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changeset 13:72bc0335b792 draft

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Uploaded v0.0.7, embed citation
author peterjc
date Fri, 28 Nov 2014 11:45:37 -0500
parents 09b5b1af9b8f
children 65d76ca44cd2
files test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.py tools/get_orfs_or_cdss/get_orfs_or_cdss.xml tools/get_orfs_or_cdss/tool_dependencies.xml
diffstat 6 files changed, 428 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta	Fri Nov 28 11:45:37 2014 -0500
@@ -0,0 +1,214 @@
+>Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis
+MNQEQLFWQRFIELAKVNFKPSIYDFYVADAKLLGINQQVANIFLNRPFKKDFWEKNFEE
+LMIAASFESYGEPLTIQYQFTEDEQEIRNTTNTRSSIVHQVQTLEPATPQETFKPVHSDI
+KSQYTFANFVQGDNNHWAKAAALAVSDNLGELYNPLFIFGGPGLGKTHILNAIGNKVLAD
+NPQARIKYVSSETFINEFLEHLRLNDMESFKKTYRNLDLLLIDDIQSLRNKATTQEEFFH
+TFNALHEKNKQIVLTSDRNPDHLDNLEERLVTRFKWGLTSEITPPDFETRIAILRNKCEN
+LPYNFTNETLSYLAGQFDSNVRDLEGALKDIHLIATMRQLSEISVEVAAEAIRSRKQTNP
+QNMVIPIEKIQTEVGNFYGVSLKELKGSKRVQHIVHARQVAMFLAREMTDNSLPKIGKEF
+GNRDHTTVMHAYNKIKTLLLDDENLEIEITSIKNKLR
+>Streptococcus_suis|ORF2 length 385 aa, 1158 bp, from 1507..2664 of Streptococcus_suis
+IINKGESMIQFSINKNIFLQALSITKRAISTKNAIPILSTVKITVTSEGITLTGSNGQIS
+IEHFISIQDENAGLLISSPGSILLEAGFFINVVSSMPDLVLDFNEIEQKQIVLTSGKSEI
+TLKGKEAEQYPRLQEVPTSKPLVLETKVLKQTINETAFAASTQESRPILTGVHFVLTENK
+NLKTVATDSHRMSQRKLVLDTSGDDFNVVIPSRSLREFTAVFTDDIETVEVFFSNNQILF
+RSEHISFYTRLLEGTYPDTDRLIPTEFKTTAIFDTANLRHSMERARLLSNATQNGTVKLE
+IANNVVSAHVNSPEVGRVNEELDTVEVSGEDLVISFNPTYLIEALKATTSEQVKISFISS
+VRPFTLIPNNEGEDFIQLVTPVRTN
+>Streptococcus_suis|ORF201 length 360 aa, 1083 bp, from complement(128035..129117) of Streptococcus_suis
+SCHGGRRMTLFGKIKEVTELQSLPGFEGQVRNHIRQKITPHVDRIETDGLGGIFGIKDTA
+VENAPRILVVAHMDEVGFMISQIKPDGTFRVVELGGWNPLVVSSQAFTLQLQDGRTIPAI
+SGSVPPHLSRGANAPGMPAIADIIFDAGFANYDEAWAFGVRPGDVLVPKNETILTANGKN
+VISKAWDNRFGVLMVTELLESLSGHALPNQLIAGANVQEEVGLRGAHASTTKFNPDIFLA
+VDCSPAGDIYGDQGKIGDGTLLRFYDPGHIMLKNMKDFLLTTAEEAGVKFQYYCGKGGTD
+AGAAHLKNHGVPSTTIGVCARYIHSHQTLYSMDDFLEAQAFLQTIVKKLDRSTVDLIKNY
+>Streptococcus_suis|ORF202 length 106 aa, 321 bp, from 128792..129112 of Streptococcus_suis
+RVKAWLETTRGFQPPSSTTRKVPSGLIWLIIKPTSSMWATTRIRGAFSTAVSLIPKIPPS
+PSVSMRSTCGVIFWRMWLRTCPSNPGKLCNSVTSLIFPKRVILLPP
+>Streptococcus_suis|ORF401 length 120 aa, 363 bp, from 265643..266005 of Streptococcus_suis
+TTGTTSPIAPKWKASSKSLRVPTSEPTTLIPSSTVFTILRSMYSDGSPTATTYPPARTLS
+IAWLKATLETAVTTVECTPPPVISLIYPGTSSTSSPLIVTSAPTSLASSNLSLLMSTAIT
+>Streptococcus_suis|ORF402 length 201 aa, 606 bp, from 265741..266346 of Streptococcus_suis
+HSLHDTEVHVFRWKSDSYYISTSTNTVNSLVEGYFGNSCYNSRVYTATSNFFNISRNIFY
+FKSVDRHICTNFFGEFQFIIIDVYGDNMSVEDFFSVLYSKVSKSTSTIDSNPLTWFQVSF
+FNRFVASNASTSDRTCLSWIKTFWNFYCIVRCYNTLLSHTTVNRVACIFYGTAESFATGC
+TIFTHTTALEEPSNADTVTNF
+>Streptococcus_suis|ORF601 length 665 aa, 1998 bp, from 409896..411893 of Streptococcus_suis
+VMIQIGKIFAGRYRIVRQIGRGGMADVYLARDLILDGEEVAVKVLRTNYQTDQIAIQRFQ
+REARAMAELDHPNIVRISDIGEEDGQQYLAMEYVNGLDLKRYIKENAPLSNDVAVRIMGQ
+ILLAMRMAHTRGIVHRDLKPQNVLLTSNGVAKVTDFGIAVAFAETSLTQTNSMLGSVHYL
+SPEQARGSKATIQSDIYAMGIILFEMLTGRIPYDGDSAVTIALQHFQKPLPSVREENANV
+PQALENVVLKATAKKLNERYKSVAEMYADLASALSMDRQNEPRVELEGNKVDTKTLPKLS
+QANVETKVPHTNSSAQVSATDKGSGKKEVAKSGNKPVSKPRPGIRTRYKVLIGAILLTVI
+AAGLMFFNTPRTVTVPDVSGQTVEKATEMIEVAGLEVGNITEEATATVDEGLVIRTSPAA
+KTTRRQGSKIDIVVATAALASIPDVVDKESDTARQELEALGFQVTIKEEYSEKVAQGLVI
+KTDPGANSSAEKGAKITLYVSKGVAPQVVPNVVGKSQENATQILQTAGFSIGTITQEYSS
+SVTAGQVISTDPVANTELAKGSIINLVISKGKELIMPDLTSGNYTYSQARSQLQALGVNA
+ESIEKQEDRSYYSTTSDIVIGQYPAAGATIDGTVTLYVSVASTRTSSDSSAGSSTSTSTS
+TGSGQ
+>Streptococcus_suis|ORF602 length 120 aa, 363 bp, from complement(410593..410955) of Streptococcus_suis
+LLSRLCSVYVCLALVLKQAYFPTSPLLSYQTPYPSQKLEQNCLYAVLSFQHWLGRVSARF
