCFMIGCD\n" " NCNEWFHGDCIRITEKMAKAIREWYCRECREKDPKLEIRYRHKKSRERDGNERDSSEP\n" " RDEGGGRKRPVPDPDLQRRAGSGTGVGAMLARGSASPHKSSPQPLVATPSQHHQQQQQ\n" " QIKRSARMCGECEACRRTEDCGHCDFCRDMKKFGGPNKIRQKCRLRQCQLRARESYKY\n" " FPSSLSPVTPSESLPRPRRPLPTQQQPQPSQKLGRIREDEGAVASSTVKEPPEATATP\n" " EPLSDEDLPLDPDLYQDFCAGAFDDHGLPWMSDTEESPFLDPALRKRAVKVKHVKRRE\n" " KKSEKKKEERYKRHRQKQKHKDKWKHPERADAKDPASLPQCLGPGCVRPAQPSSKYCS\n" " DDCGMKLAANRIYEILPQRIQQWQQSPCIAEEHGKKLLERIRREQQSARTRLQEMERR\n" " FHELEAIILRAKQQAVREDEESNEGDSDDTDLQIFCVSCGHPINPRVALRHMERCYAK\n" " YESQTSFGSMYPTRIEGATRLFCDVYNPQSKTYCKRLQVLCPEHSRDPKVPADEVCGC\n" " PLVRDVFELTGDFCRLPKRQCNRHYCWEKLRRAEVDLERVRVWYKLDELFEQERNVRT\n" " AMTNRAGLLALMLHQTIQHDPLTTDLRSSADR\"\n" "BASE COUNT 564 a 715 c 768 g 440 t\n" "ORIGIN \n" " 1 agatggcggc gctgaggggt cttgggggct ctaggccggc cacctactgg tttgcagcgg\n" " 61 agacgacgca tggggcctgc gcaataggag tacgctgcct gggaggcgtg actagaagcg\n" " 121 gaagtagttg tgggcgcctt tgcaaccgcc tgggacgccg ccgagtggtc tgtgcaggtt\n" " 181 cgcgggtcgc tggcgggggt cgtgagggag tgcgccggga gcggagatat ggagggagat\n" " 241 ggttcagacc cagagcctcc agatgccggg gaggacagca agtccgagaa tggggagaat\n" " 301 gcgcccatct actgcatctg ccgcaaaccg gacatcaact gcttcatgat cgggtgtgac\n" " 361 aactgcaatg agtggttcca tggggactgc atccggatca ctgagaagat ggccaaggcc\n" " 421 atccgggagt ggtactgtcg ggagtgcaga gagaaagacc ccaagctaga gattcgctat\n" " 481 cggcacaaga agtcacggga gcgggatggc aatgagcggg acagcagtga gccccgggat\n" " 541 gagggtggag ggcgcaagag gcctgtccct gatccagacc tgcagcgccg ggcagggtca\n" " 601 gggacagggg ttggggccat gcttgctcgg ggctctgctt cgccccacaa atcctctccg\n" " 661 cagcccttgg tggccacacc cagccagcat caccagcagc agcagcagca gatcaaacgg\n" " 721 tcagcccgca tgtgtggtga gtgtgaggca tgtcggcgca ctgaggactg tggtcactgt\n" " 781 gatttctgtc gggacatgaa gaagttcggg ggccccaaca agatccggca gaagtgccgg\n" " 841 ctgcgccagt gccagctgcg ggcccgggaa tcgtacaagt acttcccttc ctcgctctca\n" " 901 ccagtgacgc cctcagagtc cctgccaagg ccccgccggc cactgcccac ccaacagcag\n" " 961 ccacagccat cacagaagtt agggcgcatc cgtgaagatg agggggcagt ggcgtcatca\n" " 1021 acagtcaagg agcctcctga ggctacagcc acacctgagc cactctcaga tgaggaccta\n" " 1081 cctctggatc ctgacctgta tcaggacttc tgtgcagggg cctttgatga ccatggcctg\n" " 1141 ccctggatga gcgacacaga agagtcccca ttcctggacc ccgcgctgcg gaagagggca\n" " 1201 gtgaaagtga agcatgtgaa gcgtcgggag aagaagtctg agaagaagaa ggaggagcga\n" " 1261 tacaagcggc atcggcagaa gcagaagcac aaggataaat ggaaacaccc agagagggct\n" " 1321 gatgccaagg accctgcgtc actgccccag tgcctggggc ccggctgtgt gcgccccgcc\n" " 1381 cagcccagct ccaagtattg ctcagatgac tgtggcatga agctggcagc caaccgcatc\n" " 1441 tacgagatcc tcccccagcg catccagcag tggcagcaga gcccttgcat tgctgaagag\n" " 1501 cacggcaaga