transrate 0.1.0 → 0.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (47) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +16 -1
  3. data/.travis.yml +8 -0
  4. data/README.md +45 -43
  5. data/Rakefile +36 -0
  6. data/bin/transrate +98 -50
  7. data/deps/deps.yaml +55 -0
  8. data/lib/transrate.rb +19 -4
  9. data/lib/transrate/assembly.rb +93 -182
  10. data/lib/transrate/bowtie2.rb +37 -13
  11. data/lib/transrate/cmd.rb +19 -0
  12. data/lib/transrate/comparative_metrics.rb +239 -19
  13. data/lib/transrate/contig.rb +212 -0
  14. data/lib/transrate/contig_metrics.rb +76 -0
  15. data/lib/transrate/read_metrics.rb +83 -41
  16. data/lib/transrate/samtools.rb +73 -0
  17. data/lib/transrate/transrater.rb +31 -11
  18. data/lib/transrate/version.rb +1 -1
  19. data/test/data/150uncovered.l.fq +892 -0
  20. data/test/data/150uncovered.r.fq +892 -0
  21. data/test/data/Os.protein.2.fa +95 -0
  22. data/test/data/Os.protein.fa +199 -0
  23. data/test/data/assembly.2.fa +26 -0
  24. data/test/{assembly.fasta → data/assembly.fasta} +0 -0
  25. data/test/data/bridging_reads.l.fastq +20 -0
  26. data/test/data/bridging_reads.r.fastq +20 -0
  27. data/test/data/sorghum_transcript.fa +4 -0
  28. data/test/data/tiny.sam +4 -0
  29. data/test/helper.rb +33 -2
  30. data/test/test_bowtie.rb +54 -0
  31. data/test/test_cmd.rb +15 -0
  32. data/test/test_comp_metrics.rb +177 -0
  33. data/test/test_contig.rb +61 -0
  34. data/test/test_contig_metrics.rb +50 -0
  35. data/test/test_inline.rb +10 -9
  36. data/test/test_read_metrics.rb +68 -0
  37. data/test/test_samtools.rb +22 -0
  38. data/test/test_transrate.rb +40 -0
  39. data/test/test_transrater.rb +68 -0
  40. data/transrate.gemspec +16 -10
  41. metadata +232 -57
  42. data/lib/transrate/express.rb +0 -37
  43. data/lib/transrate/log.rb +0 -16
  44. data/lib/transrate/rb_hit.rb +0 -33
  45. data/lib/transrate/reciprocal_annotation.rb +0 -105
  46. data/lib/transrate/usearch.rb +0 -66
  47. data/test/test_test.rb +0 -41
data/test/data/Os.protein.2.fa ADDED
@@ -0,0 +1,95 @@
1
+ >LOC_Os03g60760.1|PACid:24121828
2
+ MEVEMGHGEEVAAAMEEEELQGWETPRREECRIPVVPPQCPAPPRKRPVALPELGKERREPPKGGYFQPPDLESLFVLAP
3
+ PRRQASSCA
4
+ >LOC_Os03g08270.3|PACid:24121831
5
+ MSIEERTLSLINKTTALNPNAQEFVPSSLRSINDVSNRSDTSRISVSGSSKDTIADQQDPVIPSNPDEEAHRYWQEQLPD
6
+ DITPDFKVLGQDEMPGPDNISLTGLSINDSIGASLFSPNQTSNLQHRASPFIRDTLSTRSKIEFPSPTYVEEQSRATIMS
7
+ PTASAMSPTAAPWVKTVRNGVQYNANRRDASHYNGDSSIGAPVQNLTDAYFGSRRSFSSTMDIMSQLENKVDGRFNQNLR
8
+ SLSFGHSSPPSPASYGQNGLANYNKEAFGLANNTYRSHSAVLADDILSPSAGREHISLDAPRGRYNTTNLPVSGLGSSRG
9
+ SQFMASSFNGNHDIVSNNTLQNIAGVQTGPAWLEADTAANMFLESKDEAHDFASLRHALLEQDRQVLLTGANPLAKELNI
10
+ KELYNLQSRLAQEKARDVYRQRFQMPEFQGLVQEQNTPIDLCGLHVSEAIHALNYELNNRRKIARSTGRRLQVIIISSTR
11
+ TPARLTAAVEQYLLEHGIQYTQAQPGLFRVLLQ
12
+ >LOC_Os10g39590.1|PACid:24095156
13
+ MSMITVKVKTLTGKEVEVSIEATETVARIKEQVEAAEGIPPPQQTLIYGGRQLADDMTAEMCDLRHGSELHLVLALRGGL
14
+ L*
15
+ >LOC_Os10g41970.1|PACid:24095158
16
+ MRGSRMNPGDRRTRSTMSIVIVMSLCCFFYILGAWQKSGTGRGDSIALRVTKETDCTILPNLHFETHHSLGGVNPLVMTD
17
+ KVFEPCHIRYSDYTPCQDQNRAMNFPRENMNYRERHCPTETKKLRCLIPAPKGYVTPFPWPKSRDYVPYANAPYKNLTVE
18
+ KAVQNWVQFEGDVFRFPGGGTMFPNGANAYIDELASVIPFTDGTIRTALDTGCGVASWGAYLMDRNVLTMSFAPRDSHEA
19
+ QVQFALERGVPAVIGVLGTIKLPYPSGSFDMAHCSRCLISWKSNDAMYMFEVDRVLRPGGYWILSGPPINWKTNHQAWKR
20
+ SKEDLEAEQNVIEKIAEMLCWGKIHEKGDTVIWRKKADSNECHNKDDHPSKMCKIQDADDVWYKKMEGCITPFPEEAQLR
21
+ KFPERLFAAPPRILQGRTPGVTEEIFEEDNKLWKKYVSTYKRINKLIGSLRYRNIMDMNAGLGSFAAIIDSPISWVMNVV
22
+ PTISEKNTLGIIYERGLIGIYHDWCEAFSTYPRTYDLIHANGLFSLYQNKCNMEDILLEMDRILRPEGAVILRDNVEVLN
23
+ KVRRTVMGMRWKSKLLDHEDGPHIPEKILVSVKKYWVGNEEENSS*
24
+ >LOC_Os09g38670.1|PACid:24136581
25
+ MPFASCLLASSSSTMMARPGAVKNIESWDEFTKHFVKSEDKLVVLVFMAPWSEPWKLMRPAVEKMASGLKSEEAEVCTIS
26
+ VDRFNTLGRLLRVEALPTFVLVKRHRAVARVVGVNRDDLHSSINKHLAPPSSSPQPINIS*
27
+ >LOC_Os09g26780.1|PACid:24136584
28
+ MAGRATATATAAGKDRSSFAVTCSLLSQFLKEKKGGGGGLQGLGLGLRPAPAAPPAAGAGGAFRPPPTTMNLLSGLDAPA
29
+ VEVEPNTAETAADELPLIKAPADQQSDESASEAAGEKAQQLTIFYGGKVVVFENFPSTKVKDLLQIVSTGDGVDKNTGTA
30
+ ATQSLPRPAHNSLPDLPIARRNSLHRFLEKRKGRMNANAPYQANCTAAPSKQANGDKSWLGFGQEMTIKQEI*
31
+ >LOC_Os12g21920.1|PACid:24147808
32
+ MPTPSTATRRPSTVTRFALCLSSPPSTPLPTPVAAAHADADAAAAVIGRPKGEGREWEERSRSQRTPSPPNSESPPKANW
33
+ GIASNNCYSRMIIASAALTSDRRMSNACDRMLAAVIPSPTAQPHAGHKGRDVCVLGYASPCPCPHLAGATAMNAT*
34
+ >LOC_Os12g24659.1|PACid:24147809
35
+ MADDKVISAIGPYFGKKLDLELIYGKKWQCSKEAALDSSTWQLNHQFMLI*
36
+ >LOC_Os01g36294.1|PACid:24116931
37