+LYQPCSLLVQPWVHSDDPWIEPKLNLHTFLQPTYSARLIFLPLLLVQHFLRPEVRWHSLL
+>Streptococcus_suis|ORF801 length 428 aa, 1287 bp, from 561960..563246 of Streptococcus_suis
+KSSRDCESCLLLFVILKVMQADRRKTFGKMRIRINNLFFVAIAFMGIIISNSQVVLAIGK
+ASVIQYLSYLVLILCIVNDLLKNNKHIVVYKLGYLFLIIFLFTIGICQQILPITTKIYLS
+ISMMIISVLATLPISLIKDIDDFRRISNHLLFALFITSILGIMMGATMFTGAVEGIGFSQ
+GFNGGLTHKNFFGITILMGFVLTYLAYKYGSYKRTDRFILGLELFLILISNTRSVYLILL
+LFLFLVNLDKIKIEQRQWSTLKYISMLFCAIFLYYFFGFLITHSDSYAHRVNGLINFFEY
+YRNDWFHLMFGAADLAYGDLTLDYAIRVRRVLGWNGTLEMPLLSIMLKNGFIGLVGYGIV
+LYKLYRNVRILKTDNIKTIGKSVFIIVVLSATVENYIVNLSFVFMPICFCLLNSISTMES
+TINKQLQT
+>Streptococcus_suis|ORF802 length 333 aa, 1002 bp, from 563382..564383 of Streptococcus_suis
+RMEKVSIIVPIFNTEKYLRECLDSIISQSYTNLEILLIDDGSSDSSTDICLEYAEQDGRI
+KLFRLPNGGVSNARNYGIKNSTANYIMFVDSDDIVDGNIVESLYTCLKENDSDLSGGLLA
+TFDGNYQESELQKCQIDLEEIKEVRDLGNENFPNHYMSGIFNSPCCKLYKNIYINKGFDT
+EQWLGEDLLFNLNYLKNIKKVSYVNRNLYFARRGIQSTTNTFKKDVFIQLENLEEKTFDL
+FVKIFGGQYEFSVFKETLQWHIIYYSLLMFKNGDESLPKKLHIFKYLYNRHSLDTLSIKR
+TSSVFKRICKLIVANNLFKIFLNTLIREEKNND
+>Streptococcus_suis|ORF1001 length 374 aa, 1125 bp, from 694014..695138 of Streptococcus_suis
+HYLLFQGGILMKVFASPSRYIQGKHVLFQGAEAIGKLGTKPLILCDDLVYGIIGEKFLSY
+LVEEGMQVHRVAFNGEASDKEIQRVVEIGKEQASDVVIGLGGGKTIDSAKAIADLLGVPV
+VIAPTIASTDAPTSALSVIYSEEGAFERYIFYKKNPDLVLVDTAIICQAPPRLLASGIAD
+GLATWVEARAILQSNGTTMAGGGQTLAGIAIAQTCEQTLFEYGLQAMASCEAKVVTAALE
+NIVEANTLLSGLGFESAGLAAAHAIHNGFTALEGDIHHLTHGEKVAYGTLTQLFLENRPK
+EELEKYIRFYQALNLPTTLEELHLADASYEELLKVGQQATIEGETIHGMPFAISAEDVAE
+ALMAVDYYVRSLDK
+>Streptococcus_suis|ORF1002 length 366 aa, 1101 bp, from 695283..696383 of Streptococcus_suis
+RIDLKEISMAYVVAVVGATGAVGAQMIKMLEESTLPIEKVRFLASARSAGKTLQFKGQDI
+VIEETTETAFEGVDIALFSAGGSTSAKYAPYAVKAGAVVVDNTSYFRQNPDVPLVVPEVN
+AHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLERIIVSTYQAVSGAGMGAILETQAQL
+RSVLNDGVEPKAVEANILPSGGDKKHYPIGFNAIPQIDLFTENDYTYEEMKMTKETKKIM
+EDDSIAVSATCVRIPVLSAHSESVYIETKEIAPIDEVKAAIASFPGAVLEDDVANQIYPQ
+AINAVGSRDTFVGRIRKDLDKENGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAE
+LKFELK
+>Streptococcus_suis|ORF1201 length 144 aa, 435 bp, from 842957..843391 of Streptococcus_suis
+FQTIKEKSRLMNIKKLILTLLTLTLTIVPCACGNQSNSNDSQLSGTYSYEKGGIDGSEMG
+FEDEELTLHYELKVSGDENILNINLLSERGNNVKYLYSEKVTIDTDKQIISDSNGTELEY
+SVSGDSVTIPDLAGDSGETVTLKR
+>Streptococcus_suis|ORF1202 length 343 aa, 1032 bp, from 843537..844568 of Streptococcus_suis
+VKVMYIFETTEQNNSKANDFETKSLLYLMSFKSDSTDIDTFFVDCFNDITGASSDLLKLW
+DVQAKNISSLRPKTIGKSLITLFQNFISSVDFYEYILFIPKLKENYLMDISLTEFKIDNF
+KDIAKIQEGLEEEYKRRKKLGALNLKQLSQLNTFLEQIHFVTGDSSKAIYIKNIIQFKSN
+IRDDNFFESVFNEVRSKQTELKNINIHNISINSIEEVLKLNKHLTKRQLETLVVNRIIGV
+ELFKQRIPNDFFDVINDKSSSDRKDIIQDCNANLSRLLFDKNSNKKKFWSLLEQILILVE
+EKDDIYQILNRIKQYQIPKIINDDYTLLYLISMVKEGMEENAC
+>Streptococcus_suis|ORF1401 length 409 aa, 1230 bp, from 991071..992300 of Streptococcus_suis
+GDNMKYPTLLDRFLVYVKENTRSDENSTTTPSTQNQVEFAQNILLPEMERIGLQNVHYLP
+NGFAVGTLPANDPSLTRKIGFIAHMDTADFNAEGVNPQIIENYDGNPIALGTSGYELHPK
+DFPQLANYHGQILITTDGTTLLGSDDKSGIAEIMTAIEFLIQNPDIKHCEIRVGFGPDEE
+IGVGADKFDVKDFDVDFAYTMDGGPLGELQYETFSAAGAKIDFLGRNVHPGSAKDQMINA
+FQMAIDFHNALPETDRPEKTEGYEGFFHLMNMEGSVDTASTTYIIRDFEEEDFQARKQLM
+LDIAEKMNANFDTPRVIVNLHDQYYNMKKIIEKDMTPINIAKDVMENLGIKPLIEPVRGG
+TDGSKISFMGIPTPNIFAGGENMHGRFEFVSLETMEKAVDVILGIVAYK
+>Streptococcus_suis|ORF1402 length 144 aa, 435 bp, from 992392..992826 of Streptococcus_suis
+YNRTIKKKWSFIMTEETLAQGILIGIWGTTLLFSFIWYILVAISNYILFKKAGYAGWKSL
+IPIYNLYIQQCITFGYEKRWFILFLLIPLAGPLYGIYLVYNFGRSFGLSAVQAIFYVLLT
+PIFNLYIAFNDGSRYQGPQEFFID
+>Streptococcus_suis|ORF1601 length 141 aa, 426 bp, from complement(1127307..1127732) of Streptococcus_suis
+VHPLHGRSLLIYFDCFAYEGGGIMTIQALAMFLASLGFLYFIFRNINKNKILFEHAFMWI
+VIGFGLIVFALFDVIPIKLAYLFGFGLTSNFLLSVAIFVLLVIGFLHSMALSQQKQQIKN
