Adding back in all input files we had before

tests/data/fasta/msa/BBA0001.tfa

@@ -0,0 +1,265 @@
+>seq001
+MAGKRKRANAPDQTERRSSVRVQKVRQKALDEKARLVQERVKLLSDRKSEICVDDTELHE
+KEEENVDGSPKRRSPPKLTAMQKGKQKLSVSLNGKDVNLEPHLKVTKCLRLFNKQYLLCV
+QAKLSRPDLKGVTEMIKAKAILYPRKIIGDLPGIDVGHRFFSRAEMCAVGFHNHWLNGID
+YMSMEYEKEYSNYKLPLAVSIVMSGQYEDDLDNADTVTYTGQGGHNLTGNKRQIKDQLLE
+RGNLALKHCCEYNVPVRVTRGHNCKSSYTKRVYTYDGLYKVEKFWAQKGVSGFTVYKYRL
+KRLEGQPELTTDQVNFVAGRIPTSTSEIEGLVCEDISGGLEFKGIPATNRVDDSPVSPTS
+GFTYIKSLIIEPNVIIPKSSTGCNCRGSCTDSKKCACAKLNGGNFPYVDLNDGRLIESRD
+VVFECGPHCGCGPKCVNRTSQKRLRFNLEVFRSAKKGWAVRSWEYIPAGSPVCEYIGVVR
+RTADVDTISDNEYIFEIDCQQTMQGLGGRQRRLRDVAVPMNNGVSQSSEDENAPEFCIDA
+GSTGNFARFINHSCEPNLFVQCVLSSHQDIRLARVVLFAADNISPMQELTYDYGYALDSV
+HGPDGKVKQLACYCGALNCRKRLY
+>seq002
+MPRHFGAVPGVVPGMAFVNRQELRDAGVHLPTQAGISGSASEGADSIVLSGGYEDDRDEG
+DVILYTGEGGRDPLTGHQVKPQQLVRGNLALAISHRDGLPLRVTRGHRHSSQFSPQSGYQ
+YAGLYRVDDHWREVGRSGFLIWRFRLTRLENQDAHHAGADPQHPDSQHPERRPTLVQRIV
+RDTATARAVKALYDHRCQVCGERLETPAGAYAEAAHIRPLGAPHHGPDVAGNILCLCPNH
+HVLFDFGAFSVGDDLRLLGLPGRLHVHPQHAVDREHLAYHRRHYALQAGLEWGCSVPLT
+>seq003
+MGVMENLMVHTEISKVKSQSNGEVEKRGVSVLENGGVCKLDRMSGLKFKRRKVFAVRDFP
+PGCGSRAMEVKIACENGNVVEDVKVVESLVKEEESLGQRDASENVSDIRMAEPVEVQPLR
+ICLPGGDVVRDLSVTAGDECSNSEQIVAGSGVSSSSGTENIVRDIVVYADESSLGMDNLD
+QTQPLEIEMSDVAVAKPRLVAGRKKAKKGIACHSSLKVVSREFGEGSRKKKSKKNLYWRD
+RESLDSPEQLRILGVGTSSGSSSGDSSRNKVKETLRLFHGVCRKILQEDEAKPEDQRRKG
+KGLRIDFEASTILKRNGKFLNSGVHILGEVPGVEVGDEFQYRMELNILGIHKPSQAGIDY
+MKYGKAKVATSIVASGGYDDHLDNSDVLTYTGQGGNVMQVKKKGEELKEPEDQKLITGNL
+ALATSIEKQTPVRVIRGKHKSTHDKSKGGNYVYDGLYLVEKYWQQVGSHGMNVFKFQLRR
+IPGQPELSWVEVKKSKSKYREGLCKLDISEGKEQSPISAVNEIDDEKPPLFTYTVKLIYP
+DWCRPVPPKSCCCTTRCTEAEARVCACVEKNGGEIPYNFDGAIVGAKPTIYECGPLCKCP
+SSCYLRVTQHGIKLPLEIFKTKSRGWGVRCLKSIPIGSFICEYVGELLEDSEAERRIGND
+EYLFDIGNRYDNSLAQGMSELMLGTQAGRSMAEGDESSGFTIDAASKGNVGRFINHSCSP
+NLYAQNVLYDHEDSRIPHVMFFAQDNIPPLQELCYDYNYALDQVRDSKGNIKQKPCFCGA
+AVCRRRLY
+>seq004
+MSTLLPFPDLNLMPDSQSSTAGTTAGDTVVTGKLEVKSEPIEEWQTPPSSTSDQSANTDL
+IAEFIRISELFRSAFKPLQVKGLDGVSVYGLDSGAIVAVPEKENRELIEPPPGFKDNRVS
+TVVVSPKFERPRELARIAILGHEQRKELRQVMKRTRMTYESLRIHLMAESMKNHVLGQGR
+RRRSDMAAAYIMRDRGLWLNYDKHIVGPVTGVEVGDIFFYRMELCVLGLHGQTQAGIDCL
+TAERSATGEPIATSIVVSGGYEDDEDTGDVLVYTGHGGQDHQHKQCDNQRLVGGNLGMER