agctgctcga acgcattcgc cgagagcagc agagtgcccg cactcgcctt\n" " 1561 caggaaatgg aacgccgatt ccatgagctt gaggccatca ttctacgtgc caagcagcag\n" " 1621 gctgtgcgcg aggatgagga gagcaacgag ggtgacagtg atgacacaga cctgcagatc\n" " 1681 ttctgtgttt cctgtgggca ccccatcaac ccacgtgttg ccttgcgcca catggagcgc\n" " 1741 tgctacgcca agtatgagag ccagacgtcc tttgggtcca tgtaccccac acgcattgaa\n" " 1801 ggggccacac gactcttctg tgatgtgtat aatcctcaga gcaaaacata ctgtaagcgg\n" " 1861 ctccaggtgc tgtgccccga gcactcacgg gaccccaaag tgccagctga cgaggtatgc\n" " 1921 gggtgccccc ttgtacgtga tgtctttgag ctcacgggtg acttctgccg cctgcccaag\n" " 1981 cgccagtgca atcgccatta ctgctgggag aagctgcggc gtgcggaagt ggacttggag\n" " 2041 cgcgtgcgtg tgtggtacaa gctggacgag ctgtttgagc aggagcgcaa tgtgcgcaca\n" " 2101 gccatgacaa accgcgcggg attgctggcc ctgatgctgc accagacgat ccagcacgat\n" " 2161 cccctcacta ccgacctgcg ctccagtgcc gaccgctgag cctcctggcc cggacccctt\n" " 2221 acaccctgca ttccagatgg gggagccgcc cggtgcccgt gtgtccgttc ctccactcat\n" " 2281 ctgtttctcc ggttctccct gtgcccatcc accggttgac cgcccatctg cctttatcag\n" " 2341 agggactgtc cccgtcgaca tgttcagtgc ctggtggggc tgcggagtcc actcatcctt\n" " 2401 gcctcctctc cctgggtttt gttaataaaa ttttgaagaa accaaaaaaa aaaaaaaaaa\n" " 2461 aaaaaaaaaa aaaaaaaaaa aaaaaaa\n" "//\n"; return result; } template void testHelperReadGenBankSingle(TRecordReader & reader) { using namespace seqan; CharString buffer, k, v; // First record. // Read GENBANK headers, split ID header, skip rest. SEQAN_ASSERT_EQ(readRecord(buffer, reader, GenBankHeader()), 0); SEQAN_ASSERT_EQ(buffer, CharString("LOCUS SCU49845 5028 bp DNA PLN 21-JUN-1999")); splitGenBankHeader(k, v, buffer); SEQAN_ASSERT_EQ(k, CharString("LOCUS")); SEQAN_ASSERT_EQ(v, CharString("SCU49845 5028 bp DNA PLN 21-JUN-1999")); while (nextIs(reader, GenBankHeader())) SEQAN_ASSERT_EQ(readRecord(buffer, reader, GenBankHeader()), 0); // Read GENBANK sequence. SEQAN_ASSERT(nextIs(reader, GenBankSequence())); DnaString seq; SEQAN_ASSERT_EQ(readRecord(seq, reader, GenBankSequence()), 0); SEQAN_ASSERT_EQ(length(seq), 5028u); // Second record. // Read GENBANK headers, split ID header, skip rest. SEQAN_ASSERT_EQ(readRecord(buffer, reader, GenBankHeader()), 0); SEQAN_ASSERT_EQ(buffer, CharString("LOCUS AB031069 2487 bp mRNA PRI 27-MAY-2000")); splitGenBankHeader(k, v, buffer); SEQAN_ASSERT_EQ(k, CharString("LOCUS")); SEQAN_ASSERT_EQ(v, CharString("AB031069 2487 bp mRNA PRI 27-MAY-2000")); while (nextIs(reader, GenBankHeader())) SEQAN_ASSERT_EQ(readRecord(buffer, reader, GenBankHeader()), 0); // Read GENBANK sequence. SEQAN_ASSERT(nextIs(reader, GenBankSequence())); SEQAN_ASSERT_EQ(readRecord(seq, reader, GenBankSequence()), 