+LIQEVSMAKKRISELEEHHAE
+>Streptococcus_suis|ORF1602 length 241 aa, 726 bp, from complement(1127663..1128388) of Streptococcus_suis
+REKMKVLMIIPAYNEEESILQTVQGIIDYKNSVNFQLDYVVINDGSTDSTKEILIQNKLN
+AVHLVQNLGIGGAVQTGYKYALDNDYDVAVQFDGDGQHDIRSLNGLIQPILVGQADMVIG
+SRFVGDTLSEFQTSFMRRFGIGVISNMIKLTTGNRIWDTTSGYRLGNRKVIAQFAKRYPI
+KYPEPESTVHLLKQNFQVVEAPANMFERAGGVSSITPFKSIRYMVEVCSSILIASLMKEG
+E
+>Streptococcus_suis|ORF1801 length 128 aa, 387 bp, from 1263312..1263698 of Streptococcus_suis
+RLHDSCSICFLFIHGNIAGNRPCKEIGILQNNPHVTAQAFTRIITDVFPINQYTSLLWII
+ETIEEIHNRRLTRPSMPNQSNCFSFFCSNGNIFQNWSVFFIAKVHVFKHDLPLFNFQNTI
+TVVLQLFF
+>Streptococcus_suis|ORF1802 length 578 aa, 1737 bp, from complement(1264661..1266397) of Streptococcus_suis
+RRYMFRLIFDYIKRHKWLYLLVAVTLIIYDATLLLPTQIIQRMVDILTKNELTQAILVQE
+MTLLLLVTVLNYATAFIWHLKLFQASVNFKFDMQQRAFKKLVTMRTPFYEKFRSGDVMTR
+FSTDVDGLMEMVGYGLMIVVYAGGMLAFIIPTMFFIDWKISLVALLPMLFMTLCIFFIGR
+KQDKAIDANREAVAQLNNEVLEVIEGIRVTRAYSKKANQKAQFQARTKQLAQGGDRITSL
+QSLYNPLATVCLGLSTIFVLLMGAQAVKAGQLTLGQVIALQLYVGSLLEPFWTLADFILV
+YQTGKTSFEKLQELIETGDDLEADGSKEIAELSSISFKNYSFSYPQAERASLQDINWTLK
+AGQTVGIVGKTGSGKTTLVRQFLRQYPIGQGNFFINHQSILDFKRSSIEEKIGYVPQEHI
+LFSRSVGENIALGKVASSSEEIEQAIATAAFSQDLKRMSDGLDTMIGERGVSISGGQKQR
+ISIARAFLREPDLLILDDSLSAVDARTERQIIQNIQKERAGKTNVIVTHRLSAVNHADWV
+LVLDEGRIVEEGRPADLLAQRGWYYEQYQRQQSQEGGE
+>Streptococcus_suis|ORF2001 length 415 aa, 1248 bp, from complement(1398025..1399272) of Streptococcus_suis
+EDFIMKMKTFLKCASVCAFASFLVACGNASSSDKVEIEYFSQKPEMQATLQEIIDDFEKE
+NPTIDVKFSNVPDAGTVLKTRMANNEAPDVINIYPQNADFKAYAADGRFLEIGDDAGLNH
+LKDGAVTPYLVNEKNYTLPLTANAYGIYYNKDKFKELGLEVPTTYAEFVALVDKIKADGS
+AAPFALSLNDAWSLNGYHQLAWVTVAGGFDGAEDILIRSAKGAIQDDATTKAVLERLQLL
+KDNGQKGATGALYADAVAAFAAGDALMLPQGTWAATAVNQQEPEFEYGMFTFPGDKEGGD
+YTIGAADLALSISADTEHPEESKKFLEYLSRPEVIQKYYDVDGSPTSVEGVDTEGKFEET
+AGVTQYAFTDKHVVWLQSEWESEEEFWNITVEMVKNPNSAELVKKLNAFFDPMKK
+>Streptococcus_suis|ORF2002 length 732 aa, 2199 bp, from complement(1399273..1401471) of Streptococcus_suis
+DHKEEIGEMNVIEIYNEKQIFHLKTREFSYIIQVLETGDLVHRYFGKKIEKFSDGNKITY
+LDRSFSPSPITGDRTYSLDVLPLEYSSNGLGDFRTSALDVRNEFGVTLDLKYKEYRLYKG
+KKELRGLPASFGNQEEVESLEIDLYDQLTDITVTLQYSVFEEASYLARSATIQTGKYPCK
+LEKVLSATLDFPHQDFIVHSLAGRYAYEKEWTQTPLTKGQYSIGSIRGASSHSRTPFLAL
+VSPDASEDKGDVYAAHLVYSGNFTAFVETTAMETSRLGLGLESHYFSWQLDKDDRFQTPE
+VLLSYTDKGFTGMTQNSHHFITKHLIRSSFVNKPRPILINNWEATYFEFTEEKILQLAQV
+ASRAGIELFVLDDGWFGKRNNDESSLGDWKVNLDKLPNGLNGLAERINELGMKFGLWFEP
+EMISIDSDLYREHPDWAIRTEGRLPIYSREQLVLDLTKQEVCDYIIDSVSSILESANISY
+VKWDMNRNITNIPEGLANDQRFEFHHRYMLGLYRVLDHLTKRFPDILFESCAGGGGRNDL
+GIMYYMPQAWASDDTDAIERLSIQEGTSLIYPPSSIGAHVSAVPNHQVGRITPLATRGNV
+AMMGGAFGYELDLTKLSEKELDEISQQIETYHSIRETIQFGQLYRLKKTSNTWAANYVSQ
+DKNQVVFTFVKILAKPEAPLLHVRLKGLDPDALYECPQLGETFYGDELMNIGLTMPHVQK
+DYFSVQYIFNKI
+>Streptococcus_suis|ORF2201 length 272 aa, 819 bp, from complement(1531599..1532417) of Streptococcus_suis
+DCSKIKIIDLAVGKLKLLSSKRKGAFMEIIRSKANHLVKQVKKLQQKKYRTSSYLIEGWH
+LLEEAMEAGANIEHIFVVEEYFEKVAGLANVTVVSPEIMQELADSKTPQGVVAQLALPSQ
+RLPETLDGKFLVLEDVQDPGNVGTMIRTADAAGFDGVFLSDKSADIYNMKVLRSMQGSHF
+HLPVYRMPISSILTALKSNQIQILATTLSSQSVDYKEITPHSSFALVMGNEGQGISDLVA
+DEADQLVHITMPGQAESLNVAIAAGILLFSFI
+>Streptococcus_suis|ORF2202 length 101 aa, 306 bp, from 1532445..1532750 of Streptococcus_suis
+MSCQKEKLMRKVKMIASGRVQGVGFRWSVQFLAVEIGDIYGRVWNNDDGTVTILAQSDNA
+EKLSHFIHEIRKGPSRMAKVIYLDVTLANFEDYKDFQVSYR
+>Streptococcus_suis|ORF2401 length 141 aa, 426 bp, from 1658030..1658455 of Streptococcus_suis
+ASITVPIARTVGSAFSSWISATKRTVSNNSSMFWLNLAEISTNSDSPPQAVEITPCSANS
+PMTRSGFAPGLSILLIATMIGTLAAFEWLIASIVCGMTPSSAATTRMVKSVTDAPRARIE
+VKAACPGVSKKVIFLPASSIW
+>Streptococcus_suis|ORF2402 length 266 aa, 801 bp, from 1658515..1659315 of Streptococcus_suis
+GVQQGCFTMVNVSHDSHNRWAFCHLFFIEVALFYEETLNICVIDLYLFFRFNTIINHEEF