+SMHYGIEVRVIRGIKYENSISSKVYVYDGLYKIVDWWFAVGKSGFGVFKFRLVRIEGQPM
+MGSAVMRFAQTLRNKPSMVRPTGYVSFDLSNKKENVPVFLYNDVDGDQEPRHYEYIAKAV
+FPPGIFGQGGISRTGCECKLSCTDDCLCARKNGGEFAYDDNGHLLKGKHVVFECGEFCTC
+GPSCKSRVTQKGLRNRLEVFRSKETGWGVRTLDLIEAGAFICEYAGVVVTRLQAEILSMN
+GDVMVYPGRFTDQWRNWGDLSQVYPDFVRPNYPSLPPLDFSMDVSRMRNVACYISHSKEP
+NVMVQFVLHDHNHLMFPRVMLFALENISPLAELSLDYGLADEVNGKLAICN
+>seq005
+MVHSESSILSSLRGGDGGGIPCSKDELAINGSYTDPMGRRKSKRFKVAAESEFSPDFGSI
+TRQLRSRRMQKEFTVETYETRNVSDVCVLSSQADVELIPGEIVAERDSFKSVDCNDMSVG
+LTEGAESLGVNMQEPMKDRNMPENTSEQNMVEVHPPSISLPEEDMMGSVCRKSITGTKEL
+HGRTISVGRDLSPNMGSKFSKNGKTAKRSISVEEENLVLEKSDSGDHLGPSPEVLELEKS
+EVWIITDKGVVMPSPVKPSEKRNGDYGEGSMRKNSERVALDKKRLASKFRLSNGGLPSCS
+SSGDSARYKVKETMRLFHETCKKIMQEEEARPRKRDGGNFKVVCEASKILKSKGKNLYSG
+TQIIGTVPGVEVGDEFQYRMELNLLGIHRPSQSGIDYMKDDGGELVATSIVSSGGYNDVL
+DNSDVLIYTGQGGNVGKKKNNEPPKDQQLVTGNLALKNSINKKNPVRVIRGIKNTTLQSS
+VVAKNYVYDGLYLVEEYWEETGSHGKLVFKFKLRRIPGQPELPWKEVAKSKKSEFRDGLC
+NVDITEGKETLPICAVNNLDDEKPPPFIYTAKMIYPDWCRPIPPKSCGCTNGCSKSKNCA
+CIVKNGGKIPYYDGAIVEIKPLVYECGPHCKCPPSCNMRVSQHGIKIKLEIFKTESRGWG
+VRSLESIPIGSFICEYAGELLEDKQAESLTGKDEYLFDLGDEDDPFTINAAQKGNIGRFI
+NHSCSPNLYAQDVLYDHEEIRIPHIMFFALDNIPPLQELSYDYNYKIDQVYDSNGNIKKK
+FCYCGSAECSGRLY
+>seq006
+MERNGGHYTDKTRVLDIKPLRTLRPVFPSGNQAPPFVCAPPFGPFPPGFSSFYPFSSSQA
+NQHTPDLNQAQYPPQHQQPQNPPPVYQQQPPQHASEPSLVTPLRSFRSPDVSNGNAELEG
+STVKRRIPKKRPISRPENMNFESGINVADRENGNRELVLSVLMRFDALRRRFAQLEDAKE
+AVSGIIKRPDLKSGSTCMGRGVRTNTKKRPGIVPGVEIGDVFFFRFEMCLVGLHSPSMAG
+IDYLVVKGETEEEPIATSIVSSGYYDNDEGNPDVLIYTGQGGNADKDKQSSDQKLERGNL
+ALEKSLRRDSAVRVIRGLKEASHNAKIYIYDGLYEIKESWVEKGKSGHNTFKYKLVRAPG
+QPPAFASWTAIQKWKTGVPSRQGLILPDMTSGVESIPVSLVNEVDTDNGPAYFTYSTTVK
+YSESFKLMQPSFGCDCANLCKPGNLDCHCIRKNGGDFPYTGNGILVSRKPMIYECSPSCP
+CSTCKNKVTQMGVKVRLEVFKTANRGWGLRSWDAIRAGSFICIYVGEAKDKSKVQQTMAN
+DDYTFDTTNVYNPFKWNYEPGLADEDACEEMSEESEIPLPLIISAKNVGNVARFMNHSCS
+PNVFWQPVSYENNSQLFVHVAFFAISHIPPMTELTYDYGVSRPSGTQNGNPLYGKRKCFC
+GSAYCRGSFG
+>seq007
+MQGVPGFNTVPNPNHYDKSIVLDIKPLRSLKPVFPNGNQGPPFVGCPPFGPSSSEYSSFF
+PFGAQQPTHDTPDLNQTQNTPIPSFVPPLRSYRTPTKTNGPSSSSGTKRGVGRPKGTTSV
+KKKEKKTVANEPNLDVQVVKKFSSDFDSGISAAEREDGNAYLVSSVLMRFDAVRRRLSQV
+EFTKSATSKAAGTLMSNGVRTNMKKRVGTVPGIEVGDIFFSRIEMCLVGLHMQTMAGIDY
+IISKAGSDEESLATSIVSSGRYEGEAQDPESLIYSGQGGNADKNRQASDQKLERGNLALE