+ MAKVHELSTKGMAVDMTELFSTFSNDLICRLVSGKNFQGEGRNKLFRQLFKANSVLLAGFNLKDYYPGLARLKAVSMVMC
38
+ AKARNTRKLWDELLDEIIDERMSKQQCEHDEGNDQDEMNFVNVLLLQEQGITREHLKAILVDMYQAGTETSSVVLVFAMA
39
+ ELMQKPHLMAKLQAELRTTIPKQGHELITERDLTDMTYLKAVIKETLRLHPPTPLLLPHLAMADCNIDGYTVRSGTRVIV
40
+ NAWAIGRNSESWEAAEEFLPERFVDDGSAANVDFIGTDFQFLPFGAGRRICPGINFASASMEIILANLLYHFDWDVSAEA
41
+ AIDKDGIDMAEAFGLSVQLKEKLLLVPVDYKDGMQDSAVILL*
42
+ >LOC_Os01g36410.1|PACid:24116932
43
+ MAGVGGRLGTATARVVRRMMTRLKDGGAPWDYEEAYPVLYLGGGEGGAGDRQWEPGAVGLALSLRASALAGGGGYGLATA
44
+ AAVVGFAGGRHGGRGVCFADAGQWLSRRRQQRSGSSRLVAPGRGAASVGRGGCEGSAGRGRASGRGGAEASSALHSLAAR
45
+ FAGRGGMGGLGATTFGSHPMCSMKCLQGKRWERGERDGVLGHWQVGSRVLGPTDQRSTGIGEMRNISSQGFFFREG*
46
+ >LOC_Os12g22750.1|PACid:24148077
47
+ MSGVPPAAAGGDGTGGAPPGAGAGGGAPGAGAANNNINGGNSASQSSGGPFSRCILLLFPLLALSLYCHVRYVPVPDLHD
48
+ ASSMLLSYCNVSVPDIHDAHRKENGAFNTRKRRAFSAASLYVRPCSGMLRPPLSSELGGGGSEEEEGEPRGERE*
49
+ >LOC_Os12g22780.1|PACid:24148079
50
+ MEDLHDWECRFTPRKLASLNKWSSRAGLSPMELQSCAGEVTDKVTAIAWGGRIRYLHLAFGGSSCWRYVVGLREGNKNVG
51
+ AIVKGFHDGVAMGVFSLVDSREAAEAPTASHGDGLESQCGGSHAAVQGEHNLEPWAEACVCSIAF*
52
+ >LOC_Os02g55190.1|PACid:24133604
53
+ MAMERNAAPRVSASSSAAASPSTVGALLSKASVAAAPAREIPSPRSLLSRILHRSGGGGGFGCRLRLPRYCSSGAAAKED
54
+ AAAEYVEVEVEAEAAAPKVVGRQAVDRESPRSSLGKKAAEEVSPASLGLGASLMLLLSKSAAELNRMAELRAQMERLVLD
55
+ TKGEEEARSSNHPNASDDHADITKEEPTAFSGGALSRCSRTAAAPGNAGHHAAVPMDQMEAELEAELTLLQCATPRRDRQ
56
+ LEIGDDEEESTDTHAATFADADDDTDGADDEEEEEEESGAAAQGGVSARELERRLHELLQWRHEERIAELETALERARKR
57
+ LQEKEREVCWWRNTAKLVTRHKDDSRLR*
58
+ >LOC_Os02g56470.1|PACid:24133605
59
+ MVPQSGVGTKAVDYEVEQRDGGRVVKRKEAGLTRGSHGGVPVATSSVGRDMLAVSDIQAETPYAQLNAASVPGEAGRQGR
60
+ WGSLPTARTLCRPCLLAADLSDELALTPIHQLRRLTSCT*
61
+ >LOC_Os03g56500.1|PACid:24123297
62
+ MSGEAESREASRQRRRRERAAAVERFVGVPLADVVRENSLVHLPPAAAARLRVVHPSWASHMSSPLFAVAHAAAPRRVSG
63
+ VFVPSAGFLPFDGDDDAVPSPSLSFVPASSELVVLSSSRGVACCFSPADDAYAVCNPATASWTAVPSPPWRSWPRPAIVV
64
+ LFDTSAYNFRGDFTLVCPFESEPGSSGAYCFQVFTSGTGAWWVTDAMSPAEGLVAASGVAAGATAWWRTSIGTAVGYTPV
65
+ TGRVDLVTCPGDSDQWEIGLAAGMLHCAVIDGGDVVVFRLHEHGIWEVTTRVAVAEILQPSQPPPPARATTSTEIVASQQ
66
+ HDESGAEEEEGSRAVVAAANAPLRLDDGVRLLGFQGAEVEVVVLAGRRLVAFDARTRRRREVAVPDEVDAAWDGAEHAAH
67
+ INTLALIAPAALAAEPPLAKPPADP*
68
+ >LOC_Os03g30530.1|PACid:24123298
69
+ MPSRMMQAFAQEASDFDRQMGCMAGMFQIFDRRRLLTARQRGGARGTAPPGSHVLPNSNSNVSIQNPVASNNTLDKTFSK
70
+ SMTENSSLSMESSRASSSSSSCSSFSSTDINRPIQQELSYINKERFAGKPPRSSQTKSVKCSKTEAKTKDPHTGFRDIVK
71
+ ESINRETHGMTIKTSTKESRKGLHKDSPRPLLISKSTDGTYVIGIDRSTGVPGYVHESSRPPRFSCDDRQLLRSVEAQDS
72
+ KKPSAKLKELPRLSLDSRKESMNPCSRLKNSGYIRTDDNLLDVLKHQESPSHQRASSVVAKLMGLEGTTPDIHETARSPT
73
+ PVHGTQIDQPSHCQRIKNQDHSVPVQKNHSPVLKTNPSPRIIPEAAPWRQNERAVTGRAAEVKPRTASIYADIQRRLRGL
74
+ ELSECNKELRALRILSTLHKKDGPSQSDNNPELTAIQKKASEQIVDSENFQSPIVIMKPARCITKPDASDTLVAPLSRPK
75
+ GIRRLRHEETSFTRKNENSDSKRNHSPNESAHSSGEEPVNSARSPRLSSSLSPRLAQKKADSERRSRPPVLPTSPGKKSK
76
+ ETVSPRGRLRSRHSQTKSNSDNDNVLHIPETKINLAKQIDVGVVDHPNPLNANSPYIHQSKIASTPNREEMPTILPADKK
77
+ >LOC_Os03g56724.1|PACid:24125111
78
+ MSCEKLSRQSLHLVLNEGRGLFSLRHMDVSKLFYPSTAEALEAEAKAKKKKNGTNKIGSIGRLPTPSIHYQPYTWSASNP
79
+ YSSLCALALFGERSKNKILCTDMAGHTSIYNPELRSFMRMPDLNSPKRYNSCVAVSIPGASAHAMSNFDIDTDHSLYIMD
80
+ IDPTYWCSSEVLAYDPVEECWCWGPLPQPPFFQDREYKVPLKPRFMVVDSTKICVSTTTATYSFDMVTRDWNKVGDWVLP
81
+ FNAEYVPELGHCLGMSDGGPFDLCILDNLSTAAGSPPPVVRHVGMEFELPENWSQVYRDLVNLGSLRFCIVNGYTIENER
82
+ YECDFNPVTVFTGVEVLPTSSEQGLLMIKHKSKCIMTYIMFVL*
83
+ >LOC_Os03g49850.1|PACid:24125112
84
+ MTPGLEGVDPAVLDSGAADSPLLTSVTSTMRMTVVARATATIATSHARVDLAAPDSGAADPPPPSSAMMMTIMTTRARMT
85
+ TMTMASRARADPSGAELGRGRFANVGLRSCGDCCGDRVP*
86
+ >LOC_Os01g11360.1|PACid:24119702
87
+ MAARGSRSCAWPCGLGMAGGGQEGSGNRQGVGDGVPPDGGRDSEARRKMVTALGGYGSPRGCGVPRQWQSEHCESDKVEA
88
+ DPIEQIQRGFSIYRANTEGKGVVDGGFTCFAMGIGRVVSAGTAAASAESRLRRLLEMLLVVVSNIGTYQTRGILVKDLLK
89
+ *
90
+ >LOC_Os01g44140.1|PACid:24119703
91
+ MTVAAAAAAAADDAGRPGAAAARLRVMWRVVRAAEALALAVLLSRSLPLLPVAAGAAGAVLRVGASFLLHPCSVFLLANG
92
+ IVVLLVALSRRDRPSSSSSSSSSSSCSDDHDDVHDQFLSFAGAHLPPLPAAITGAAAADQEEGAVFEDKQAVHVTPARAA
93
+ PRRSRSEKVGRGRRPTRAASPELRRSESERCRRRRRSLSSSSASLADWGMEEDDGGEKEEEEFRRAVEAFIAKQQTRFHR
94
+ EESFVLVAGAGAGDETSAAAAAVEVK*
95
+
data/test/data/Os.protein.fa ADDED
@@ -0,0 +1,199 @@
1
+ >ChrUn.fgenesh.mRNA.8|PACid:24093257
2
+ MSHSSGASDASSTSDEEPVPAPSTSVLQTVNIRSHVPVVLDLDVSNYSQWRCSFESVLGKFGLEAHVQEPPALDLRTAEW
3
+ RRADHCVVNWLHNSIAKNVFDVVYKPRASAFTVWSDIEGVFRDNAVQRSVYLETEFRSINQGDMTITQYTAKLKQLADGL
4
+ RDINMPVSEPSQVLNLLRGLNTKFRSLRASIADRNPPHTFMTARSYLLLAELQMQHDAKAEAGEALYAGTGSSSGTSDTT
5
+ GQPRPKGRGKRRGRGGGAPPGGAPSTPGGGAGAGHDGQPRPPAPWGYNPWTGFVQAWPFPFRAPGAGVLGPRPPFQAQQA