+DSISIQRLVLSRHNSHKEEFFHNFSRFTFDSFCNFCDGHASSIFKFSWQFVELAFCDRFG
+RLVSLAFFIFLVVIPVTCSLISHLILTISISLLFPWTIFFVTIKVTFFIWSSLFLTTGIY
+SSFCNLLWYRCNKCRFHKWFAFHNRFFKLNFFWLLRLLFSFLSLTKTFFTGTSILRILFC
+FQSSSTRFEVNFRSCWFCSLSLFKAS
+>Streptococcus_suis|ORF2601 length 100 aa, 303 bp, from 1790150..1790452 of Streptococcus_suis
+LKDGYQRLVVEGFADIAETFLQTETNLMTTVIFIARHDDDRPIAFPLGSLNQVNMTLVHG
+SKGPKNNCYCLFHNLPFYCFLYFISYSFLKPKSRVFYIFL
+>Streptococcus_suis|ORF2602 length 823 aa, 2472 bp, from complement(1790482..1792953) of Streptococcus_suis
+ERGVVRMKISRGLQGVYEDAQLIAQRYSSDYLETWHLLLAFVINPDTVAGAILAEYPADV
+LDYERAVYMVMGRRYHEELESFFFLPSSKRVKELQVFAEKIAEIVKSKGLGTEHIFMGML
+LDKRSTASQILDQVGFHFEDSDDKVRFLDLRKNLEAKAGFTKEHLKAIRTMTKGGKPKQA
+TVGNMMGMTQSQSGGLEDYTRDLTALARSGQLEPVIGRDEEISRMLQILSRKTKNNPVLV
+GDAGVGKTALALGLAQRIANGEVPASLVNMRILELDLMNVIAGTRFRGDFEERMNNIIND
+IEEDGRVILFIDELHTIMGSGSGIDSILDAANILKPALSRGTLRTVGATTQDEYQKHIEK
+DAALVRRFAKVTIEEPSVADSVAILQGLKPAYEAHHKVTISDQAVVTAVAYAKRYLTSKN
+LPDSAIDLLDEASATVQNRAKGQVEEGGLTALDQALMAGKYKTVTQLLLKAQEAENQATS
+YSLEVTEEDILATLSRLSGIPVTKLSQTDAKKYLNLEQELHKRVIGQEEAISAVSRAIRR
+NQSGIRTGHRPIGSFMFLGPTGVGKTELAKALAEILFDDESALIRFDMSEYMEKFAASRL
+NGAPPGYVGYEEGGELTEKVRNKPYSVLLFDEVEKAHPDIFNVLLQVLDDGVLTDRKGRK
+VDFSNTVIIMTSNLGATALRDDKTVGFGALDLSKSQEHVEKRIFEALKKAYRPEFINRID
+EKVVFHSLTEADMQDVVKVMVKPLIAVAASKGITLKLQASALKLLAKEGYDPEMGARPLR
+RLLQTKLEDPLAEMLLRGELPAGVTLKVGVKAEQLKFDSVKAG
+>Streptococcus_suis|ORF2801 length 1006 aa, 3021 bp, from complement(1921434..1924454) of Streptococcus_suis
+TQTKEYEMIEFRKKAVQLASLMSVFFLCTYSFTDAMYIMAESLSTDGASTIRRTYIEDKK
+EDKDRLNIELVESLSSPKTIGQKITIDKQSLATQNFNEKGIVVITQKGLELKKDDLEKGW
+KLDESYNEKDLAITKSETEKRSLSNELDVLSKTVEELPVYGENYHSYRLLPTTELDYSAD
+NVSLTLSFTKVSEVIKGELVAVVDAEHIAYFKAEPSVFKEYSQVNEKPSSTEDVNVVSPS
+QDPPVSETKENVPDNPESQGSSTVPESEQAVDALVEQRGVICIKLTKSSSEQEEGIEDTE
+NEAIEGATFEVRNVESENLVYTGQTDKDGLLTISNLPLGNYAVIQKSTIDGYEISATKEV
+VELTVAQSRQTVSISNSPKNPLEGLMLNSILDSSLIPRSARVARSLLDTSLLDNPTVTGN
+ANATTTTTVFGNKTTTITREESNIKYIFKPITISIPGVYQSYSQDGVLKKKEVVVDSNTN
+TTKIIWEYTTTVGGVNSNITSIRNAFSTTTDSGLGEPKITSIMKDGVAITPNTTYYGNFD
+NFKSATDNLPVGNGTYVYTIETPVVIPSDNYSLDYRSEVTVDAPKGSKLTYNGTSVTLTQ
+KETRTLSTADTITLPAKNDGGPLGDLKVDTVNTSNTNRTIGKYRDNDDKVIEWTSSQLND
+TSTTQSFTFDVALDSSQAAHEYKVYIYEPSNGTYTETKAEKVATPGNQITVDNVPAGAVA
+LVKTVTNVKDEKVNHTISGAQLEALKGDIKIQKNWEADSDKVDVTFTVNGGSLTNRKETL
+SANNTQITIANVDKFSGMRSTATKKRIYYDVTEAVPSGYILSSAQTDWENLYYVFTNKKD
+NTTTPVFPPDTCGNYGVSSIDLVSINYVMYKSGSKIWGGFDGSMKMNLKIPAFARAGDSF
+TLELPPELKLSHVANPNVAWSTVSANGKVIAKVYHEKDNLIRFVLTTEAYSVQEYNGWFE
+IGVPTSNVIKINNRETTELYKTGVLPNLPEWYTTTTRNQTLIKRSR
+>Streptococcus_suis|ORF2802 length 252 aa, 759 bp, from complement(1925855..1926613) of Streptococcus_suis
+LEARMQQYFVNGRAPQGMFQISDKDTAKHMFSVMRLQAGDQIVLVFDDGIKRLARVVDSQ
+SQSVEIIEELTDNVELPISVTIAMGFPKGDKLEFVAQKATELGMSALWAFPADWSVVKWD
+GKKLAKKAEKLEKIAQGAAEQSKRNRIPAVRLFEKKSDFLAQLAGFDQIILAYEEAAKEG
+EQANLVKILSGLEIGQSVLVIVGPEGGVSPEEVAAFEGAGAVKTGLGPRILRAETAPLYA
+LSTISYATELLR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta	Fri Nov 28 11:45:37 2014 -0500
@@ -0,0 +1,194 @@
+>Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis
+MNQEQLFWQRFIELAKVNFKPSIYDFYVADAKLLGINQQVANIFLNRPFKKDFWEKNFEE
+LMIAASFESYGEPLTIQYQFTEDEQEIRNTTNTRSSIVHQVQTLEPATPQETFKPVHSDI
+KSQYTFANFVQGDNNHWAKAAALAVSDNLGELYNPLFIFGGPGLGKTHILNAIGNKVLAD
+NPQARIKYVSSETFINEFLEHLRLNDMESFKKTYRNLDLLLIDDIQSLRNKATTQEEFFH
+TFNALHEKNKQIVLTSDRNPDHLDNLEERLVTRFKWGLTSEITPPDFETRIAILRNKCEN
+LPYNFTNETLSYLAGQFDSNVRDLEGALKDIHLIATMRQLSEISVEVAAEAIRSRKQTNP
+QNMVIPIEKIQTEVGNFYGVSLKELKGSKRVQHIVHARQVAMFLAREMTDNSLPKIGKEF
+GNRDHTTVMHAYNKIKTLLLDDENLEIEITSIKNKLR
+>Streptococcus_suis|ORF101 length 112 aa, 339 bp, from complement(72006..72344) of Streptococcus_suis
+LQFNFYVYTTWKIQFHQSVNCFLSWVDDVDQTFVCTHFELLTRIFVLVSRTDDCVEATFC