+NSLRKGNGVRVVRGEEDAASKTGKIYIYDGLYSISESWVEKGKSGCNTFKYKLVRQPGQP
+PAFGFWKSVQKWKEGLTTRPGLILPDLTSGAESKPVSLVNDVDEDKGPAYFTYTSSLKYS
+ETFKLTQPVIGCSCSGSCSPGNHNCSCIRKNDGDLPYLNGVILVSRRPVIYECGPTCPCH
+ASCKNRVIQTGLKSRLEVFKTRNRGWGLRSWDSLRAGSFICEYAGEVKDNGNLRGNQEED
+AYVFDTSRVFNSFKWNYEPELVDEDPSTEVPEEFNLPSPLLISAKKFGNVARFMNHSCSP
+NVFWQPVIREGNGESVIHIAFFAMRHIPPMAELTYDYGISPTSEARDESLLHGQRTCLCG
+SEQCRGSFG
+>seq008
+MGSSHIPLDPSLNPSPSLIPKLEPVTESTQNLAFQLPNTNPQALISSAVSDFNEATDFSS
+DYNTVAESARSAFAQRLQRHDDVAVLDSLTGAIVPVEENPEPEPNPYSTSDSSPSVATQR
+PRPQPRSSELVRITDVGPESERQFREHVRKTRMIYDSLRMFLMMEEAKRNGVGGRRARAD
+GKAGKAGSMMRDCMLWMNRDKRIVGSIPGVQVGDIFFFRFELCVMGLHGHPQSGIDFLTG
+SLSSNGEPIATSVIVSGGYEDDDDQGDVIMYTGQGGQDRLGRQAEHQRLEGGNLAMERSM
+YYGIEVRVIRGLKYENEVSSRVYVYDGLFRIVDSWFDVGKSGFGVFKYRLERIEGQAEMG
+SSVLKFARTLKTNPLSVRPRGYINFDISNGKENVPVYLFNDIDSDQEPLYYEYLAQTSFP
+PGLFVQQSGNASGCDCVNGCGSGCLCEAKNSGEIAYDYNGTLIRQKPLIHECGSACQCPP
+SCRNRVTQKGLRNRLEVFRSLETGWGVRSLDVLHAGAFICEYAGVALTREQANILTMNGD
+TLVYPARFSSARWEDWGDLSQVLADFERPSYPDIPPVDFAMDVSKMRNVACYISHSTDPN
+VIVQFVLHDHNSLMFPRVMLFAAENIPPMTELSLDYGVVDDWNAKLAICN
+>seq009
+MDKSIPIKAIPVACVRPDLVDDVTKNTSTIPTMVSPVLTNMPSATSPLLMVPPLRTIWPS
+NKEWYDGDAGPSSTGPIKREASDNTNDTAHNTFAPPPEMVIPLITIRPSDDSSNYSCDAG
+AGPSTGPVKRGRGRPKGSKNSTPTEPKKPKVYDPNSLKVTSRGNFDSEITEAETETGNQE
+IVDSVMMRFDAVRRRLCQINHPEDILTTASGNCTKMGVKTNTRRRIGAVPGIHVGDIFYY
+WGEMCLVGLHKSNYGGIDFFTAAESAVEGHAAMCVVTAGQYDGETEGLDTLIYSGQGGTD
+VYGNARDQEMKGGNLALEASVSKGNDVRVVRGVIHPHENNQKIYIYDGMYLVSKFWTVTG
+KSGFKEFRFKLVRKPNQPPAYAIWKTVENLRNHDLIDSRQGFILEDLSFGAELLRVPLVN
+EVDEDDKTIPEDFDYIPSQCHSGMMTHEFHFDRQSLGCQNCRHQPCMHQNCTCVQRNGDL
+LPYHNNILVCRKPLIYECGGSCPCPDHCPTRLVQTGLKLHLEVFKTRNCGWGLRSWDPIR
+AGTFICEFAGLRKTKEEVEEDDDYLFDTSKIYQRFRWNYEPELLLEDSWEQVSEFINLPT
+QVLISAKEKGNVGRFMNHSCSPNVFWQPIEYENRGDVYLLIGLFAMKHIPPMTELTYDYG
+VSCVERSEEDEGFLVCPYLSSSLWPSSSEIHFLINSKGRAWYDKIYRKLASQGNVSSGLD
+SVKDEPEKLREEQMEGDGFKEKLSDSVLIDEKLEEYSDCDRTATTSRSHTDPVSSQSTHQ
+TPESFRTPITCDDDTFVSVSGISRDVSNLIPFATETPASPVQEKMANTRSFSNNSVKGNQ
+DEFFIEDFDVGPMDTIDLYDMTFREDPSDFDDNLLYAMRDRTKQLRSFKRKIMDAIKSKR
+RREKEYEQLAIWFGDADMGCDLVNDKEQSTTSIDSKSSQTNVPVVSEDSEWEIL
+>seq010
+MMMTQRISPSNKRRRVSFVRDFPQFSVKDESDIGGDDVATIKENLDGKEDSNCVGVAYRD
+HHRPKEESFDSIMKKAGFNVANGNLGNGKFPPSKRNVPLPCEGKVQPLSVEEGIKLMAYE
+SQRRRCFGKPLVSTKVVQKHRYSPAKKKLSNATALRVRHSPMKKLSNASRLRANAHRPTQ