6
+ MTAQHLLPALPPASPGVQSTGAWDNSALYSALQSAGVATTTPPSAADWFLISSSHVRLLHLPRRLPHLLVVQAADDRLEA
7
+ TIAYCDNISSVYMSKNPVHHKRTKHIELDIHFVREKVALGELRVLPIPSAHQFADVFTKGLPSSMFNEFRASLCVDRRST
8
+ AGSGALTSSTTEYSPTMLSISEFRYGSLASVARLIDRSSCTCTYLVLGNAPMALESSKVFAKAAVFAMCMIVALTSPSNH
9
+ FCPSQELSSAVTDVLTCAYAVLLSALRRSWSRDNWRTNRHCPQCDNIPHPLAHSYARSGGISNNVEVGEVMGPSESVRSA
10
+ RGEVAVVARLALWLRRDKKKHARPRGKRIGASTIKGTSSSADARFDTQIPGSSTHKYQRGVCGDFINLKIYRSNLSEVSI
11
+ GPFRGWALDFTGQIYPSSSKGHWFVLVAMDYFTKWAEAVPPENITCTEANG*
12
+ >ChrUn.fgenesh.mRNA.7|PACid:24093258
13
+ MDRRSRHWRDGGRGRTGGGSAGVIEVEDGLTPGGGGAMEVDGRSAESRGGAVEAEGGAAEVHGGCGKAESAWWRRKAEAP
14
+ WKRRRCIGGGRRRRRDRAQRNAMGRGGAAFVACGLVGGRYHVSVMVKTTNGSRDSNNASGSEEQINGPRASGASDNSPSP
15
+ PHENPTIDQVLDNQTQMMTMMMQQMQQQYHQVLQQSKLLKFLRVKPPTFSGTTNPIEANDWLHAIEKKLNLLQCNDQEKV
16
+ AFATHQLQGPVSVWWDNYMVTRPAGTEVTWSEFCQSFNKAQVPEGIVAQKKREFRSLQQGTKTVIEYLHEFNRLARYAPE
17
+ DVRTDAERQEKFLSGLDDELINQLISRDYEDFEKLHCPYHPGSFNKNYNSGSHSNKEAQSAPEVILGTFPINWTPAVILF
18
+ DSGATHSFISKRFAGAHGLSLVKLKIPMRVHTPGGGMTTTHYCPSVTVEIQGLIFLANLILLESKDLDVILGMDWLTRHR
19
+ GATGEEQEVVVEKTTKKLEDITIVREYPEVFPDDLTTMPPKRDIEFRIDLAPGTAPIHKRPYRMGANELAEVKKQVDEQL
20
+ QKGYIRSSTSPWGAPLRIREEDIPKTAFITRYGLFECTIMSFGLTNAPAFFMNLMNKVFMEFLDKFVVVFINDILIYSKF
21
+ EEEHEQHLRLVLEKLKEHQLYAKFSKCDFWLKKVQFLGHVISAQGVAVDPANVESVTKWTPPRTVTQGLRCVLMQDGKVV
22
+ AYASRKLRPHEGNYLTHDLELATVVHALKIWRHYLIGNRCERRWLELIKDYDMGIHYHPGKANVVADALSRKSYCNVAWV
23
+ EELCCEAQPTLVEQVRIAQASDPEIAKLKKNMRVGKARGFTEDEHETIWMGERLCVPENKELKDLILIEAHQTQYSIHPG
24
+ STKMYQDLKEKFWWVSMRREIAEFIALCGVCQRVKAEHQRPAGLLQPLQIPEWKWEEIGMDFITGLPRTSSGHNSIWVVI
25
+ DRLTKVAHFIPVHTTYSGKRLAELYLARIMCLHGVVGNFL*
26
+ >ChrUn.fgenesh.mRNA.71|PACid:24093259
27
+ MAVRRRGSVAGDSNQAAREVAAHGAKGGGVGQRRLRTRERRVRGGGPHQRAWRPAQRMKAAVTTGDAEARTADGDT*
28
+ >ChrUn.fgenesh.mRNA.11|PACid:24093260
29
+ MTWRKFRTDRAGKAVMAIEEVQALRKEFDAQQASNYQQPVHKKVRKDLYYAFHGRSSHTTEQCRNIRQRGNVQDPRPQQG
30
+ ATVEAPREAVQEQAPPAEQRQDAQRRVIQVITRADPPSQLSKRQKKMQIRTVHSITSAGEGAPQYLNQLISFGPEDAEGV
31
+ MFPHQDPLVILAEIAGFEVRRILVDGGSSADVIFAEAYAKMGLPTQALTPAPASLRRFGGEAVEVLGQALLLIAFGSGEN
32
+ RREVQLQRHLRPCNPEQVRSHFPPQLSQAQDARPDRSDSARITGGDMGEEEAESILEVLKKNIDIFAWSPDEVGGVSTDL
33
+ IIHHLAVKPDGKPRKQKLRKMSADRQEVAKAEVQKLLRAGVIQESNHPEWLANPMLVRKSNDKWRMCVDFTDLNKACPKD
34
+ DFPLPRIDQLVDSIAGCELMSFLDAYSGYHQIHMNPPDIPKTAFITPFGTFCHLRMPFGLRNAGATFARQVYKVLCKQLG
35
+ RNVEAYVDDIVVKSRKAFDHTSDLQETFDNLRAADIKLNPEKCVFGIRAGKLLGFLVSERGIEANPEKIDAILQMKPPSS
36
+ VHEIQKLAGRIAALSQFLSKAAERGLPFFKTLRGAGKFNWTPECQAVFDELKQYLQSPPALISPAPGSELLQYLAASPVA
37
+ ISAVLIQETEFGQKPVYFVSEALQGVKTRYIEMEKLAYALVMASRKLKHYFQAHKVIVPSQYSLGEILRGKEVTSRLSKW
38
+ AAELSPFDLHFVARTAVKSQVLADFVAEWTPVFAPEPEPVEQLWVMCSDGSWSHKGAGIAAVLISPNGVPIRYAARLQFD
39
+ TTNNTAEYEAILLGLRKAKVLGVRRFLIQTDSKLVAGHVDKSFEAKEEGMKRYLEAVRSMEKCFTGITVEHLPRGQNEEA
40
+ DALAKSAACGGPHSPGILFEVLHAPSVPMDSLEVMAIDQVKLGEDPYDWRIPFVKHLETGWLLEDEAEAKRLQLRATKYK
41
+ MVSGQLYRSGVLQPLLRCISFAEGEEMAKEIHQGLCGAHQAARTVASKVFRQGVYWPTVLKVCVEQIKKCESCQRHGRTQ
42
+ TAPQYDLQPIAPIWPFARWGLDIIGPFPVARNGYKFAIVAVEYFSRWIEAEPLGAITSAAVQKFVWKNIVCRFGVPKEFI
43
+ TDNGKQFDSDKFREMCEGLNLEIRFASVAHP*
44
+ >ChrUn.fgenesh.mRNA.52|PACid:24093261
45
+ MDGRDRTGPRRLTGEGLDDASDDVTDDGGGSAEETARTAHARRRTAARGRKRRTPGRSGQHGEHTDDQSDGGGGTNDDGD
46
+ EERAAATFGLSTATMLRRVPTAAKGRTRTATTWRPRRRSSRATATTGATAELGWSGGGDGEARAHGARTIPATRGKGEGC
47
+ DNYGTYTCPDGEESATLMHAVHMLSAMDAVSVERDKAAHDRENWNGGKICKLESKVYRLQKELAELKGETPPPAPKLRLT
48
+ ARKRTCPPPRLQLASKIRVIGEAVPDRAEPMVNTRTGSGSGSGSGATNNEGDPTLAQILAQQTQLINLLVQQAQNQQANN
49
+ QNQNPPPPPQNKLADFLHLHGPAAEWWDHFRQGRAEGEPITWQEFTAAFKKTHIPTGVVALKKREFRALNQGSRSVTEYL
50
+ HDFNRLARYAPEDVRSDEERQEKFLEGLNDELSYALMSTDFRDFQQLVDKAIRQEDKYNRMEQKKRRAAQFKAQQGSNQR
51
+ PCLVTGPQAPSYPQGGSSSVVRPQRQFYNNNTGNRGNDNRNMVARPAATPAQNQPVRKEQGSKPVVCFNCGDPGHYADKC
52
+ PKPRRVKNAPASNNSNVPAPKARVNHVAAAEAQNAPDVVLGTFPVNSIPATVLFDSGATHSFLSKSFASNHGMEVISLGR
53
+ PLLVNTPGNQVFSTQYCLSVTIEIEEVPFPSSLILLESKDLDVILGMDWLSRHRGVIDCANRKVTLTNSNGETISFFASS
54
+ LKSHGVILNQVVLQEIPIVQDYPDVFPEDLPGMPPKRDIEFRIDLVPGTNPIHKRPYRMAANELAEVKRQVDDLLQKGYI
55
+ RPNTSPWGAPVIFVEKKDHTQRMCVDYRALNEVTIKNKYPLPRIDDLFDQLEGATVFSKIDLRSGYHQLRIREEDIPKTA
56
+ FTTRYGLFECTVMSFGLTNAPAFFMNLMNKVFMEYLDKFVVVFIDDILIYSKTKEEHEEHLRLALEKLREHQLYAKFSKC
57
+ EFWLSEVKFLCHVISSGGVAVDPSNVESVLSWKQPKTVSEIRSFLGLAGYYRRFIENFSKIARPMTRLLQKEVKYKWTED
58
+ CERSFQELKKRLVTAPVLILPDSRKGFQVYCDASRLGLGCVLMQEGKVVAYASRQLRPHENNYPTHDLELAAVVHALKIW
59
+ RHYLFGNRTEIYTDHKSLKYIFTQPDLNMRQRRWLELIKDYDMEIHYHPGKANVVADALSRKSYCNMSEGRRLPWELCQE
60
+ FERLNLGIVSKGFVAALEAKPTLFD*
61
+ >ChrUn.fgenesh.mRNA.61|PACid:24093262
62