+WKWNWTCYLSTCTCCSFNDFCSCCIKCTVFVRFQADANFFVCHLFLLFVYLT
+>Streptococcus_suis|ORF201 length 360 aa, 1083 bp, from complement(128035..129117) of Streptococcus_suis
+SCHGGRRMTLFGKIKEVTELQSLPGFEGQVRNHIRQKITPHVDRIETDGLGGIFGIKDTA
+VENAPRILVVAHMDEVGFMISQIKPDGTFRVVELGGWNPLVVSSQAFTLQLQDGRTIPAI
+SGSVPPHLSRGANAPGMPAIADIIFDAGFANYDEAWAFGVRPGDVLVPKNETILTANGKN
+VISKAWDNRFGVLMVTELLESLSGHALPNQLIAGANVQEEVGLRGAHASTTKFNPDIFLA
+VDCSPAGDIYGDQGKIGDGTLLRFYDPGHIMLKNMKDFLLTTAEEAGVKFQYYCGKGGTD
+AGAAHLKNHGVPSTTIGVCARYIHSHQTLYSMDDFLEAQAFLQTIVKKLDRSTVDLIKNY
+>Streptococcus_suis|ORF301 length 105 aa, 318 bp, from complement(191714..192031) of Streptococcus_suis
+NQGQTVRFFHIRGNFCQKFIIGNTCGSCQMQFIPNIVLDKLGNLNRRADAQLIFCYIQVS
+LIDRHGLHQISIAMENFSNLSPNFLIFFIIARNENRLRTTLISLF
+>Streptococcus_suis|ORF401 length 120 aa, 363 bp, from 265643..266005 of Streptococcus_suis
+TTGTTSPIAPKWKASSKSLRVPTSEPTTLIPSSTVFTILRSMYSDGSPTATTYPPARTLS
+IAWLKATLETAVTTVECTPPPVISLIYPGTSSTSSPLIVTSAPTSLASSNLSLLMSTAIT
+>Streptococcus_suis|ORF501 length 104 aa, 315 bp, from 336857..337171 of Streptococcus_suis
+KDLIRKSSLLVYKLFSPSRTMSKSIVAWRMIYSDEDPIRRRSKAFRPVAPSNIRSAPVSF
+GISIASRVLGLPNSMRICTSVRPALRASCLYSSRRSSASLSKDS
+>Streptococcus_suis|ORF601 length 665 aa, 1998 bp, from 409896..411893 of Streptococcus_suis
+VMIQIGKIFAGRYRIVRQIGRGGMADVYLARDLILDGEEVAVKVLRTNYQTDQIAIQRFQ
+REARAMAELDHPNIVRISDIGEEDGQQYLAMEYVNGLDLKRYIKENAPLSNDVAVRIMGQ
+ILLAMRMAHTRGIVHRDLKPQNVLLTSNGVAKVTDFGIAVAFAETSLTQTNSMLGSVHYL
+SPEQARGSKATIQSDIYAMGIILFEMLTGRIPYDGDSAVTIALQHFQKPLPSVREENANV
+PQALENVVLKATAKKLNERYKSVAEMYADLASALSMDRQNEPRVELEGNKVDTKTLPKLS
+QANVETKVPHTNSSAQVSATDKGSGKKEVAKSGNKPVSKPRPGIRTRYKVLIGAILLTVI
+AAGLMFFNTPRTVTVPDVSGQTVEKATEMIEVAGLEVGNITEEATATVDEGLVIRTSPAA
+KTTRRQGSKIDIVVATAALASIPDVVDKESDTARQELEALGFQVTIKEEYSEKVAQGLVI
+KTDPGANSSAEKGAKITLYVSKGVAPQVVPNVVGKSQENATQILQTAGFSIGTITQEYSS
+SVTAGQVISTDPVANTELAKGSIINLVISKGKELIMPDLTSGNYTYSQARSQLQALGVNA
+ESIEKQEDRSYYSTTSDIVIGQYPAAGATIDGTVTLYVSVASTRTSSDSSAGSSTSTSTS
+TGSGQ
+>Streptococcus_suis|ORF701 length 182 aa, 549 bp, from 489284..489832 of Streptococcus_suis
+LGKSVALSSLSRVTIYRGENLGKLRFFVAYLTSRYIIDIQNEGRMNMNIKEVSDVTGLSA
+DTIRYYERVGLIPKIARKSSGVRDFVENDVAVLEFVRCFRSAGMSIERLIEYMGLVQAGD
+STVEARIDLLKEEREVLQSRLSKIQQALERLDYKIENYQTILRGAENQLFTDGSGSCKKD
+RE
+>Streptococcus_suis|ORF801 length 428 aa, 1287 bp, from 561960..563246 of Streptococcus_suis
+KSSRDCESCLLLFVILKVMQADRRKTFGKMRIRINNLFFVAIAFMGIIISNSQVVLAIGK
+ASVIQYLSYLVLILCIVNDLLKNNKHIVVYKLGYLFLIIFLFTIGICQQILPITTKIYLS
+ISMMIISVLATLPISLIKDIDDFRRISNHLLFALFITSILGIMMGATMFTGAVEGIGFSQ
+GFNGGLTHKNFFGITILMGFVLTYLAYKYGSYKRTDRFILGLELFLILISNTRSVYLILL
+LFLFLVNLDKIKIEQRQWSTLKYISMLFCAIFLYYFFGFLITHSDSYAHRVNGLINFFEY
+YRNDWFHLMFGAADLAYGDLTLDYAIRVRRVLGWNGTLEMPLLSIMLKNGFIGLVGYGIV
+LYKLYRNVRILKTDNIKTIGKSVFIIVVLSATVENYIVNLSFVFMPICFCLLNSISTMES
+TINKQLQT
+>Streptococcus_suis|ORF901 length 241 aa, 726 bp, from 628396..629121 of Streptococcus_suis
+NSPMRLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKVAL
+EGSAYYLLHKPAGVVSAVTDQEHQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGP
+LGYRMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSR
+ATIKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGTYRQLTPNEMEHLFTYF
+D
+>Streptococcus_suis|ORF1001 length 374 aa, 1125 bp, from 694014..695138 of Streptococcus_suis
+HYLLFQGGILMKVFASPSRYIQGKHVLFQGAEAIGKLGTKPLILCDDLVYGIIGEKFLSY
+LVEEGMQVHRVAFNGEASDKEIQRVVEIGKEQASDVVIGLGGGKTIDSAKAIADLLGVPV
+VIAPTIASTDAPTSALSVIYSEEGAFERYIFYKKNPDLVLVDTAIICQAPPRLLASGIAD
+GLATWVEARAILQSNGTTMAGGGQTLAGIAIAQTCEQTLFEYGLQAMASCEAKVVTAALE
+NIVEANTLLSGLGFESAGLAAAHAIHNGFTALEGDIHHLTHGEKVAYGTLTQLFLENRPK
+EELEKYIRFYQALNLPTTLEELHLADASYEELLKVGQQATIEGETIHGMPFAISAEDVAE
+ALMAVDYYVRSLDK
+>Streptococcus_suis|ORF1101 length 124 aa, 375 bp, from complement(764791..765165) of Streptococcus_suis
