Mercurial > repos > peterjc > get_orfs_or_cdss

changeset 15:2eb9e86f5f35 draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/get_orfs_or_cdss commit e8aac97bf20ccd42402cace482c6d93b90cb3608
author peterjc
date Tue, 12 May 2015 11:27:35 -0400
parents 65d76ca44cd2
children e29fef81c126
files test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.sample_C10.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.xml
diffstat 6 files changed, 31 insertions(+), 598 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta	Mon Apr 06 05:21:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,119 +0,0 @@
->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|ORF291 length 760 aa, 2283 bp, from complement(184307..186589) of Streptococcus_suis
-KRGEFMRFNQFSFIKKETSVYLQELDTLGFQLIPDASSKTNLETFVRKCHFLTANTDFAL
-SNMIAEWDTDLLTFFQSDRELTDQIFYQVAFQLLGFVPGMDYTDVMDFVEKSNFPIVYGD
-IIDNLYQLLNTRTKSGNTLIDQLVSDDLIPEDNHYHFFNGKSMATFSTKNLIREVVYVET
-PVDTAGTGQTDIVKLSILRPHFDGKIPAVITNSPYHQGVNDVASDKALHKMEGELAEKQV
-GTIQVKQASITKLDLDQRNLPVSPATEKLGHITSYSLNDYFLARGFASLHVSGVGTLGST
-GYMTSGDYQQVEGYKAVIDWLNGRTKAYTDHTRSLEVKADWANGKVATTGLSYLGTMSNA
-LATTGVDGLEVIIAEAGISSWYDYYRENGLVTSPGGYPGEDLDSLTALTYSKSLQAGDFL
-RNKAAYEKGLAAERAALDRTSGDYNQYWHDRNYLLHADRVKCEVVFTHGSQDWNVKPIHV
-WNMFHALPSHIKKHLFFHNGAHVYMNNWQSIDFRESMNALLSQKLLGYENNYQLPTVIWQ
-DNSGEQTWTTLDTFGGENETVLPLGTGSQTVANQYTQEDFERYGKSYSAFHQDLYAGKAN
-QISIELPVTEGLLLNGQVTLKLRVASSVAKGLLSAQLLDKGNKKRLAPIPAPKARLSLDN
-GRYHAQENLVELPYVEMPQRLVTKGFMNLQNRTDLMTVEEVVPGQWMNLTWKLQPTIYQL
-KKGDVLELILYTTDFECTVRDNSQWQIHLDLSQSQLILPH
->Streptococcus_suis|ORF292 length 216 aa, 651 bp, from 185183..185833 of Streptococcus_suis
-AVGKDHLTLDPISVEQIIAVMPVLIVVTAGAVQGSTLGSQSFFVGCFIAEEVTCLQTLGV
-GQGGQAVQIFAWIATRAGHQPVFTVVVIPRGNPCFCDDDFQSVHASCCQGIGHGTEIRQS
-RRRYLTIGPIGLDLKRASVVCVGLGATVQPVNHRFIALHLLVVARCHVARRAQRANTRHM
-EAGKAASEEVVIEGVRSNVPQFFSSRADRQVPLVQV
->Streptococcus_suis|ORF583 length 391 aa, 1176 bp, from 397805..398980 of Streptococcus_suis
-RKKMKKQFELIATAAAGLEAVVGREIRNLGYECQVENGRVRFQGDVKSIIETNIWLRSAD
-RIKIIVGQFPAKTFEELFQGVFNLDWENYLPLGCKFPISKAKCVKSKLHNEPSVQAISKK
-AVVKKLQKHFSRPEGVPLQEMGAEFKIEVSILKDVATVMIDTTGSSLFKRGYRVEKGGAP
-IKENMAAAILQLSNWYPDKPLIDPTCGSGTFCIEAAMLAKNIAPGLKRSFAFEEWPWVED
-QLVVALRKEAQASIKTDLVLDITGSDIDARMIEIAKKNAFAAGVEQDIVFKQMRVQDLRT
-DKINGVIISNPPYGERLLDDEAIVTLYREMGETFEPLKTWSKFILTSDELFETRFGQQAD
-KKRKLYNGTLKVDLYQFFGQRVKRQVQEVQG