+ MKEMRVTKDDTDYAPADEIGLSQLADAPEATKPSQSPRQIN*
63
+ >ChrUn.fgenesh.mRNA.67|PACid:24093263
64
+ MTTASLVHPSASSSSSSTRAEVEVVGGVFVCSDSCSGDIVRNLIVDYGSGKITLTAACIQFCVPCTRPQPLLPPLCHSGP
65
+ INTCFATADDRGRSRFRHYH*
66
+ >ChrUn.fgenesh.mRNA.75|PACid:24093264
67
+ MSSKVTFQIVHGEGNIRFGPDGVDLSDFVMTSKGIDRPAERTFQSIYSWLLRGFRIDQEVYTMSVSVVVSRAIEGYFWEL
68
+ MPMDSTTAWRRYVEMAFERSWPLVIFVSVQEKDTNVSMRTEDVEGPSNAGDVVGPSMENEENQPREEQAMGMADEGERVG
69
+ IIVDEMEREDSDNEQAEDDASSDEEGDVMATDWANEDFSGLVISEGDHVPWEYKENEVIEGARYAHKDEMKEAVKHWAVS
70
+ LQREFRVVKHIENKFKYTISYAKAWRAKQKIIEMRYGTFEASYDNLPRLLATIAQRNNNTYYDLHTFTSVDDRTKSVLQR
71
+ AFFSLGACINAFVHCRPVLCIDGTFMTGKYRGQILTAIGCDGNNQVLPMAFAFVESENTESWYWFLERVHIAVVRMRPNV
72
+ CLIHDRHAGMLRAIDYLQNGWDEKGLPAKWPDVRSRWCMRHMGANFYKQFKNKHLMDLFKRLCAQNQEKKFNELWDKLDE
73
+ LTTKQTDEQSRRPQVEGEEPPIPLGALHDDPPTMRRRSGSSIRNFSQWIENEPKEKWSLLFDTDGSRYGIMTTNLAEVYN
74
+ WVMRGVRVLPLVAIVEFILHGTQAYFRDRYKKIGPSMADNNIVFGNVVTKYMEDKIKKARRHRVVAQGTQVRRYEIMCVD
75
+ RSRRGIYRKQAIQECVLKADGGCTCSCMKPKLRHLPCSHVLAAAGDCGISPNVYVSNYFRKEAIFHTWSEEIYGFGISGS
76
+ YTTLSAQVFYIPDPSKLRVKKGRRQTRRIRNDMDESEAGGRTLRCSKCDLRGHTYKKCPKNAEVPSGADASPSGQASDGM
77
+ AYDTPALLNRGIDRNHRSFLSAVEGAQLGTFRPRTSREWLRVDPRHVPWLRAAGLLPLCRLVEAAADDRDPAKRWDADRS
78
+ LLAALVDRWRPETHTFHLPCGEMAPTLQDVSYLLGLPLAGAPVGPVAGVVGWKEDITARFEQVMRLPHLGPTNTLPPYST
79
+ VGPSKAWLLQFTADLLHPDADDYSVRRSLEAYLLWLFGWVMFTSTHGHAVDFRLVHYARSIADAQPQDVPQWSWGSAVLA
80
+ ATYRALCEACTKTDAGAIIAGCPMLLQLWAAERFAIGRPVVDSAPYGVGRSAQWPEDGPTMGTYWCRRGRRYAHVQVRRG
81
+ YPDFVFEFDRLQPSDVIWEPYTEEVVAARAPLGLSSLCTRDQAYWLTILPMVFDIFVEPHCPQRVMRQFGLRQVFPGNVQ
82
+ PTVPPADHSLTRRGQLAGALWAPRVQQYVDDWVLATEEVINELFPHTEENYRDYLRWYLPRTRARVTFTPDAPEPHVAAV
83
+ TDAYPTHRDRDYFVAADAARDISADITAVQVRLNRGLHLTDVEQRATFDRMQEKMRAVMRVFSCRSAVDVVPPAGPDLVC
84
+ LRARSQARPGASASSAGAFATSSGAFASSSSHGASIPRPHAGYAAGIFGTGASSSHAGRTGPTSQFYDDDLHGADHQDVL
85
+ GSSQLGGAPEAHTQEQPEVTPVQAGRVGRAVPPDRLTYSQGHIRAQGRRDRVIFIHMVLEQLMLTTTHFRRFTVVPYPVA
86
+ RTVHNSTHEKRQLELSLSTFGVAC*
87
+ >ChrUn.fgenesh.mRNA.32|PACid:24093265
88
+ MEFCSKIFKSYYKYEGIVRHYTVPHKPQQNGVAERFPKQFWAEAVSTACYLINQSPIYTIDKKTHFEVWSSSPANYSDLR
89
+ VFGCTAYAHIDNGKLKPRAIKCIFHGYLSGVKGYKLWCPETKKIQVATVEQSPKCSIAKDKPKGNTKPPQRYIEETNIIA
90
+ YALSVVEEIEEQMDVKTAFLHGGLEEDIYMEQPEGFVVPRKDNLVCRLKKSLYGLKQSPRQWYMRFDSFMIPQKFRRSNF
91
+ YSCVYLKVVDGSAIYLFLYVNDMLIAAKDKSKIAKLKAQLSSEFEMKDLGAAKQILVSTPLAAHFRLSSNLYPQSDYDIE
92
+ FIPRVPYSSAVGSLMYAIVYSRPNLSHALSVVSRYMANPGKEHWKAVQWIFIYLHGTSSGCLQFGGSRDGLVGCKDLDFA
93
+ GDLDRRRSLTGYVFTIGGCAVSWKASLQAAIALSTTEAEYMAISKACNEAIWFRALYTQLCEVTSCINIFCDSQSAICLI
94
+ KYQMFHERTKYIDVRYHFIRGVNA*
95
+ >ChrUn.fgenesh.mRNA.29|PACid:24093266
96
+ MAEGIVGLLITKLSAVLARDATTLLGASQLLKEVSALRGLFSEIHDVKEELESMQAFLQGAELFRDTDKTTSVFVKKIRD
97
+ LAFEIEDVVDEFTYKLDDKHGGFVDRVKKRIKHVKTWHRLAHKLQEIKRRLEAADRRNVRYGMRGIQMKGGCSDAHSKSA
98
+ GQTSYFAREEDLVGIKENKEKLIQWLTGDRELGSKITTIWGMGGVGKTTLVQHVYNTIKVEFDAAAWIAVSKSYDVEDLM
99
+ KKMAKDFGLRIDIVNMENRSLIEMMHRYLQGKRYIVIMDDVWGVDVWFKVRHVFPTNCISRFIITSRIHEVALLATRNSV
100
+ IQLEPLHEHHSWELFCKEAFWNNDNKTCPLELKYLAQKFVEKCNGLPIAIACIGRLLSCKQLTYSEWENMYKQLEIQLTN
101
+ NAIFDVSNILKLSLEDLPYNLKNCLMYCTIFPEDYLIHRRKIIRHWITAGFIQEIGNKTLEQVAEGYLNELVNRSLLQVV
102
+ RRNEFGRLRQCQMHDIIHLLALNKSNEERFCQIYNGSRKVLVAGTRRLSIQNENVEQLDRSGATYLRALHVFKSHINIDL
103
+ LRPILKSSNMLSTLDLENVQINMLPNEVFDLFNLRYLGLHNTNIETLPESLGRLQNLEVLDAFETNLSYLPKHVVKLEKL
104
+ RYLYAGTFFRDHEIIGAFGGIEMPNGLRHLTGLQALQCVKASSEILHEVGALRELRTLGVANVKSEYSADLCAAITKLSH
105
+ LIHLEITAPGEMEVLHLEGLHLPMTVSWLGIEGILEKTSMPQVLSSWSHVSTLTRLRLAFCRLDEDSFSSLLVLHGLYCL
106
+ EISTKGFIGKRLKFSAGSFPNLRTLIVGGAPELNQVDIENGAMQSLDYLLFIECPNLRDLPHGIEHLTVLEKLCLLEASE
107
+ ELIQRLRKMRDSDECDEDLMKISHIRNVTVGQIQKQIWERIR*
108
+ >ChrUn.fgenesh.mRNA.15|PACid:24093267
109
+ MSWHRAGVLLLGAQSCLPVPGVPAVGGIGSVLLSMARMGWKLCHVFRPYTVVMAGSVTRRGLDMTGFVLELRGMCVVLGY
110
+ PHGVDYQARPLPEQEGDDAEPHAAWEVTAVILAGSPERTSLAVTAGGDSFPAACQNAALLAIGTLHQRYPDELQHSPYRY
111
+ HPRRGGARDYATFRDASSEDDATIVHLARMVEVYDAARIDFHQMVRRGMVENNLKILELRQENLQLKKDLDAVEAQLHQL
112
+ KIAQGEVCRPKRRRVCRSQKITARKSTSRPELVRQSLAWTCFVETPRAEPAPVVPQEGEASGFGSTEDALLLTFRPGPSQ
113
+ RRNAATGDGNQPEGSNHNHQGNPPPPPPPPPPPPPDTNAILTQILAQQANMMTAFLYHLQNPPQHNAPPPPPQHSKLAEF
114
+ LRIRPPTFSSSNNPVDALDWLHAVGKKLDTVQCSDEEKVIFAAHQLQGPASLWWDHFQATQPEGQPITWARFTAAFRRTH
115
+ VPAGVVALKKREFRELKQGNRSVMEYLHEFNNLARYASEDVREDEEKQEKFLAGMDPELSVRLVSGDYPDFQRLVDKSIR
116
+ LEAKHKELESHKRRLANFRNQQGANQRVRYTNPYPGGSSSQQQQQQQQPRSTPRPQFVVRVPQPQQQQSQQGTRAPRPPT
117
+ PTVQPGQGRRDAQGPQRLCFNCFEPGHFADKCPKPRRQQGQAPPRSNNGGKDVIRGRVNHVTAEDVLTTPDVIVGTFLIH
118
+ SIPATILFDSGASHSFISVPFVGRNQLGVERLRNPLLITTPGGVMTAKYYSPAVPIEIQGIPFPSDLILLDTKNLDVILG
119