+IQAFWHEEIGHALLVFSLGRKLHHPQPDDQYKPCGREFGEFVLFPRSIPPKCSHQNAPEP
+ENVSPLLSLWQSPLVSCGLFQNDQSAPQLLRDRLVDCRVQWPNTYEGISYLSIQQQALYG
+HHRF
+>Streptococcus_suis|ORF1201 length 144 aa, 435 bp, from 842957..843391 of Streptococcus_suis
+FQTIKEKSRLMNIKKLILTLLTLTLTIVPCACGNQSNSNDSQLSGTYSYEKGGIDGSEMG
+FEDEELTLHYELKVSGDENILNINLLSERGNNVKYLYSEKVTIDTDKQIISDSNGTELEY
+SVSGDSVTIPDLAGDSGETVTLKR
+>Streptococcus_suis|ORF1301 length 750 aa, 2253 bp, from 915023..917275 of Streptococcus_suis
+FSEYDILGQLFYNRRSMEMKKKLLMLLASILPVFFIFTGIKADDTIDVVFDNAYAPFEFK
+DSDQIYKGLDVDIINEVAKRSGWTMNQSFPGFDAAVNAVQAGSADALMAGTTITEARKKV
+FTFSDPYFDTKIVIATTKANTISSYKDLKGKTVGVKNGTAAQNFLEENKDKYGYNVKTFD
+TGDLMYNSLSAGAVDAVMDDEAVIQYAIQQGQDLSIDIEGEAIGSFGFSVKKGSQYEYLV
+EDFNKALAEMKKDGTYEIIMNKWLGASTTSTESTDYSSRLSLTGNASAKATPVKSSYTIV
+ADSSFAPFEYQDESGNYVGIDMELIKAIAEHQGFTITIQNPGFDAALNAVQAGQADAVIA
+GMSITDARKEIFDFSNAYYTSNILLAVKNGSDIASYEDLKGKTVGAKNGTASYSFLEENK
+SKYGYTLKAFDEASSMYDSLNSGSIDALMDDEAVLLYAIQQGRNFATPIPGEKSGEYGFA
+VKKGANPELIEMFNNGLAALVESGKYDEILNKYFNSTEEASTTTSTVDETTIVGLLKNNY
+GQLLSGLGITIGLALLSFAIAIVIGIIFGMFAVSPVKALRVTSSVFVDVVRGIPLMIVAA
+FIFWGIPNLIESMTGQQSPINDFVAGTIALSLNSGAYIAEIVRGGIQAVPAGQMEASRSL
+GISYGTTMRKIILPQAGKIMLPNFINQFVITLKDTTIISAIGLVELFQAGKIIIARNYQS
+FRMYAILAIIYLVVITLLTRLARKLEKGGK
+>Streptococcus_suis|ORF1401 length 409 aa, 1230 bp, from 991071..992300 of Streptococcus_suis
+GDNMKYPTLLDRFLVYVKENTRSDENSTTTPSTQNQVEFAQNILLPEMERIGLQNVHYLP
+NGFAVGTLPANDPSLTRKIGFIAHMDTADFNAEGVNPQIIENYDGNPIALGTSGYELHPK
+DFPQLANYHGQILITTDGTTLLGSDDKSGIAEIMTAIEFLIQNPDIKHCEIRVGFGPDEE
+IGVGADKFDVKDFDVDFAYTMDGGPLGELQYETFSAAGAKIDFLGRNVHPGSAKDQMINA
+FQMAIDFHNALPETDRPEKTEGYEGFFHLMNMEGSVDTASTTYIIRDFEEEDFQARKQLM
+LDIAEKMNANFDTPRVIVNLHDQYYNMKKIIEKDMTPINIAKDVMENLGIKPLIEPVRGG
+TDGSKISFMGIPTPNIFAGGENMHGRFEFVSLETMEKAVDVILGIVAYK
+>Streptococcus_suis|ORF1501 length 100 aa, 303 bp, from 1057210..1057512 of Streptococcus_suis
+RYETCSFIRSAAIVYWIRSFVPIEKKSTSLANWSASIAAAGISIMIPTWISSATATPSAN
+KFAFSSSRIAFAARNSVNKATIGNMIRSLPCTDERRRARN
+>Streptococcus_suis|ORF1601 length 141 aa, 426 bp, from complement(1127307..1127732) of Streptococcus_suis
+VHPLHGRSLLIYFDCFAYEGGGIMTIQALAMFLASLGFLYFIFRNINKNKILFEHAFMWI
+VIGFGLIVFALFDVIPIKLAYLFGFGLTSNFLLSVAIFVLLVIGFLHSMALSQQKQQIKN
+LIQEVSMAKKRISELEEHHAE
+>Streptococcus_suis|ORF1701 length 153 aa, 462 bp, from complement(1195146..1195607) of Streptococcus_suis
+ESFFFGEYPYLVYNGLNTCSYNAKEVFKMIQSIGQVMLYVNDIEASAQFWKEKMGFERVE
+KQVQGPQTSYIIAPKSDSEVQFVLHDKAEVAEMEPELNLGTPSILMTSVDVAKTYEELVE
+RGVTTNPVMDLGFMKVISFADNDGNYYAIREVK
+>Streptococcus_suis|ORF1801 length 128 aa, 387 bp, from 1263312..1263698 of Streptococcus_suis
+RLHDSCSICFLFIHGNIAGNRPCKEIGILQNNPHVTAQAFTRIITDVFPINQYTSLLWII
+ETIEEIHNRRLTRPSMPNQSNCFSFFCSNGNIFQNWSVFFIAKVHVFKHDLPLFNFQNTI
+TVVLQLFF
+>Streptococcus_suis|ORF1901 length 276 aa, 831 bp, from 1325729..1326559 of Streptococcus_suis
+PAGSTPSRWKGDEIMVYTSLKSPEKDYTYDLHIAHLYGDLMNTYGDNGNILMLKYVAEKL
+GARVQVDIVSLTDEFDKNFYDIAFFGGGQDYEQSILAKDLPTKKDSLADFIENDGVMLAI
+CGGFQLLGQYYIEAGGRKIDGLGIMGHYTLNQTNNRYIGDIKIHNDEFNETYYGFENHQG
+RTFLADNQKPLGKVVYGNGNNKEDGGEGLHYKNTFGSYFHGPILSRNANLAYRLVTTALR
+KKYGQDIQLASYADILSKEVAEEYGDVKSKAEFDTQ
+>Streptococcus_suis|ORF2001 length 415 aa, 1248 bp, from complement(1398025..1399272) of Streptococcus_suis
+EDFIMKMKTFLKCASVCAFASFLVACGNASSSDKVEIEYFSQKPEMQATLQEIIDDFEKE
+NPTIDVKFSNVPDAGTVLKTRMANNEAPDVINIYPQNADFKAYAADGRFLEIGDDAGLNH
+LKDGAVTPYLVNEKNYTLPLTANAYGIYYNKDKFKELGLEVPTTYAEFVALVDKIKADGS
+AAPFALSLNDAWSLNGYHQLAWVTVAGGFDGAEDILIRSAKGAIQDDATTKAVLERLQLL
+KDNGQKGATGALYADAVAAFAAGDALMLPQGTWAATAVNQQEPEFEYGMFTFPGDKEGGD
+YTIGAADLALSISADTEHPEESKKFLEYLSRPEVIQKYYDVDGSPTSVEGVDTEGKFEET
+AGVTQYAFTDKHVVWLQSEWESEEEFWNITVEMVKNPNSAELVKKLNAFFDPMKK