->Streptococcus_suis|ORF584 length 487 aa, 1464 bp, from 398981..400444 of Streptococcus_suis
-EDIVGEKNSHHLPLDEEKVLDFEVAKDLTIEEAVKKHKEIEAGVTEDDGLLDRYIKQHRA
-EIESQKFETKINHLPLVEVADEEKNQGHESAEEVEANESSLTEVSEEIAPIVEELSVTPM
-ETLEETVIASTVAMEGLSSVADDSSLELEEDETEDLDHSEGADRDQKKKFYFWSAVGLSM
-IGVMATALVWMNSVNKSNTATSSSSTSTSQTSSTASSSTDANVTAFEQLYNSFFTDSSLT
-KLKNSEFGKLAELKVLLEKLDKNSDSYTKAKEQYDHLEKAIAAIQAINGQFDKEVVVNGE
-IDTTATVKSGESLSATTTGISAVDSLLASVVNFGRSQQEVASATVASEAAVTRNQGADET
-VSTGVPATTEVASTTVSGSTTDFGIAVPAGVVLQRDRSRVPYNQAMIDDVNNEAWNFNPG
-ILENIVTISQQRGYITGNQYILEKVNIINGNGYYNMFKPDGTYLFSINCKTGYFVGNGAG
-HSDALDY
->Streptococcus_suis|ORF873 length 343 aa, 1032 bp, from 605439..606470 of Streptococcus_suis
-TLGEETMTNVFKGRHFLAEKDFTRAELEWLIDFSAHLKDLKKRNIPHRYLEGKNIALLFE
-KTSTRTRAAFTVASIDLGAHPEYLGANDIQLGKKESTEDTAKVLGRMFDGIEFRGFSQKM
-VEELAEFSGVPVWNGLTDAWHPTQMLADYLTVKENFGKLEGLTLVYCGDGRNNVANSLLV
-TGAILGVNVHIFSPKELFPEEEVVALAEGFAKESGARVLITDNADEAVKGADVLYTDVWV
-SMGEEDKFAERVALLKPYQVNMELVKKAENENLIFLHCLPAFHDTNTVYGKDVAEKFGVE
-EMEVTDEVFRSKYARHFDQAENRMHTIKAVMAATLGDPFVPRV
->Streptococcus_suis|ORF874 length 113 aa, 342 bp, from complement(605625..605966) of Streptococcus_suis
-VSNIVTAITTVNQSQAFQLAKVFFDSQVVRQHLSWVPCICQTIPYWHTGEFCQFFHHFLT
-ETTEFNTVEHTSQNFSSIFCRFFLTKLDVICTKIFWMGTKVNRCYCEGSTSTC
->Streptococcus_suis|ORF1165 length 105 aa, 318 bp, from 811613..811930 of Streptococcus_suis
-AYNESVKRKECHLMKQVNMSKIINYLTILGLLILLSAFFLDNWIRDWFFPSSWGNVATML
-ILPLLGALILILSIYYKKLWTGLISIFLIISFPLIFGIGYFIFGP
->Streptococcus_suis|ORF1166 length 125 aa, 378 bp, from 811867..812244 of Streptococcus_suis
-YLLNNLISSDIRYWLLYIWPLEGVVMNLTLLKRLNLVLYGIAIFLFVMLFLPIGQWFDIV
-NVNFKLTFFIIPFFGLASLPTAIYTKNVRQILLSVLLVALYFILFSLITALSGLFHLNFY
-SFFFK
->Streptococcus_suis|ORF1455 length 114 aa, 345 bp, from 1026973..1027317 of Streptococcus_suis
-SCKLSLHIRWESWMGQGFYCYRFKLIHLRTNSNPFSFFRHLNSHFQHLRNEWTVMLPDSV
-LDQDISTSHCRCHHKGTRFDTILHHLMFCASQFFYTSNRNRLCTCPLNFCPHFV
->Streptococcus_suis|ORF1456 length 116 aa, 351 bp, from complement(1027944..1028294) of Streptococcus_suis
-YGNACNSRPPTCDKSYSCWETLIYMGLNLVQFHFLISWYNGNMVISILQFFSHILFIYLA
-HHLLVTTVDWSRWLKVTGDNQRKINLLILFLAIALGYLVSTFFLELLMMGRSFANM
->Streptococcus_suis|ORF1747 length 335 aa, 1008 bp, from complement(1225218..1226225) of Streptococcus_suis
-RMLNTDDTVTIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARG
-LASKKTTTVGVVIPNIANAYFATLAKGIDDIADMYKYNIVLANSDENDEKEINVVNTLFS
-KQVDGIIFMGYHLTDKIRAEFSRSRTPIVLAGTVDLEHQLPSVNIDYAAASVDAVNLLAK