+ MNWLAQFQGVVDCARRTVTLYRGPEQPVLFFAPPTSVSSSELHQIGLSEISIVREFGDVFPEELPGMPPKREIEFRIDLA
120
+ PGTTPLYKRPYRMAANELAEVKKQLEELKEKGYIRPSTSPWGAPVIFVEKKDKTKRMCVDYRALNEVTIKNKYPLPRIDD
121
+ LFDQLKGATVFSKIDLRSGYHQLRIREEDIPKTAFTTRYGLYEFTVMSFGLTNAPAFFMNLMNKVFMEYLDKFVVVFIDD
122
+ ILIYSQSEEDHQHHLRLVLGKLREHQLYAKLSKCEFWLSEVKFLGHVISVKGVAVDPETVTAVTDWKQPKTVTQVRSFLG
123
+ LAGYYRRFIENFSKIARPMTQLLKKEEKFVWSPQCEKAFQTLKEKLVSLPVLILPDTRKDFMVYCDASRQGLGCVLMQDG
124
+ HVVAYASRQLRPHEGNYPTHDLELAAVVHALKIWRHYLIGNRCEIYTDHKSLKYIFTQSDLNLRQRRWLELIKDYDVGIH
125
+ YHPGKANVVADALSRKSHCNTLNVRGIPPEFNQQMEALNLSIVGRGFLAALEAKPTLLDQIREAQKNDPDMHGLLKNMKQ
126
+ GKAAGFTEDEHGTLWNGNRVCVPDNRELKQLILQEAHESPYSIHPGSTKMYLDLKEKYWWVSMKREIAEFVALCDVCQRV
127
+ KAEHQRPAGLLQPLQVPEWKWDEIGMDFITGLPKTQGGYDSIWVVVDRLTKVARFIPVKTTYGGNKLAELYFARIVSLHG
128
+ IPKKIVSDRGSQFTSHFWKKLQEELGTRLNFSTAYHPQTDGQTERLNQILEDMLRACVLDFGKTWDKSLPYAEFSYNNSW
129
+ HFMKRCMGANAGHRYCGTKLGKAKFQTKGKLAPRFVGPFRIIARRGEVAYQLELPASLGNVHDVFHVSQLKKCLRVPSEQ
130
+ ADSEHIEVREDLTYVERPVKILDTMERRTRNRVIRFCKVQWSNHAEEEATWEREDELKAAHPDLFASSSESRGRDSV*
131
+ >ChrUn.fgenesh.mRNA.65|PACid:24093268
132
+ MATWRRGTGREADGTGPRRRDVGGDGQRQRAARERRWNVMVTAARGGATARGGDSSAGREAAAAERGDGDGDGPRRRGAR
133
+ GRLGAVWQRRGKG*
134
+ >ChrUn.fgenesh.mRNA.80|PACid:24093269
135
+ MRLEEEVEREDDRRQDSRPLDQTAAVLGTARSRVLLLRPPSSPLLWPDLGGREGGEESVAGCCAVLRAAGYCVVFHAARS
136
+ PPGLHAPPRRRLLWPLPPPSMSLAGSKRRGEEVKGEGRGRDEGCYERTNKCNNYEELRNWDFYKSTLVQKKKARQVVVLF
137
+ RMSYPSSELNFEAAIVIRASWLKGSRRYLITEGMSAFIVYFGEGEILENESGVDLSNFRQCTLHHPNPDTLTMPEVWRRG
138
+ YEYVMLVQACQGRVPTESAAGQSSNREELGSSSHEEDEVVAPHRGGDVGPDIQNLSIQGDEVVNHHPTGEADEGEDIPAI
139
+ VEEIERVDRHAIEDEENLAAEENDDEDEQQVEEVPMPASWNQEDPGYIAENSCHDSIWFYGDGQINLGAMFRDKTGLQDV
140
+ VKSWSFKTQRQFRVVKSNKTEYTVVCETEGCTFRLHGHVPKYESYWIVSKLHEHSCLIRNTRESHRNLTAAYVANKYYKE
141
+ IIEGDDLPVRHIIKLVEKACIHAFQCPRPVLCVDGTFLTGKYRGQILTAVGADANNQIIPVAFAFVESENYESWLWFLQH
142
+ LKWGVVQKRTSICIIHDRNAGLLKAIKELQEDGDGAYYWPDMHSRWCMRHMGANFFKQFNSRRLMNMFKWLCKANQSTKF
143
+ DELWKQLDEATRTHTRSKQTNSNPKDVHVPQALEPMDDLIPSNGKKRRSSKNIKCFTHWIECKPNDKWALLHDTNGARHG
144
+ IMTTNLAEAYNAVLCKLRPLSLTAIVEGIMHRTTMWMRTRRAAALQQMSNAQTPFCKKMAEYLQEKANKARFHTVITTGN
145
+ VRRRWEVTCRTKGGFGSSTGVITHEVTLGHESDNTCSCSCNKPKLLHKPCSHVLAACAKIKLDSTSYVSTFYLKDRVLNA
146
+ WSAEILGWRSLQHLVETGGDNRIYVPDLDLLKAGKGRRQTRRLRNDMDASEAGGPVRRCEECLQYGHRTRDCKNNKEGTS
147
+ SPVEPRQQRARRNRRGSQDIEEEWPYPLLSKEIDARHRAKKIYDGNSCSSLAVLIPRTAGLLSAAGLLTFVQMTQARMHY
148
+ DAREPKQKLMGAHSKRRQNIDKSLLMALVDRWRPETHTFHLPCGEMTITLQDVSMLTGLPLAGQAIVLPDPPEDWRDDIV
149
+ SRYACILSRYAIGDTDDDEDKIFFSEKETHGPTLKWLSQFEVRYMPDDVQEYQLTLYLEAYLLWLFGWVLFTGSHGNTVD
150
+ ARLIPLARQIAEGNISPSAQFSWGSAILAATYRGFCDACIKTGQREAIFTGCPLLVMLWSYERFSFGRPYMSVVVAHKDD
151
+ YTDAVDDRPTFGTRWCYGPPQWARIQVHNVYEYFTEAFESLRENEVRWTPYTNEEAILRAPHGVSILCYRDEAYWMTRKM
152
+ LVYDIFVEGQNRQADNRYRRSMHSRMTPWIEAWSQALNDVVHETRAYDHNTYKQYMAWYTSQTRIRLLAPEDPDERGPPT
153
+ IDQIYDMQLAPPAHLTTDIAGELVKEAKTLWEKLRDGMAGTNQEVMAAVDSLRRKGKRIMRLASCRHSSDIYNPATSRRT
154
+ FEPMRERPSTSSRPSTSSRPSASARRSSDGRVGVRSTSFREPPTIPTIPEITEISERLGGFGSTQEGTRMVRPVPHMPPA
155
+ RPQMIRQMAPDVPTSHWQGGFAPFAGPTQPVPLHAPTYGTNPWQGQSMDYGGTSFGGGVQGYMDLLQQGDWLFGQYSSHP
156
+ NEIRYMQAPSTGSFRPELMSGFRPYTTSYGDMSSFGGGSSSVPNELRTSQTDDAPQVTQPTQPEVGEGNDNDPRRSNRER
157
+ HEPNRLSLSGPRHAARQRKKTTKKRGGTSTTTTDHDDDDEYN*
158
+ >ChrUn.fgenesh.mRNA.70|PACid:24093270
159
+ MSSKVTFQIVHGEGNIRFGPDGVDLSDFVMTSKGIDRPAERTFQSIYSWLLRGFRIDQEVYTMSVSVVVSRAIEGYFWEL
160
+ MPMDSTTAWRRYVEMAFERSWPLVIFVSVQEKDTNVSMRTEDVEGPSNAGDVVGPSMENEENQPREEQAMGMADEGERVG
161
+ IIVDEMEREDSDNEQAEDDASSDEEGDVMATDWANEDFSGLVISEGDHVPWEYKENEVIEGARYAHKDEMKEAVKHWAVS
162
+ LQREFRVVKHIENKFKYTISYAKAWRAKQKIIEMRYGTFEASYDNLPRLLATIAQRNNNTYYDLHTFTSVDDRTKSVLQR
163
+ AFFSLGACINAFVHCRPVLCIDGTFMTGKYRGQILTAIGCDGNNQVLPMAFAFVESENTESWYWFLERVHIAVVRMRPNV
164
+ CLIHDRHAGMLRAIDYLQNGWDEKGLPAKWPDVRSRWCMRHMGANFYKQFKNKHLMDLFKRLCAQNQEKKFNELWDKLDE
165
+ LTTKQTDEQSRRPQVEGEEPPIPLGALHDDPPTMRRRSKVEARHRCPLSVTGTNFRPD*
166
+ >ChrUn.fgenesh.mRNA.17|PACid:24093271
167
+ MWDALETKFGVSNAGNELYVMEQFYDYKMVDDRSVVEQAHEIQILAKELENNSSKLPDKFVAGGIIAKLPHSWSDFVTSL
168
+ KHKRRRRQRTTTTKRSREVLAPIWCRRRTLMHLITITRRSNQMPNPRQQLILRRKGKERQMTTALCAVGRGSSLLMGNGL
169
+ LVVVHGVGTVTLEFTSRKIAQLKNM*
170
+ >ChrUn.fgenesh.mRNA.68|PACid:24093272
171
+ MGSCCCMGCNDDDGGSGGGDGGLDPKGFLLALMIALVLFMICHRPQPRRNNYVVYRCY*
172
+ >ChrUn.fgenesh.mRNA.47|PACid:24093273
173
+ MVNTRASGSGNNNNEGNPTLAQVLAQQTQLMNMMIQQMQNQLNQGNNNAPPAQNKLADFLRVRPPTFSSTTNPVEAGDWL
174
+ HTIEMKLELLQCTDQEKVVFASHQLQGPASEWWDHFWMNRAEGQPITWADFTEAFKKTHIPTGVVSLKKREFRALKQKDQ
175
+ TVAEYLHEFNRLARYAPEDVRTDEERQEKFLEGLKDELSVTLISHDYADFQQLVDKAIRLEDKKNRMDNRKRKMTVFQEA