+HKDERRSGVLSVIQRNRLSKDLTPRQKVQEVLRIFTLVFDELDRNKAARRGGSETAKSRI
+DYQTWTILREMGMQVNSQKRIGSVPGIKVGDKIQFKAALSVIGLHFGIMSGIDYMYKGNK
+EVATSIVSSEGNDYGDRFINDVMIYCGQGGNMRSKDHKAIKDQKLVGGNLALANSIKEKT
+PVRVIRGERRLDNRGKDYVYDGLYRVEKYWEERGPQGNILFKFKLRRTCQPYVDF
+>seq011
+MSQKRSLVFAIRDFPPGCGTHIDVSSSLNHPAEKAFKHPRTGDVSGENLSFAEAKPEGTC
+LKRESADQDHIFAAPEHNAKREPAGQDHVVAATTVAYATSSHRQKVEIGNSDCDPTPREK
+VLEVLSLFKQVYNQLDRDKKARRGGDFLDATSRIDLKTLTVLEKMGKQVNTEKRIGSVPG
+INIGDVFQYKTELRVVGLHSKPMCGIDYIKLGDDRITTSIVASEGYGYNDTYNSGVMVYT
+GEGGNVINKQKKTEDQKLVKGNLALATSMRQKSQVRVIRGEERLDRKGKRYVYDGLYMVE
+EYWVERDVRGKSVYKFKLCRIPGQLPLT
+>seq012
+MCLVGLHRNTAGGIDSLLAKESGVDGPAATSVVTSGKYDNETEDLETLIYSGHGGKPCDQ
+VLQRGNRALEASVRRRNEVRVIRGELYNNEKVYIYDGLYLVSDCWQVTGKSGFKEYRFKL
+LRKPGQPPGYAIWKLVENLRNHELIDPRQGFILGDLSFGEEGLRVPLVNEVDEEDKTIPD
+DFDYIRSQCYSGMTNDVNVDSQSLVQSYIHQNCTCILKNCGQLPYHDNILVCRKPLIYEC
+GGSCPTRMVETGLKLHLEVFKTSNCGWGLRSWDPIRAGTFICEFTGVSKTKEEVEEDDDY
+LFDTSRIYHSFRWNYEPELLCEDACEQVSEDANLPTQVLISAKEKGNVGRFMNHNCWPNV
+FWQPIEYDDNNGHIYVRIGLFAMKHIPPMTELTYDYGISCVEKTGEDEVIYKGKKICLCG
+SVKCRGSFG
+>seq013
+MGLVGLHSGTIDMEFIGVEDHGDEEGKQIAVSVISSGKNADKTEDPDSLIFTGFGGTDMY
+HGQPCNQKLERLNIPLEAAFRKKSIVRVVRCMKDEKRTNGNIYIYDGTYMITNRWEEEGQ
+NGFIVFKFKLVREPDQKPAFGIWKSIQNWRNGLSIRPGLILEDLSNGAENLKVCLVNEVD
+KENGPALFRYVTSLIHEVINNIPSMVDRCACGRRSCGSKHVFREKLSVSSSLVISAKKSG
+NVARFMNHSCSPNVFWQSIAREQNGLWCLYIGFFAMKHIPPLTELRYDYGKSRGGGKKMC
+LCRTKKCCGSFG
+>seq014
+MTRVNQLPCDCVSTAEESLTSGTCITPTHVTSLSSPLDRSGDVDPLPVSDESGGSKADES
+MTDADETKKRKRILSGDCEADENNKSDGEIASLNDGVDAFTAICEDLNCSLCNQLPDRPV
+TILCGHNFCLKCFDKWIDQGNQICATCRSTIPDKMAANPRVNSSLVSVIRYVKVAKTAGV
+GTANFFPFTSNQDGPENAFRTKRAKIGEENAARIYVTVPFDHFGPIPAEHDPVRNQGVLV
+GESWENRVECRQWGVHLPHVSCIAGQEDYGAQSVVISGGYKDDEDHGEWFLYTGRSRGRH
+FANEDQEFEDLNEALRVSCEMGYPVRVVRSYKDRYSAYAPKEGVRYDGVYRIEKCWRKAR
+FPVCRYLFVRCDNEPAPWNSDESGDRPRPLPNIPELETASDLFERKESPSWDFDEAEGRW
+RWMKPPPANHEQRERMKMAMTCLLLFVLIILVGSSSILYQY
+>seq015
+MTRVNQLPCDCVSTAEESLTSGTCITPTHVTSLSSPLDRSGDVDPLPVSDESGGSKADES
+MTDADETKKRKRILSGDCEADENNKSDGEIASLNDGVDAFTAICEDLNCSLCNQLPDRPV
+TILCGHNFCLKCFDKWIDQGNQICATCRSTIPDKMAANPRVNSSLVSVIRYVKVAKTAGV
+GTANFFPFTSNQDGPENAFRTKRAKIGEENAARIYVTVPFDHFGPIPAEHDPVRNQGVLV
+GESWENRVECRQWGVHLPHVSCIAGQEDYGAQSVVISGGYKDDEDHGEWFLYTGRRSYKD
+RYSAYAPKEGVRYDGVYRIEKCWRKARFPDSFKVCRYLFVRCDNEPAPWNSDESGDRPRP