-NNKKIAFVSGPLVDDINGKVRFAGYKQGLKDNGIEFNEGLVFESKYKYEEGYALAERILN
-AGATAAYVAEDEIAAGLLNGVSDMGIKVPEDFEIITSDDSLVTKFTRPNLTSINQPLYDI
-GAIAMRMLTKIMHKEELENREVVLNHGIKVRKSTK
->Streptococcus_suis|ORF1748 length 377 aa, 1134 bp, from 1226384..1227517 of Streptococcus_suis
-TKISLFLPLHARKVSTMSKLHHVKSYLEANKMDLAIFSDPVSIYYLTGYHSDPHERHMML
-FVMPDHDSLLFLPALDVERAVATVDFPVAGYMDSENPWQIIKSKLPQKSFSAICAEFDNL
-NLTRYHGLQSIFSQPFSDITPLINTMKLIKSRDEIEKMLVAGEFADKAMQVGFNNISLDV
-TETDIIAQIEFEMKKQGISKMSFETMVLTGDNAANPHGIPSTNKIENNALLLFDLGVEAL
-GYTSDMTRTVAVGKPDQFKKDIYNLTLEAHMAAVNMIKPGVTAGEIDYAARSVIEKAGYG
-EYFNHRLGHGLGMSVHEFPSIMEGNDLVIEEGMCFSVEPGIYIPGKVGVRIEDCGYVTKN
-GFEVFTKTPKELLYFEG
->Streptococcus_suis|ORF2037 length 234 aa, 705 bp, from complement(1422380..1423084) of Streptococcus_suis
-KSMTKTALITGVSSGIGLAQAGIFLENGWRVFGIDLASKPDLAGDFHFLQLDLTGDLSPV
-FSWCQSVDVLCNTAGILDDYRPHLDISEDELAQIFAVNFFAVTRLTRPYLQQMVDRQSGI
-IINMCSIASSLAGGGGSAYTASKHALAGFTKQLALDYAKDKVQIFGIAPGAVQTGMTQKD
-FEPGGLADWVADQTPIGRWTQPSEIAELTFMLATGKLASMQGQIITIDGGWSLK
->Streptococcus_suis|ORF2038 length 112 aa, 339 bp, from 1422849..1423187 of Streptococcus_suis
-SSKMPAVLQRTSTDWHQEKTGDKSPVRSSCRKWKSPAKSGLLARSIPKTRQPFSKKIPAC
-ARPMPLETPVMRAVLVMDFYPVGRKDIARGRAPHGEAFTLAGHVDEEIGRRL
->Streptococcus_suis|ORF2329 length 160 aa, 483 bp, from 1612284..1612766 of Streptococcus_suis
-LIETNWFHHLTGQEGLDVLFFHNLGFRITDQLYLEVRKFHLLQGLSQLLRRWSQESRVKG
-ARYIERNHPLDTCFLQQFNRLIHCSHLASDDDLGWCVVVGWGNNPRGNSRTDFFNQVDIC
-VENSNHLTSPCWRSQFHIFTTLSNQGNRIFKGQSSRCHQS
->Streptococcus_suis|ORF2330 length 329 aa, 990 bp, from complement(1613050..1614039) of Streptococcus_suis
-ARKKDEGIMKTKITELLDIKYPIFQGGMAWVADGDLAGAVSNAGGLGIIGGGNAPKEVVK
-ANIDKVKSITDKPFGVNIMLLSPFADDIVDLVIEEGVKVVTTGAGNPGKYMERLHAAGIT
-VIPVVPSVALAKRMEKLGVDAVIAEGMEAGGHIGKLTTMTLVRQVVEAVSIPVIAAGGIA
-DGAGAAAAFMLGAEAVQVGTRFVVATESNAHQAYKEKVLKAKDIDTTVSASIVGHPVRAI
-KNKLSSAYAAAEKDFLAGKISADAIEELGAGALRNAVVDGDVTNGSVMAGQIAGLVSKEE
-SCEDILKDIYYGAAKVIREEASRWASVGE
->Streptococcus_suis|ORF2619 length 107 aa, 324 bp, from 1802386..1802709 of Streptococcus_suis
-QLCVGSNPINSLFRRNFFVCCISSQSSCYVHTMWFVGIIVEIIVARYIIIAMGNFQCVCP
-CRRWSNVLNFRNDTIIQPHVFVLNIQTGVNDCNHHSATICLIFRTCF
->Streptococcus_suis|ORF2620 length 192 aa, 579 bp, from complement(1803558..1804136) of Streptococcus_suis
-RLKIPCFQRKEVTMYDSFDKGWFVLQTYSGYENKVKENLLQRAHTYNMLENILRVEIPTQ
-TVQVEKNGEVKEVEENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLE
-EEIRQILVSMGQTVQEFDIDVKVGDTVRIIDGAFTDYTGKITEIDNNKVKMVISMFGNDT
-IAEVNLSQIAEL
--- a/test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta	Mon Apr 06 05:21:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,214 +0,0 @@
->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
--- a/test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta	Mon Apr 06 05:21:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
->Streptococcus_suis|ORF1 length 457 aa, 1374 bp, from 1..1374 of Streptococcus_suis
-MNQEQLFWQRFIELAKVNFKPSIYDFYVADAKLLGINQQVANIFLNRPFKKDFWEKNFEE
-LMIAASFESYGEPLTIQYQFTEDEQEIRNTTNTRSSIVHQVQTLEPATPQETFKPVHSDI
-KSQYTFANFVQGDNNHWAKAAALAVSDNLGELYNPLFIFGGPGLGKTHILNAIGNKVLAD
-NPQARIKYVSSETFINEFLEHLRLNDMESFKKTYRNLDLLLIDDIQSLRNKATTQEEFFH
-TFNALHEKNKQIVLTSDRNPDHLDNLEERLVTRFKWGLTSEITPPDFETRIAILRNKCEN
-LPYNFTNETLSYLAGQFDSNVRDLEGALKDIHLIATMRQLSEISVEVAAEAIRSRKQTNP
-QNMVIPIEKIQTEVGNFYGVSLKELKGSKRVQHIVHARQVAMFLAREMTDNSLPKIGKEF
-GNRDHTTVMHAYNKIKTLLLDDENLEIEITSIKNKLR
->Streptococcus_suis|ORF292 length 216 aa, 651 bp, from 185183..185833 of Streptococcus_suis
-AVGKDHLTLDPISVEQIIAVMPVLIVVTAGAVQGSTLGSQSFFVGCFIAEEVTCLQTLGV
-GQGGQAVQIFAWIATRAGHQPVFTVVVIPRGNPCFCDDDFQSVHASCCQGIGHGTEIRQS
-RRRYLTIGPIGLDLKRASVVCVGLGATVQPVNHRFIALHLLVVARCHVARRAQRANTRHM
-EAGKAASEEVVIEGVRSNVPQFFSSRADRQVPLVQV
->Streptococcus_suis|ORF583 length 391 aa, 1176 bp, from 397805..398980 of Streptococcus_suis
-RKKMKKQFELIATAAAGLEAVVGREIRNLGYECQVENGRVRFQGDVKSIIETNIWLRSAD
-RIKIIVGQFPAKTFEELFQGVFNLDWENYLPLGCKFPISKAKCVKSKLHNEPSVQAISKK
-AVVKKLQKHFSRPEGVPLQEMGAEFKIEVSILKDVATVMIDTTGSSLFKRGYRVEKGGAP
-IKENMAAAILQLSNWYPDKPLIDPTCGSGTFCIEAAMLAKNIAPGLKRSFAFEEWPWVED
-QLVVALRKEAQASIKTDLVLDITGSDIDARMIEIAKKNAFAAGVEQDIVFKQMRVQDLRT
-DKINGVIISNPPYGERLLDDEAIVTLYREMGETFEPLKTWSKFILTSDELFETRFGQQAD
-KKRKLYNGTLKVDLYQFFGQRVKRQVQEVQG
->Streptococcus_suis|ORF874 length 113 aa, 342 bp, from complement(605625..605966) of Streptococcus_suis
-VSNIVTAITTVNQSQAFQLAKVFFDSQVVRQHLSWVPCICQTIPYWHTGEFCQFFHHFLT
-ETTEFNTVEHTSQNFSSIFCRFFLTKLDVICTKIFWMGTKVNRCYCEGSTSTC
->Streptococcus_suis|ORF1165 length 105 aa, 318 bp, from 811613..811930 of Streptococcus_suis
-AYNESVKRKECHLMKQVNMSKIINYLTILGLLILLSAFFLDNWIRDWFFPSSWGNVATML
-ILPLLGALILILSIYYKKLWTGLISIFLIISFPLIFGIGYFIFGP
->Streptococcus_suis|ORF1456 length 116 aa, 351 bp, from complement(1027944..1028294) of Streptococcus_suis
-YGNACNSRPPTCDKSYSCWETLIYMGLNLVQFHFLISWYNGNMVISILQFFSHILFIYLA