+>Streptococcus_suis|ORF2101 length 366 aa, 1101 bp, from 1460501..1461601 of Streptococcus_suis
+SLRRITMKSKFPSSWTDQLTLLGFEDFTPIQVQAFEPIANGKSLLAISPTGTGKTLAYLW
+PSLLALTPKKAQQLLILAPNTELAGQIFEVCKTWSETIGLTAQLFLSGSSQKRQIERLKK
+GPEILIGTPGRIFELIKLKKIKMMNINTIVLDEFDQLFSDSQYQFVEKIINYVPRDHQLI
+YMSATAKFDRQKIAEDIESIDLSEQKLDNIQHCYMMVDKRERLETLRKFANIPDFRALAF
+FNSLSDLGASEDKLLYNGVNAVSLVSDVNVKFRKVIIERFKNHELNLLLATDMVARGIDI
+DNLECVLNFEVPFDQEAYTHRSGRTGRMGKEGLVITLVSSPSELKQLKKYASVQEVILKN
+QELYKI
+>Streptococcus_suis|ORF2201 length 272 aa, 819 bp, from complement(1531599..1532417) of Streptococcus_suis
+DCSKIKIIDLAVGKLKLLSSKRKGAFMEIIRSKANHLVKQVKKLQQKKYRTSSYLIEGWH
+LLEEAMEAGANIEHIFVVEEYFEKVAGLANVTVVSPEIMQELADSKTPQGVVAQLALPSQ
+RLPETLDGKFLVLEDVQDPGNVGTMIRTADAAGFDGVFLSDKSADIYNMKVLRSMQGSHF
+HLPVYRMPISSILTALKSNQIQILATTLSSQSVDYKEITPHSSFALVMGNEGQGISDLVA
+DEADQLVHITMPGQAESLNVAIAAGILLFSFI
+>Streptococcus_suis|ORF2301 length 102 aa, 309 bp, from 1597247..1597555 of Streptococcus_suis
+IDVIKDASEIFHSIPIEFYIGVKMIENRLVVTRYNLTVINFGYQSCPGIFRLDGIPKVRS
+CIFQMLYQVIPNCFSRIGILNSFSWSRTDNFIFHQETLLMLR
+>Streptococcus_suis|ORF2401 length 141 aa, 426 bp, from 1658030..1658455 of Streptococcus_suis
+ASITVPIARTVGSAFSSWISATKRTVSNNSSMFWLNLAEISTNSDSPPQAVEITPCSANS
+PMTRSGFAPGLSILLIATMIGTLAAFEWLIASIVCGMTPSSAATTRMVKSVTDAPRARIE
+VKAACPGVSKKVIFLPASSIW
+>Streptococcus_suis|ORF2501 length 630 aa, 1893 bp, from complement(1722511..1724403) of Streptococcus_suis
+GEMMMLQINHSLRQSEGVLEEICSSLGLDCQLELEVGGKESLRIEGSAGSYRIRAPKEHM
+IYRGLLVLASQLAQGETDIQILERPAYRQLGFMEDCSRNAVLTVEASKILIRQLALIGYS
+HFQLYMEDTYQLRDEPYFGYFRGAYTKEELQAIEEECHRYGMEFIPCIQTLAHLIAYLKW
+NISSIQAIRDVDNILLIGDERTYALIDKMFEALSHLKTRTINIGMDEAHLVGLGQYLNQH
+GYQKRSLIMCQHLERVLDIADKYGFHCSMWSDMFFQLLTASKDYTGQLEIDSEIQAYLDR
+LKDRVTLIYWDYYQTSRESYGQKLASHQQLGDQIAFASGAWKWIGFTPDNDFSMRIAPKA
+HAACQEYGVQEVTVTAWGDNGGECATFSILPSLHAWAELQYRGNLGCLAEHFYQLHQVSL
+DDFLQLDLPNKTPSHPGPGHHGFNPSRYILYQDILCPLLQEHIDAEKDNAFYQELAPRLA
+EIGSRAKGYAYLFDTQAKLCQVLATKAAISVGIRQAYQEGNRQVLAEKVDGLQQLRIDLE
+SFYQALSYQWMVEKKVFGLDTVDIRLGGLDARIRRAIQRLQAYLNNEVPKLDELEVPILP
+YDDFHQDKGFIATTANQWQIIATASTIYTT
+>Streptococcus_suis|ORF2601 length 100 aa, 303 bp, from 1790150..1790452 of Streptococcus_suis
+LKDGYQRLVVEGFADIAETFLQTETNLMTTVIFIARHDDDRPIAFPLGSLNQVNMTLVHG
+SKGPKNNCYCLFHNLPFYCFLYFISYSFLKPKSRVFYIFL
+>Streptococcus_suis|ORF2701 length 215 aa, 648 bp, from 1851361..1852008 of Streptococcus_suis
+SLHPHEASHDNGKHDLHEVTHKGSKATDCLQVGFQHPGHQVERCKNRHVRDKHHQGLQDS
+KTIADKEVEVQEFIGYFLELGILIFFLYKRLNHTNPTEVFLSNTVHLVHEGLEFPKTWSH
+LPHDNCHNSHNQDHHENNHPPEFWHGPHCHDKGSDKQQWNPHQHCKEHHDKVLDLIDIVS
+HPNNQVPCVKLFDISIREALDLPKGLLTNICRYPL
+>Streptococcus_suis|ORF2801 length 1006 aa, 3021 bp, from complement(1921434..1924454) of Streptococcus_suis
+TQTKEYEMIEFRKKAVQLASLMSVFFLCTYSFTDAMYIMAESLSTDGASTIRRTYIEDKK
+EDKDRLNIELVESLSSPKTIGQKITIDKQSLATQNFNEKGIVVITQKGLELKKDDLEKGW
+KLDESYNEKDLAITKSETEKRSLSNELDVLSKTVEELPVYGENYHSYRLLPTTELDYSAD
+NVSLTLSFTKVSEVIKGELVAVVDAEHIAYFKAEPSVFKEYSQVNEKPSSTEDVNVVSPS
+QDPPVSETKENVPDNPESQGSSTVPESEQAVDALVEQRGVICIKLTKSSSEQEEGIEDTE
+NEAIEGATFEVRNVESENLVYTGQTDKDGLLTISNLPLGNYAVIQKSTIDGYEISATKEV
+VELTVAQSRQTVSISNSPKNPLEGLMLNSILDSSLIPRSARVARSLLDTSLLDNPTVTGN
+ANATTTTTVFGNKTTTITREESNIKYIFKPITISIPGVYQSYSQDGVLKKKEVVVDSNTN
+TTKIIWEYTTTVGGVNSNITSIRNAFSTTTDSGLGEPKITSIMKDGVAITPNTTYYGNFD
+NFKSATDNLPVGNGTYVYTIETPVVIPSDNYSLDYRSEVTVDAPKGSKLTYNGTSVTLTQ
+KETRTLSTADTITLPAKNDGGPLGDLKVDTVNTSNTNRTIGKYRDNDDKVIEWTSSQLND
+TSTTQSFTFDVALDSSQAAHEYKVYIYEPSNGTYTETKAEKVATPGNQITVDNVPAGAVA
+LVKTVTNVKDEKVNHTISGAQLEALKGDIKIQKNWEADSDKVDVTFTVNGGSLTNRKETL
+SANNTQITIANVDKFSGMRSTATKKRIYYDVTEAVPSGYILSSAQTDWENLYYVFTNKKD
+NTTTPVFPPDTCGNYGVSSIDLVSINYVMYKSGSKIWGGFDGSMKMNLKIPAFARAGDSF
+TLELPPELKLSHVANPNVAWSTVSANGKVIAKVYHEKDNLIRFVLTTEAYSVQEYNGWFE
+IGVPTSNVIKINNRETTELYKTGVLPNLPEWYTTTTRNQTLIKRSR