+LPNIPELETASDLFERKESPSWDFDEAEGRWRWMKPPPANHEQRERMKMAMTCLLLFVLI
+ILVGSSSILYQY
+>seq016
+MAEQPRINSALVSVIRMAKVSKNANSAVSAAAYHYIRNDDRPDKAFTTERAKRAGKANAS
+SGQIFVTIPPDHFGPILAENDPKRSIGVLVGDTWEDRLECRQWGAHFPHVAGIAGQSTHG
+AQSVALSGGYVDDEDHGEWFLYTGSGGRDLSGNKRTNKEQSSDQKFEKLNAALRISCLKG
+YPVRVVRSHKEKRSSYAPEAGVRYDGVYRIEKCWRKISVQGKFKVCRYLFVRCDNEPAPW
+TSDIYGDRPRPLPKVDELKGATDISERKGTPSWDFDEKEGWKWVKPPPISRKPNLSGDPA
+TDKEIRRVARRAQMSVTERLLKEFGCSICKQVMKEPLTTPCAHNFCKLCLVGTYGSQSSM
+RERSRGGRTLRAQKIVKKCPSCPTDICDFLENPQINREMMDLIESLQRKAVEEGDTKTSS
+DVSNGAESSGDDGNNEALEKGEDDSSLKDDGSLKDDGKVVKAVVVIKEEDLQPKKSKGED
+EKEQGDKKMDSADVVDIAVEKKQATKRASEKAEKKQARKRKGDAVATNDGKRMKTGGDAM
+ETAAEEDAPLSGGTPVKRNSRKSSEVDAKGGGGSPVVSSPRRVTRSNAKASGEADGSPAT
+RTRRATRAEA
+>seq017
+MTPATQYPCDPEGVCMRCKSMPPPEESLTCGTCVTPWHVSCLLSPPETLSATLQWLCPDC
+SGETNPLPVSGVAAGYGSVGSDLVAAIHSIEADETLSAEEKAKKKQQLLSGKGVVDEDDE
+EEKKKTSKGKKPIDVLSHFECSFCMQSLQKPVSVRVLFALALMLVWFLESTPCGHNACLK
+CFLKWMGQGHRSCGTCRSVIPESMVTNPRINLSIVSAIRLARVSEKADARTSKVVHYVDN
+EDRPDKAFTTERAKKTGNANASSGKIFVTIPRDHFGPIPAENDPVRNQGLLVGESWKGRL
+ACRQWGAHFPHVSGIAGQASYGAQSVVLAGGYDDDEDHGEWFLYTGRTNTVQAFDQVFLN
+FNEALRLSCKLGYPVRVVRSTKDKRSPYAPQGGLLRYDGVYRIEKCWRIVGIQMCRFLFV
+RCDNEPAPWTSDEHGDRPRPLPNVPELNMATDLFERKESPSWDFDEGEDRWRWMKPPPAS
+KKAVKNVLDPEERKLLREAIKSANPNTMRARLLKEFKCQICQKVMTNPVTTPCAHNFCKA
+CLESKFAGTALVRERGSGGRKLRSQKSVMKCPCCPTDIAEFVQNPQVNREVAEVIEKLKK
+QEEEENAKSLDEGQCSGTSHEEEDDEQPKKRIKLDTDAEVSATVVESDMK
+>seq018
+MARDIQLPCDGDGVCMRCKSNPPPEESLTCGTCVTPWHVSCLSSPPKTLASTLQWHCPDC
+SGEIDPLPVSGGATGFESAGSDLVAAIRAIEADESLSTEEKAKMRQRLLSGKGVEEDDEE
+EKRKKKGKGKNPNLDVLSALGDNLMCSFCMQLPERPVTKPCGHNACLKCFEKWMGQGKRT
+CGKCRSIIPEKMAKNPRINSSLVAAIRLAKVSKSAAATTSKVFHFISNQDRPDKAFTTER
+AKKTGKANAASGKIYVTIPPDHFGPIPAENDPVRNQGLLVGESWEDRLECRQWGAHFPHV
+AGIAGQSTYGAQSVALSGGYKDDEDHGEWFLYTGSGGRDLSGNKRTNKEQSFDQKFEKSN
+AALKLSCKLGYPVRVVRSHKEKRSAYAPEEGVRYDGVYRIEKCWRKVGVQVCRYLFVRCD
+NEPAPWTSDENGDRPRPIPNIPELNMATDLFERKETPSWDFDEGEGCWKWMKPPPASKKS
+VNVLAPEERKNLRKAIKAAHSNTMRARLLKEFKCQICQQVLTLPVTTPCAHNFCKACLEA
+KFAGKTLVRERSTGGRTLRSRKNVLNCPCCPTDISDFLQNPQVNREVAEVIEKLKTQEED
+TAELEDEDEGECSGTTPEEDSEQPKKRIKLDTDATVSATIR
+>seq019
+MAIQTQLPCDGDGVCMRCQVTPPSEETLTCGTCVTPWHVSCLLPESLASSTGDWECPDCS
+GVVVPSAAPGTGISGPESSGSVLVAAIRAIQADVTLTEAEKAKKRQRLMSGGGDDGVDDE
+EKKKLEIFCSICIQLPERPVTTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNP
+RINLALVSAIRLANVTKCSGEATAAKVHHIIRNQDRPDKAFTTERAVKTGKANAASGKFF
+VTIPRDHFGPIPAANDVTRNQGVLVGESWEDRQECRQWGVHFPHVAGIAGQAAVGAQSVA
+LSGGYDDDEDHGEWFLYTGSGGRDLSGNKRVNKIQSSDQAFKNMNEALRLSCKMGYPVRV
+VRSWKEKRSAYAPAEGVRYDGVYRIEKCWSNVGVQGLHKMCRYLFVRCDNEPAPWTSDEH
+GDRPRPLPDVPELENATDLFVRKESPSWGFDEAEGRWKWMKSPPVSRMALDTEERKKNKR
+AKKGNNAMKARLLKEFSCQICRKVLSLPVTTPCAHNFCKACLEAKFAGITQLRDRSNGVR
+KLRAKKNIMTCPCCTTDLSEFLQNPQVNREMMEIIENFKKSEEEAEVAESSNISEEEEEE
+SEPPTKKIKMDNNSVGDTSLSA
+>seq020
+MAIQTQLPCDGDGVCMRCQVNPPSEETLTCGTCVTPWHVSCLLPESLASSTGDWECPDCS
+GVVVPSAAPGTGISGPESSGSVLVTAIRAIQADVTLTEAEKAKKRQRLMSGGGDDGVDDE
+EKKKLEIFCSICIQLPERPVTTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNP
+RINLALVSAIRLANVTKCSGEATAAKVHHIIRNQDRPDKAFTTERAVKTGKANAASGVLV
+GESWEDRQECRQWGVHFPHVAGIAGQAAVGAQSVALSGGYDDDEDHGEWFLYTGSGGRDL
+SGNKRVNKIQSSDQAFKNMNEALRLSCKMGYPVRVVRSWKEKRSAYAPAEGVRYDGVYRI
+EKCWSNVGVQGLHKMCRYLFVRCDNEPAPWTSDEHGDRPRPLPDVPELENATDLFVRKES
+PSWGFDEAEGRWKWMKSPPVSRMALDTEERKKNKRAKKGNNAMKARLLKEFSCQICRKVL
+SLPVTTPCAHNFCKACLEAKFAGITQLRDRSNGVRKLRAKKNIMTCPCCTTDLSEFLQNP
+QVNREMMEIIENFKKSEEEAEVAESSNISEEEGEEESEPPTKKIKMDKNSVGGTSLSA
+>seq021
+MAIETQLPCDGDGVCMRCQVNPPSEETLTCGTCVTPWHVPCLLPESLASSTGEWECPDCS
+GVVVPSAAPGTGNARPESSGSVLVAAIRAIQADETLTEAEKAKKRQKLMSGGGDDGVDEE
+EKKKLEIFCSICIQLPERPITTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNP
+RINLALVSAIRLANVTKCSVEATAAKVHHIIRNQDRPEKAFTTERAVKTGKANAASGKFF
+VTIPRDHFGPIPAENDVTRKQGVLVGESWEDRQECRQWGAHFPHIAGIAGQSAVGAQSVA
+LSGGYDDDEDHGEWFLYTGSGGRDLSGNKRINKKQSSDQAFKNMNESLRLSCKMGYPVRV
+VRSWKEKRSAYAPAEGVRYDGVYRIEKCWSNVGVQGSFKVCRYLFVRCDNEPAPWTSDEH
+GDRPRPLPNVPELETAADLFVRKESPSWDFDEAEGRWKWMKSPPVSRMALDPEERKKNKR
+AKNTMKARLLKEFSCQICREVLSLPVTTPCAHNFCKACLEAKFAGITQLRERSNGGRKLR
+AKKNIMTCPCCTTDLSEFLQNPQVNREMMEIIENFKKSEEEADASISEEEEEESEPPTKK
+IKMDNNSVGGSGTSLSA
+>seq022
+MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD
+YEVRLNDTIQLLVRQSLVLPHSTKERDSELSDTDSGCCLGQSESDKSSTHGEAAAETDSR
+PADEDMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEE
+DVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYD
+AEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGP
+SCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYC
+PECRNDASEVVLAGERLRESKKNAKMASATSSSQRDWGKGMACVGRTKECTIVPSNHYGP
+IPGIPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGSYSLVLAGGYEDDVDHGNFFTYTG
+SGGRDLSGNKRTAEQSCDQKLTNTNRALALNCFAPINDQEGAEAKDWRSGKPVRVVRNVK
+GGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVWRYLLRRDDDEPGPWTKEGKDRIKK
+LGLTMQYPEGYLEALANREREKENSKREEEEQQEGGFASPRTGKGKWKRKSAGGGPSRAG
+SPRRTSKKTKVEPYSLTAQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEE
+TFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQT
+VLNQLFPGYGNGR
+>seq023
+MWIQVRTMDGKETHTVNSLSRLTKVQELRKKIEEVFHVEPQLQRLFYRGKQMEDGHTLFD
+YDVRLNDTIQLLVRQSLALPLSTKERDSELSDSDSGYGVGHSESDKSSTHGEGAAEADDK
+TVWEDTDLGLYKVNEYVDVRDNIFGAWFEAQVVQVQKRALSEDEPCSSSAVKTSEDDIMY
+HVKYDDYPEHGVDIVKAKNVRARARTVIPWENLEVGQVVMANYNVDYPRKRGFWYDVEIC
+RKRQTRTARELYGNIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALRNT
+GKSGPSCRFCKDDENKPCRKCACHVCGGREAPEKQLLCDECDMAFHLYCLKPPLTSVPPE
+PEWYCPSCRTDSSEVVQAGEKLKESKKKAKMASATSSSRRDWGKGMACVGRTTECTIVPA
+NHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNY
+FTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVV
+RNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKD
+RTRQLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRAS
+KKSKLEPYTLSEQQANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELV
+FRPVTTVCQHNVCKDCLDRSFRAQVFSCPACRFELDHSSPTRVNQPLQTILNQLFPGYGS
+GR

tests/data/fastq/methylated_dna/bisulfite-seq_test_data.md

@@ -0,0 +1,61 @@
+### E. coli paired-end test dataset for Bisulfite-seq applications
+
+The E. coli data set was generated using [Sherman](https://github.com/FelixKrueger/Sherman) as 10,000 reads of paired-end data, with average methylation levels of 80% in CpG context, and 10% in non-CG context. The files can be found in the folder: genaral/fastq/dna, and are called:
+
+```
+Ecoli_10K_methylated_R1.fastq.gz
+Ecoli_10K_methylated_R2.fastq.gz
+```
+
+```bash
+Sherman --non_dir --genome /bi/scratch/Genomes/E_coli/ --paired -n 10000 -l 100 --CG 20 --CH 90
+```
+
+The data is non-directional, so it should produce roughly 25% mapping to each of the `OT`, `CTOT`, `CTOB` and `OB` strands. Thus, the data can be used for bisulfite mapping in standard (= directional), `--pbat` and `--non_directional` mode.
+
+A test alignment should look roughly like this:
+
+`bismark --genome /bi/scratch/Genomes/E_coli/ -1 Ecoli_10K_methylated_R1.fastq.gz -2 Ecoli_10K_methylated_R2.fastq.gz --non_dir`
+
+```
+Bismark report for: Ecoli_10K_methylated_R1.fastq.gz and Ecoli_10K_methylated_R2.fastq.gz (version: v0.22.3)
+Bismark was run with Bowtie 2 against the bisulfite genome of /bi/scratch/Genomes/E_coli/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
+Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
+
+Final Alignment report
+======================
+Sequence pairs analysed in total:       10000
+Number of paired-end alignments with a unique best hit: 9320
+Mapping efficiency:     93.2%
+Sequence pairs with no alignments under any condition:  0
+Sequence pairs did not map uniquely:    680
+Sequence pairs which were discarded because genomic sequence could not be extracted:    0
+
+Number of sequence pairs with unique best (first) alignment came from the bowtie output:
+CT/GA/CT:       2341    ((converted) top strand)
+GA/CT/CT:       2329    (complementary to (converted) top strand)
+GA/CT/GA:       2356    (complementary to (converted) bottom strand)
+CT/GA/GA:       2294    ((converted) bottom strand)
+
+Final Cytosine Methylation Report
+=================================
+Total number of C's analysed:   471997
+
+Total methylated C's in CpG context:    111011
+Total methylated C's in CHG context:    11923
+Total methylated C's in CHH context:    21433
+Total methylated C's in Unknown context:        0
+
+Total unmethylated C's in CpG context:  27790
+Total unmethylated C's in CHG context:  105877
+Total unmethylated C's in CHH context:  193963
+Total unmethylated C's in Unknown context:      0
+
+C methylated in CpG context:    80.0%
+C methylated in CHG context:    10.1%
+C methylated in CHH context:    10.0%
+Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0
+
+
+Bismark completed in 0d 0h 0m 12s
+```

tests/data/fastq/rna/paired_end_RNAseq_test_data.md

@@ -0,0 +1,8 @@
+### Paired-end RNA-seq test dataset
+
+The data here are 2x 76bp RNA-seq data from mouse (10,000 reads of paired-end data). The files can be found in the folder: genaral/fastq/rna, and are called:
+
+```
+test_R1.fastq.gz
+test_R2.fastq.gz
+```