176
+ QGSSQRQRIEPLQIGESFSAGQGQSQQLNIGGEIKLETNENTEVNIEQANQPVPVQQDQSQENNNSGRKQQVCFNCYKPG
177
+ HFARECPKPKHQQQQGQVNNIVVTGANAVPVASSRVVSSSVTAQPPVSKQQ*
178
+ >ChrUn.fgenesh.mRNA.56|PACid:24093274
179
+ MAPIATPSRSHIAGPTEHHKLQSSLAPPDCRRYAGPPIIATAIEVRSSPDPGLDTPDLDPEGQIRPFPILHHRRRPAFRV
180
+ GTRGKPRSSPTHSPHSRCRRAPQSPDPTGDTLDLDLGRSDPVVPLAACPREGGGHWRRTWRRRNQAQAQCLPRSLKPGEE
181
+ EREEGERKREGEKREGEEEEEEAAPPLPACGGVAGGSEAGEAQRGWS*
182
+ >ChrUn.fgenesh.mRNA.72|PACid:24093275
183
+ MTTASLVHPSASSSSSSTRAEVEVVGGVFVCSDSCSGDIVRNLIVDYGSGKITLTAACIQFCVPCTRPQPLLPPLCHSGP
184
+ INTCFATADDRGRSRFRHYH*
185
+ >ChrUn.fgenesh.mRNA.81|PACid:24093276
186
+ MAALTGEWRGVGSGSGIRRKRGGRGGPYDGKRGGVVGAARRGG*
187
+ >ChrUn.fgenesh.mRNA.62|PACid:24093277
188
+ MGTYLVIMLISNMAPLYSGSYFYVLAQEATIAAKGNFNHYHVQMQEMSDWILLFKRYCIYVNERYVISPAFSRRVGFVLL
189
+ DIYGVISMYGENDSLEQYLLHVAPNQKMMLYKTFMMSNSILRRNVVHDINSAKVSYFATHQSTGPNENYYGLRATMDVYG
190
+ HELKPGQLSGGALWVSHFGDDGKLSSYNAVSAGWHIDPQRYGDSRPHFYTSWTRDGYATTGCYNMDCPGFERANGAAVGP
191
+ GASIDPVSDDKSLQSITVEVPLDRTSGDWWVYYGFNSVPTGVGSYPKSLFTNMAEKANAIAFGGYVVTRRALPTPPMGSG
192
+ SHPHTNKSRAASLTNLGVINQDGNTNPINADLPTYMGNEQCYSITPVAQAECFYGGPGGCMP*
193
+ >ChrUn.fgenesh.mRNA.45|PACid:24093278
194
+ MAWPTGSGDDRRSERETATNWGRGRLFLRVLLLLVLLVGLTFHGARFDVAATAAKGSDLLLLLLYSLPTLPLPRTHNWKR
195
+ GREGQKNWTIEIESPPCPSPKMDRQWMYADQRSKEFIEGVHYFLRVAEANRQRGFICCPCNKCKNQKEYSASRTIHFHLF
196
+ ESGFMPSYNCWTSHGEQGVEMEEDEVEDDNIPDFAQYVGFEGNQTGEEEIAADGNDVADDLGQMLQDAREVCKSEKEAHK
197
+ LDKMLEDHRTSLYPGCEQGHKKLDTTLELLQWKAKNGVSDKAFGNLLKLVKNILPGGNKLPETTYEAKKIVCPLGLEVHK
198
+ IHACPNDCILYRGEEYENLEACPVCKALRYKIRRDDPGEVDGQLTKKRIPAKVMWYFPIIARLRRLFRNKGNARMLRWHA
199
+ EERQQDGMLRHPADGSQWRNIDRKFKEFGKDALSRPEFLSKIPNAYMCVKPSSRNQPRHTMTI*
data/test/data/assembly.2.fa ADDED
@@ -0,0 +1,26 @@
1
+ >scaf_Os03g60760.1
2
+ ATGGAGGTGGAGATGGGGCACGGAGAGGAGGTGGCGGCGGCGATGGAGGAGGAGGAGCTGCAGGGGTGGGAGACGCCGAGGAGGGAGGAGTGCCGCATCCCGGTGGTGCCGCCGCAGTGCCCGGCGCCGCCGAGGAAGAGGCCGGTGGCGCTGCCGGAGCTGGGGAAGGAGCGGCGGGAGCCGCCCAAGGGCGGGTACTTCCAGCCGCCGGACCTCGAGTCGCTCTTCGTGCTCGCGCCGCCGCGGAGGC
3
+ >scaf_Os03g60760.2
4
+ ATCGAGGTGGAGATGCACGGAGAGGAGGTGGCGGCGGCGATGGAGGAGGAGGAGCTGCAGGGGTGGGAGACGCCGAGGAGGGAGGAGTGCCGCATCCCGGTGGTGCCGCCGCAGTGCCCGGCGCCGCCGAGGAAGAGGCCGGTGGCGCTGCGGGAAGGAGCGGCGGGAGCCGCCCAAGGGCGGGTACTTCCAGCCCGCGCGGCCGGACCTCGAGTCGCTCTTCGTGCTCGCGCCGCGGTGGC
5
+ >scaf_Os10g39590.1
6
+ ATGAGCATGATAACGGTGAAGGTGAAGACGCTGACGGGGAAGGAGGTGGAGGTGAGCATCGAGGCGACGGAGACGGTGGCGAGGATCAAGGAGCAGGTGGAGGCGGCGGAGGGGATCCCGCCGCCGCAGCAGACGCTGATCTACGGCGGCAGGCAGCTCGCCGACGACATGACCGCCGAGATGTGCGACCTCAGGCATGGCT
7
+ >scaf_Os10g39590.2
8
+ CATCGAGGCGACGGAGACGGTGGCGAGGATCAAGGAGCAGGTGGAGGCGGCGGAGGGGATCCCGCCGCCGCAGCAGACGCTGATCTACGGCGGCAGGCAGCTCGCCGACGACATGACCGCCGAGATGTGCGACCTCAGGCATGGCTCCGAGCTGCACCTCGTTCTTGCTCTCAGGGGTGGACTACTTTGA
9
+ >scaf_Os09g38670.1
10
+ CCGCAAGGAATTGCAGTCCTGCAGATAAGAGATGCCATTTGCTAGTTGCCTCCTTGCATCTTCGAGCTCTACCATGATGGCAAGGCCCGGCGCTGTGAAGAATATTGAAAGCTGGGACGAGTTTACAAAGCATTTTGTGAAATCAGAGGACAAGCTGGTGGTGCTGGTATTCATGGCGCCGTGGTCGGAGCCGTGGAAGCTGATGAGGCCGGCGGTGGAGAAGATGGCGTCGGGGCTGAAGAGCGAGGAGGCCGAGGTGTGCACGATCAGCGTCGACCGGTTCAACACGCTGGGGCGGCTGCTGCGGGTGGAGGCGCTGCCGACGTTCGTGCTGGTGAAGAGGCACCGGGCGGTGGCTCGCGTCGTCGGCGTCAACCGGGACGATCTTCACAGCAGCATCAACAAGCACCTCGCACCACCCTCTTCTTCTCCACAACCCATTAATATTTCTTAGTGCTGTTGATGATTCTTGGTTGATTGCATGATATAATCGAGTAATGCCATGCGTCTTAATTATGAGTTGTAATTGTTTATCACATACTGTATTTGAGACATATTCAACCTTGTTTCGAGAAAAAAAAATGGAGATGAAAAAAAAATCTATTCATACTTATAGATTTTCTTTGAAGAA
11
+ >scaf_Os12g21920.1
12
+ ATGCCGACGCCCTCCACCGCCACGCGCCGCCCATCGACCGTCACACGCTTCGCTCTCTGCCTGTCGTCGCCGCCGTCGACGCCGCTGCCGACACCCGTCGCTGCCGCCCACGCCGATGCCGACGCTGCCGCTGCTGTTATCGGGAGGCCGAAAGGGGAGGGGAGAGAATGGGAGGAGAGGAGTCGTTCCCAACGAACACCATCACCACCCAACTCAGAGTCGCCGCCAAAAGCCAACTGGGGTATTGCCAGCAACAACTGCTACTCAAGAATGATCATTGCGTCGGCTGCCTTAACAAGCGATCGCCGAATGAGTAATGCCTGCGACCGCATGCTCGCGGCGGTCATACCCTCGCCCACGGCGCAACCACATGCTGGCCATAAAGGACGGGATGTTTGCGTCCTTGGTTACGCCTCACCCTGCCCTTGCCCACACCTCGCCGGCGCCACGGCCATGAATGCCACATAG
13
+ >scaf_Os01g36294.1
14