+>Streptococcus_suis|ORF2901 length 306 aa, 921 bp, from 1998013..1998933 of Streptococcus_suis
+IRDNRNCFYNTNQGEYMKERIKDFISVTLGSVVMAIGFNSFFLENNIVSGGVGGLAIALN
+ALLRWSPSDFVLYCNIPLLIICWFFLGKSVFIKTVYGAIIYPLCIKLTAGLPNLTENPLL
+AAIFGGIILGFGLGLVFLGNSSTGGTGILIQFIHKYTPLSLGLTMAIIDGIIVGLGFVAF
+DTDTVMYSIIALMTITYIVNRMMSGTQSSRNVMIISQKSEEIKDYITKVADRGVTELPII
+GGFTGVDKRMLMTTISIPEMQKLETAVLEIDETAFMVVMPASQVRGRGFSLQKDHKHYDE
+DILIPM
--- a/tools/get_orfs_or_cdss/README.rst	Wed Nov 20 12:06:24 2013 -0500
+++ b/tools/get_orfs_or_cdss/README.rst	Fri Nov 28 11:45:37 2014 -0500
@@ -31,21 +31,22 @@
 
 There are just two files to install to use this tool from within Galaxy:
 
-* get_orfs_or_cdss.py (the Python script)
-* get_orfs_or_cdss.xml (the Galaxy tool definition)
+* ``get_orfs_or_cdss.py`` (the Python script)
+* ``get_orfs_or_cdss.xml`` (the Galaxy tool definition)
 
-The suggested location is in a dedicated tools/get_orfs_or_cdss folder.
+The suggested location is in a dedicated ``tools/get_orfs_or_cdss`` folder.
 
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
 tool. One suggested location is in the filters section. Simply add the line::
 
     <tool file="get_orfs_or_cdss/get_orfs_or_cdss.xml" />
 
-You will also need to install Biopython 1.54 or later. If you want to run
-the unit tests, include this line in tools_conf.xml.sample and the sample
-FASTA files under the test-data directory. Then::
+You will also need to install Biopython 1.54 or later.
 
-    ./run_functional_tests.sh -id get_orfs_or_cdss
+If you wish to run the unit tests, also	move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    ./run_tests.sh -id get_orfs_or_cdss
 
 That's it.
 
@@ -68,6 +69,7 @@
         - Updated citation information (Cock et al. 2013).
         - Renamed folder and adopted README.rst naming.
 v0.0.6  - Corrected automated dependency defintion.
+v0.0.7  - Tool definition now embeds citation information.
 ======= ======================================================================
 
 
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.py	Wed Nov 20 12:06:24 2013 -0500
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.py	Fri Nov 28 11:45:37 2014 -0500
@@ -8,6 +8,9 @@
 minimum length (in amino acids), strand (both, forward, reverse), output
 nucleotide filename, and output protein filename.
 
+For more details, see the help text and argument descriptions in the
+accompanying get_orfs_or_cdss.xml file which defines a Galaxy interface.
+
 This tool is a short Python script which requires Biopython. If you use
 this tool in scientific work leading to a publication, please cite the
 Biopython application note:
@@ -19,7 +22,7 @@
 This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
 (formerly SCRI), Dundee, UK. All rights reserved.
 
-See accompanying text file for licence details (MIT/BSD style).
+See accompanying text file for licence details (MIT licence).
 
 This is version 0.0.3 of the script.
 """
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Wed Nov 20 12:06:24 2013 -0500
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Fri Nov 28 11:45:37 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.5">
+<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.7">
     <description>e.g. to get peptides from ESTs</description>
     <requirements>
         <requirement type="package" version="1.62">biopython</requirement>
@@ -168,4 +168,8 @@
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>
--- a/tools/get_orfs_or_cdss/tool_dependencies.xml	Wed Nov 20 12:06:24 2013 -0500
+++ b/tools/get_orfs_or_cdss/tool_dependencies.xml	Fri Nov 28 11:45:37 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.62">
-        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>