0); SEQAN_ASSERT_EQ(length(seq), 2487u); SEQAN_ASSERT(atEnd(reader)); } template void testHelperReadGenBankRecord(TRecordReader & reader) { using namespace seqan; CharString id; Dna5String seq; SEQAN_ASSERT_EQ(readRecord(id, seq, reader, GenBank()), 0); SEQAN_ASSERT_EQ(id, CharString("U49845.1 GI:1293613")); SEQAN_ASSERT_EQ(length(seq), 5028u); SEQAN_ASSERT_EQ(readRecord(id, seq, reader, GenBank()), 0); SEQAN_ASSERT_EQ(id, CharString("AB031069.1 GI:8100074")); SEQAN_ASSERT_EQ(length(seq), 2487u); } template void testHelperReadGenBankBatch(TRecordReader & reader) { using namespace seqan; StringSet ids; StringSet seqs; SEQAN_ASSERT_EQ(read2(ids, seqs, reader, GenBank()), 0); SEQAN_ASSERT_EQ(ids[0], CharString("U49845.1 GI:1293613")); SEQAN_ASSERT_EQ(length(seqs[0]), 5028u); SEQAN_ASSERT_EQ(ids[1], CharString("AB031069.1 GI:8100074")); SEQAN_ASSERT_EQ(length(seqs[1]), 2487u); } SEQAN_DEFINE_TEST(test_stream_read_genbank_single_char_array_stream) { using namespace seqan; typedef Stream > TStream; char const * genbankString = testHelperReturnGenBankFile(); TStream stream(genbankString, genbankString + strlen(genbankString)); RecordReader > reader(stream); testHelperReadGenBankSingle(reader); } SEQAN_DEFINE_TEST(test_stream_read_genbank_record_char_array_stream) { using namespace seqan; typedef Stream > TStream; char const * genbankString = testHelperReturnGenBankFile(); TStream stream(genbankString, genbankString + strlen(genbankString)); RecordReader > reader(stream); testHelperReadGenBankRecord(reader); } SEQAN_DEFINE_TEST(test_stream_read_genbank_batch_char_array_stream) { using namespace seqan; typedef Stream > TStream; char const * genbankString = testHelperReturnGenBankFile(); TStream stream(genbankString, genbankString + strlen(genbankString)); RecordReader > reader(stream); testHelperReadGenBankBatch(reader); } SEQAN_DEFINE_TEST(test_stream_read_genbank_single_mmap) { using namespace seqan; typedef String > TString; TString mmapString; mmapString = testHelperReturnGenBankFile(); RecordReader > reader(mmapString); testHelperReadGenBankSingle(reader); } SEQAN_DEFINE_TEST(test_stream_read_genbank_single_batch_mmap) { using namespace seqan; typedef String > TString; TString mmapString; mmapString = testHelperReturnGenBankFile(); RecordReader > reader(mmapString); testHelperReadGenBankRecord(reader); } SEQAN_DEFINE_TEST(test_stream_read_genbank_single_batch_concat_mmap) { using namespace seqan; typedef String > TString; TString mmapString; mmapString = testHelperReturnGenBankFile(); RecordReader > reader(mmapString); testHelperReadGenBankBatch(reader); } #endif // TEST_STREAM_TEST_STREAM_READ_GENBANK_H_