-HHLLVTTVDWSRWLKVTGDNQRKINLLILFLAIALGYLVSTFFLELLMMGRSFANM
->Streptococcus_suis|ORF1747 length 335 aa, 1008 bp, from complement(1225218..1226225) of Streptococcus_suis
-RMLNTDDTVTIYDVAREAGVSMATVSRVVNGNKNVKENTRKKVLEVIDRLDYRPNAVARG
-LASKKTTTVGVVIPNIANAYFATLAKGIDDIADMYKYNIVLANSDENDEKEINVVNTLFS
-KQVDGIIFMGYHLTDKIRAEFSRSRTPIVLAGTVDLEHQLPSVNIDYAAASVDAVNLLAK
-NNKKIAFVSGPLVDDINGKVRFAGYKQGLKDNGIEFNEGLVFESKYKYEEGYALAERILN
-AGATAAYVAEDEIAAGLLNGVSDMGIKVPEDFEIITSDDSLVTKFTRPNLTSINQPLYDI
-GAIAMRMLTKIMHKEELENREVVLNHGIKVRKSTK
->Streptococcus_suis|ORF2038 length 112 aa, 339 bp, from 1422849..1423187 of Streptococcus_suis
-SSKMPAVLQRTSTDWHQEKTGDKSPVRSSCRKWKSPAKSGLLARSIPKTRQPFSKKIPAC
-ARPMPLETPVMRAVLVMDFYPVGRKDIARGRAPHGEAFTLAGHVDEEIGRRL
->Streptococcus_suis|ORF2329 length 160 aa, 483 bp, from 1612284..1612766 of Streptococcus_suis
-LIETNWFHHLTGQEGLDVLFFHNLGFRITDQLYLEVRKFHLLQGLSQLLRRWSQESRVKG
-ARYIERNHPLDTCFLQQFNRLIHCSHLASDDDLGWCVVVGWGNNPRGNSRTDFFNQVDIC
-VENSNHLTSPCWRSQFHIFTTLSNQGNRIFKGQSSRCHQS
->Streptococcus_suis|ORF2620 length 192 aa, 579 bp, from complement(1803558..1804136) of Streptococcus_suis
-RLKIPCFQRKEVTMYDSFDKGWFVLQTYSGYENKVKENLLQRAHTYNMLENILRVEIPTQ
-TVQVEKNGEVKEVEENRFPGYVLVEMVMTDEAWFVVRNTPNVTGFVGSHGNRSKPTPLLE
-EEIRQILVSMGQTVQEFDIDVKVGDTVRIIDGAFTDYTGKITEIDNNKVKMVISMFGNDT
-IAEVNLSQIAEL
--- a/test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta	Mon Apr 06 05:21:48 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,194 +0,0 @@
->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	Mon Apr 06 05:21:48 2015 -0400
+++ b/tools/get_orfs_or_cdss/README.rst	Tue May 12 11:27:35 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to find ORFs or simple CDSs
 =======================================
 
-This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -74,6 +74,7 @@
 v0.1.0  - Tool now outputs BED formatted calls (by @erasche, Eric Rasche).
         - Using ``optparse`` for the Python command line API (Eric Rasche).
         - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
+v0.1.1  - Reorder XML elements (internal change only).
 ======= ======================================================================
 
 
@@ -86,32 +87,41 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ tar -czf get_orfs_or_cdss.tar.gz tools/get_orfs_or_cdss/README.rst tools/get_orfs_or_cdss/get_orfs_or_cdss.* tools/get_orfs_or_cdss/tool_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta test-data/get_orf_input*.bed
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    ...
 
-Check this worked::
+or::
 
-    $ tar -tzf get_orfs_or_cdss.tar.gz
-    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
-    test-data/get_orf_input.fasta
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    ...
+
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    test-data/Ssuis.fasta
+    test-data/get_orf_input.Suis_ORF.bed
     test-data/get_orf_input.Suis_ORF.nuc.fasta
     test-data/get_orf_input.Suis_ORF.prot.fasta
+    test-data/get_orf_input.fasta
+    test-data/get_orf_input.t11_bed_out.bed
     test-data/get_orf_input.t11_nuc_out.fasta
+    test-data/get_orf_input.t11_open_bed_out.bed
     test-data/get_orf_input.t11_open_nuc_out.fasta
     test-data/get_orf_input.t11_open_prot_out.fasta
     test-data/get_orf_input.t11_prot_out.fasta
+    test-data/get_orf_input.t1_bed_out.bed
     test-data/get_orf_input.t1_nuc_out.fasta
     test-data/get_orf_input.t1_prot_out.fasta
-    test-data/Ssuis.fasta
-    test-data/get_orf_input.Suis_ORF.bed
-    test-data/get_orf_input.t11_open_bed_out.bed
-    test-data/get_orf_input.t11_bed_out.bed
-    test-data/get_orf_input.t1_bed_out.bed
+    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/README.rst
+    tools/get_orfs_or_cdss/tool_dependencies.xml
 
 
 Licence (MIT)
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Mon Apr 06 05:21:48 2015 -0400
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Tue May 12 11:27:35 2015 -0400
@@ -1,18 +1,18 @@
-<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.1.0">
+<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.1.1">
     <description>e.g. to get peptides from ESTs</description>
     <requirements>
         <requirement type="package" version="1.65">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command>
-    <command interpreter="python">
-get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command>
+    <command interpreter="python">
+get_orfs_or_cdss.py -i $input_file -f $input_file.ext --table $table -t $ftype -e $ends -m $mode --min_len $min_len -s $strand --on $out_nuc_file --op $out_prot_file --ob $out_bed_file
+    </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file (nucleotides)" help="FASTA, FASTQ, or SFF format." />
         <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">