+ GTTGCACTGCAACTCTGCAAGTAGCCATGGAACAAGCAGCTGGACTAGTGTACCAACTCTTCCAACACGAAATGTTTCCCTGGACCTTCTCTGTCCTAGCCTTGTTCCCTTTCCTTCTCCTAGTGCTGCACTACTTGGCAACAAATCATAGAACACCAACAACCTGCAAGGAAACGAAGAATCATCATCCTCCCCCACCTTCACCTCCGAGGCTGCCCATCATAGGGCACCTGCACCTCATCGGTGGCCTCCTGCACGTCTCTCTTCGTGAGCTCGCTCATCGGTACGGCCCCGACCTCATGCTCCTCCACCTCGGCCAAGTCCCGAACCTCATTGTCTCCTCCCCGCGCGCCGCAGAGGCTGTCTTGCGCACGCACGACCTTGTCTTCGCGTCACGGCCATACTCCTTGATCGCCGACATACTCCTTTACGGCCCGTCTGATGTCGGGCTTTCGCCTTACGGCGAGTAGTGGCGGAGGAGGATCATCACAACGCACCTGCTGACCAACAAGAAGGTGCGGTCGTACCGTGTAGCACGAGAAGAGGAGGTGCATAAGGTAATGGCCAAAGTCCATGAGTTATCCACCAAGGGTATGGCAGTGGATATGACTGAGCTCTTCAGCACCTTCTCAAATGACCTCATATGCCGCCTTGTGTCGGGGAAGAACTTCCAAGGGGAAGGTCGAAACAAGCTGTTCCGTCAACTGTTCAAAGCAAATTCTGTACTCCTCGCAGGGTTTAACCTCAAGGACTACTACCCAGGCTTGGCAAGGCTCAAAGCTGTCTCAATGGTGATGTGTGCCAAGGCCAGGAACACGAGGAAGTTGTGGGATGAATTGCTCGACGAGATTATCGATGAGCGTATGAGCAAACAACAATGTGAGCATGATGAAGGCAATGATCAAGATGAGATGAACTTCGTAAATGTTTTGCTCCTTCAAGAGCAGGGCATCACCAGAGAACACCTTAAAGCAATTCTAGTTGACATGTATCAAGCCGGCACGGAGACGTCATCAGTGGTCTTAGTATTTGCCATGGCCGAGCTTATGCAGAAGCCACATCTCATGGCCAAGTTGCAAGCCGAACTAAGAACAACCATACCCAAGCAGGGACACGAATTGATTACTGAACGTGATCTTACCGACATGACCTACCTCAAGGCTGTCATCAAGGAGACGCTTCGGTTGCATCCACCAAC
15
+ >scaf_Os12g22750.1
16
+ ATGTCTGGAGTTCCCCCCGCCGCTGCTGGAGGAGATGGCACAGGTGGTGCGCCGCCAGGAGCTGGAGCCGGCGGTGGTGCGCCAGGAGCCGGTGCCGCGAACAACAACATCAACGGAGGCAATTCTGCCTCACAATCCAGTGGAGGGCCATTCTCGAGGTGTATCCTTCTTCTGTTCCCTTTGTTAGCGCTATCGCTTTACTGTCATGTGCGCTATGTTCCTGTTCCTGACCTTCATGATGCCTCAAGCATGTTATTGAGTTACTGTAATGTTTCTGTTCCTGACATTCATGATGCGCATAGAAAGGAAAATGGCGCCTTCAACACGCGGAAGCGGCGAGCCTTCTCGGCGGCGTCCTTGTACGTGCGCCCGTGCTCCGGCATGCTTCGGCCGCCGTTGTCGTCGGAGCTTGGAGGCGGCGGGAGTGAGGAAGAAGAGGGAGAGCCGAGAGGGGAGAGGGAATGA
17
+ >scaf_Os02g55190.1
18
+ TGGGCCACAAAATTTCTCCAAATTTTGAATTCCAGAGGCGACCAGTCCGGCTCGAAATCCCCGCCTTATAAATTACGCACGCCGACACGATACGCCCCCATCGAATTCAGGCGCAAAAACCTCCAAAACCTTTGCAATATTCCTCGTAAATCGTAATTCCCCCTCGCGATCGAGCTCGCGACGCCCATGGCGATGGAGAGAAACGCGGCGCCGCGCGTCTCGGCCTCGTCGTCGGCGGCGGCGTCGCCCTCCACCGTCGGTGCGCTCCTCTCGAAGGCCTCGGTGGCTGCCGCTCCCGCACGCGAGATCCCCTCGCCGCGGTCGCTGCTGTCGCGCATCCTCCATAGGAGTGGCGGCGGCGGCGGCTTCGGGTGTCGCCTTCGCCTCCCCCGATACTGCTCCAGCGGCGCGGCCGCCAAGGAGGACGCCGCCGCCGAGTACGTGGAGGTTGAGGTTGAGGCGGAGGCTGCGGCGCCGAAGGTGGTGGGCCGCCAAGCGGTTGATCGCGAGTCGCCTCGGAGCTCGCTCGGGAAGAAGGCGGCGGAGGAGGTGTCGCCGGCGAGCCTGGGGCTGGGCGCGAGCCTCATGCTGCTGCTCTCCAAGAGCGCGGCGGAGCTGAACAGGATGGCGGAGCTCCGCGCCCAGATGGAGCGGCTGGTGCTCGACACCAAGGGGGAGGAGGAGGCGCGGAGCAGCAACCACCCCAACGCGTCCGACGATCACGCCGACATCACCAAGGAGGAGCCCACCGCCTTCTCCGGCGGCGCATTATCCCGCTGCTCACGCACGGCCGCCGCCCCGGGAAACGCAGGGCACCACGCCGCCGTTCCAATGGACCAGATGGAAGCGGAGCTCGAGGCGGAGCTGACGCTCCTGCAATGCGCGACTCCTCGTCGGGATCGTCAACTCGAGATCGGCGACGACGAGGAGGAGTCCACGGACACCCACGCGGCCACCTTCGCCGACGCCGACGATGACACGGACGGTGCTGACGACGAGGAGGAGGAGGAGGAGGAGAGCGGGGCGGCGGCGCAGGGCGGCGTGTCGGCGAGGGAGCTGGAGAGGAGGCTGCACGAGCTGCTCCAGTGGCGGCACGAGGAGCGGATCGCGGAGCTGGAGACGGCGCTGGAGCGCGCCAGGAAGAGGCTGCAGGAGAAGGAGCGCGAGGTTTGCTGGTGGCGCAACACCGCCAAGCTCGTCACCCGCCACAAGGACGACTCCCGCCTCAGATAGCAAGAATTAATCCGCCATGAGATGAGATCAAACAAGAACAAGATCAAGATCGATCATCTCGCCTCGCAGTGATCCGTTTTGTACTCTGGTGATCATGCTGCAACTAGACTAGAAGAACAAATTCCAACCAGAAAACATTGATTGCATAAACTAACTGGGATCACAGATTCACAGGATTCGGTTGCTGCAGCCTATCAACATTTGGAGCAGATGGTAAGGTGTTTTTTACCTATCTAGTCTACGGATTGATTCCAAGATGATTGTGTTTCGGCCTTTCATTCGACCTCCAAACGTGACTAAATTAAGATGCATGGAATGACGCACAATCTCTTA
19
+ >scaf_Os03g56500.1
20
+ ATCAAGCCGTCCACTTCCCCCACGACCACCAGCGTCCGAGCGGGTCGAGGAGGCCATGTCCGGCGAAGCAGAGTCCCGCGAGGCGTCGCGGCAGCGGCGGCGGCGGGAGCGGGCTGCGGCGGTCGAGCGATTCGTCGGGGTGCCGCTCGCCGACGTGGTCAGGGAGAACTCGCTCGTGCACCTCCCGCCGGCGGCGGCGGCGCGCCTCCGCGTCGTGCACCCGTCGTGGGCGAGCCACATGTCGTCCCCGCTCTTCGCCGTCGCGCACGCGGCCGCCCCGAGGCGGGTCTCCGGGGTGTTCGTCCCATCAGCGGGGTTCCTCCCCTTCGACGGCGACGACGACGCCGTGCCGTCCCCGTCGCTCTCGTTCGTGCCGGCCTCGTCGGAGCTCGTCGTGCTGTCGTCGTCGCGCGGGGTCGCCTGCTGCTTCTCCCCCGCCGACGACGCGTACGCCGTGTGCAACCCGGCTACGGCGTCGTGGACGGCCGTCCCGTCCCCGCCGTGGCGGTCCTGGCCGCGCCCGGCGATCGTCGTCCTCTTCGACACGAGCGCCTACAACTTCCGCGGCGACTTCACGCTCGTCTGCCCCTTCGAGTCGGAGCCGGGTTCTTCCGGCGCCTACTGCTTCCAGGTGTTCACGTCCGGGACCGGCGCGTGGTGGGTCACCGACGCGATGTCGCCAGCCGAAGGGCTCGTCGCCGCGTCGGGCGTGGCGGCCGGCGCCACGGCGTGGTGGCGGACGAGCATCGGCACCGCGGTGGGGTACACCCCTGTCACGGGGCGCGTCGACCTCGTGACCTGCCCCGGCGACAGTGACCAGTGGGAGATCGGATTGGCCGCGGGCATGCTCCACTGCGCCGTGATCGACGGCGGCGACGTGGTGGTGTTCCGGCTGCACGAGCACGGAATCTGGGAGGTGACCACCAGGGTCGCCGTCGCAGAGATACTGCAACCATCTCAGCCGCCGCCGCCGGCAAGGGCGACGACGTCCACGGAGATCGTGGCGTCCCAGCAGCACGACGAGTCCGGCGCGGAGGAGGAGGAGGGCTCGCGCGCTGTTGTCGCCGCGGCGAATGCACCACTCCGGCTGGACGACGGGGTGCGGCTGCTGGGTTTCCAGGGCGCGGAGGTGGAGGTGGTGGTGCTGGCAGGGAGGCGCCTGGTGGCGTTCGACGCGCGGACGCGGCGGCGGCGCGAGGTCGCCGTGCCGGACGAGGTCGACGCGGCATGGGACGGCGCGGAGCACGCTGCGCACATCAACACCCTCGCGCTGATCGCGCCCGCCGCTCTCGCGGCCGAGCCGCCGCTCGCGAAGCCGCCGGCTGATCCATGAAGTGGCAATGGCATCGTCATCTTAGCGAATCTTACTGCAATGCATGGCGATCAATCACTCGATCTAAGAGTAAGTTTGTGGATGTGAAGTTCCATTTTGAGAAATTTAACTCGCAAGCTGCAATAAATTGTGTATATTAATCATCAGATGAGCTTTTTCCCCAGTTCAATATATGTTTTTCAAATAGTTTTTGGGTGAGGTACTTGCCAGTTGAGTTGATCTATACTTTAACAGTGGGAGAATGAATAGCTACTTTGTCACTTTTTTTTCTTTGTTTTTGGGTGTGTTAGTTGACGTCAAAATTTAAAGTTTGATTGAAATTGAAACAATGTGACGTTCAATGGAACGATGTGACGCAAAAGTTGAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAAGGTTTAGAACTTAA
21
+ >scaf_Os03g56500.2
22
+ ATCAAGCCGTCCACTTCCCCCACGACCACCAGCGTCCGAGCGGGTCGAGGAGGCCATGTCCGGCGAAGCAGAGTCCCGCGAGGCGTCGCGGCAGCGGCGGCGGCGGGAGCGGGCTGCGGCGGTCGAGCGATTCGTCGGGGTGCCGCTCGCCGACGTGGTCAGGGAGAACTCGCTCGTGCACCTCCCGCCGGCGGCGGCGGCGCGCCTCCGCGTCGTGCACCCGTCGTGGGCGAGCCACATGTCGTCCCCGCTCTTCGCCGTCGCGCACGCGGCCGCCCCGAGGCGGGTCTCCGGGGTGTTCGTCCCATCAGCGGGGTTCCTCCCCTTCGACGGCGACGACGACGCCGTGCCGTCCCCGTCGCTCTCGTTCGTGCCGGCCTCGTCGGAGCTCGTCGTGCTGTCGTCGTCGCGCGGGGTCGCCTGCTGCTTCTCCCCCGCCGACGACGCGTACGCCGTGTGCAACCCGGCTACGGCGTCGTGGACGGCCGTCCCGTCCCCGCCGTGGCGGTCCTGGCCGCGCCCGGCGATCGTCGTCCTCTTCGACACGAGCGCCTACAACTTCCGCGGCGACTTCACGCTCGTCTGCCCCTTCGAGTCGGAGCCGGGTTCTTCCGGCGCCTACTGCTTCCAGGTGTTCACGTCCGGGACCGGCGCGTGGTGGGTCACCGACGCGATGTCGCCAGCCGAAGGGCTCGTCGCCGCGTCGGGCGTGGCGGCCGGCGCCACGGCGTGGTGGCGGACGAGCATCGGCACCGCGGTGGGGTACACCCCTGTCACGGGGCGCGTCGACCTCGTGACCTGCCCCGGCGACAGTGACCAGTGGGAGATCGGATTGGCCGCGGGCATGCTCCACTGCGCCGTGATCGACGGCGGCGACGTGGTGGTGTTCCGGCTGCACGAGCACGGAATCTGGGAGGTGACCACCAGGGTCGCCGTCGCAGAGATACTGCAACCATCTCAGCCGCCGCCGCCGGCAAGGGCGACGACGTCCACGGAGATCGTGGCGTCCCAGCAGCACGACGAGTCCGGCGCGGAGGAGGAGGAGGGCTCGCGCGCTGTTGTCGCCGCGGCGAATGCACCACTCCGGCTGGACGACGGGGTGCGGCTGCTGGGTTTCCAGGGCGCGGAGGTGGAGGTGGTGGTGCTGGCAGGGAGGCGCCTGGTGGCGTTCGACGCGCGGACGCGGCGGCGGCGCGAGGTCGCCGTGCCGGACGAGGTCGACGCGGCATGGGACGGCGCGGAGCACGCTGCGCACATCAACACCCTCGCGCTGATCGCGCCCGCCGCTCTCGCGGCCGAGCCGCCGCTCGCGAAGCCGCCGGCTGATCCATGAAGTGGCAATGGCATCGTCATCTTAGCGAATCTTACTGCAATGCATGGCGATCAATCACTCGATCTAAGAGTAAGTTTGTGGATGTGAAGTTCCATTTTGAGAAATTTAACTCGCAAGCTGCAATAAATTGTGTATATTAATCATCAGATGAGCTTTTTCCCCAGTTCAATATATGTTTTTCAAATAGTTTTTGGGTGAGGTACTTGCCAGTTGAGTTGATCTATACTTTAACAGTGGGAGAATGAATAGCTACTTTGTCACTTTTTTTTCTTTGTTTTTGGGTGTGTTAGTTGACGTCAAAATTTAAAGTTTGATTGAAATTGAAACAATGTGACGTTCAATGGAACGATGTGACGGAAAAGTTGAAAGTTTGTGTGTGTAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTTGAAGAAAAAGGTTTAGAACTTAA
23
+ >scaf_Os03g56724.1
24
+ ATGAGCTGCGAGAAGTTGAGCCGTCAGTCTCTGCATTTGGTGTTGAACGAGGGTCGCGGCTTGTTCTCGCTAAGGCACATGGACGTATCAAAGCTCTTCTACCCATCAACGGCAGAAGCACTGGAAGCAGAGGCTAAAGCTAAGAAGAAGAAGAATGGCACCAACAAAATTGGGAGCATCGGCCGTTTGCCAACACCGAGCATACACTACCAGCCATATACGTGGTCTGCGTCTAATCCCTACAGTTCACTGTGTGCACTTGCTCTCTTTGGTGAGAGGAGCAAGAACAAGATCCTCTGCACGGACATGGCAGGCCACACCAGCATCTACAACCCCGAGTTGCGCTCATTCATGAGAATGCCTGATCTGAATTCGCCCAAGAGATACAATAGTTGTGTGGCTGTCTCCATCCCAGGTGCTTCTGCCCATGCCATGTCCAACTTTGACATCGACACAGACCACAGCCTGTACATCATGGATATCGATCCTACCTACTGGTGTAGTTCTGAGGTGCTTGCCTATGATCCTGTGGAGGAGTGTTGGTGCTGGGGGCCACTCCCGCAGCCGCCATTCTTTCAGGACCGAGAGTATAAGGTCCCCCTTAAGCCTCGCTTCATGGTGGTCGATAGCACCAAGATATGCGTGTCTACCACCACGGCGACCTACTCCTTTGACATGGTGACGAGAGATTGGAATAAGGTGGGTGATTGGGTGCTGCCCTTCAATGCCGAGTATGTCCCTGAGCTGGGCCACTGCCTCGGCATGTCGGATGGCGGCCCCTTTGACCTGTGCATCTTGGACAACCTCTCCACCGCCGCAGGCTCTCCTCCGCCGGTGGTGCGGCATGTCGGGATGGAGTTTGAGCTGCCGGAGAACTGGTCTCAGGTGTACCGTGACCTGGTGAACCTTGGATCACTGAGGTTTTGCATTGTCAATGGCTACACCATTGAAAACGAGCGGTACGAGTGTGACTTTAACCCAGTGACTGTCTTCACCGGCGTGGAGGTGTTGCCAACAAGCAGTGAACAGGGGCTCCTTATGATCAAGCACAAGTCCAAATGTATCATGACTTACATCATGTTCGTGCTCTGA
25
+ >scaf_Os01g11360.1
26
+ ATGGCGGCCAGAGGCAGCCGGTCCTGCGCCTGGCCGTGTGGGTTGGGGATGGCTGGAGGTGGTCAGGAGGGCAGCGGGAACCGGCAAGGAGTCGGCGATGGAGTCCCTCCGGACGGCGGTAGGGACAGCGAAGCACGGCGGAAGATGGTGACGGCGCTCGGCGGCTACGGCAGCCCTAGGGGCTGCGGCGTCCCAAGACAGTGGCAGTCTGAGCACTGTGAATCCGATAAAGTGGAAGCTGATCCCATCGAGCAAATACAGAGGGGATTTTCGATCTACAGAGCCAATACAGAGGGGAAAGGAGTGGTGGATGGGGGTTTTACCTGCTTTGCTATGGGCATCGGCAGGGTGGTCTCAGCAGGGACGGCGGCGGCCTCAGCAGAGAGTAGACTAAGGAGGCTGTTGGAGATGCTCTTAGTAGTAGTATCGAACATCGGGACATACCAAACGAGAGGGATTTTGGTCAAGGATTTACTAAAGTAG
data/test/{assembly.fasta → data/assembly.fasta} RENAMED
File without changes
data/test/data/bridging_reads.l.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @read1:1
2
+ AAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGGGG
3
+ +
4
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
5
+ @read2:1
6
+ CACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCA
7
+ +
8
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
9
+ @read3:1
10
+ CACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCA
11
+ +
12
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
13
+ @read4:1
14
+ CTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGG
15
+ +
16
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
17
+ @read5:1
18
+ ACGACGCGCACCACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGC
19
+ +
20
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
data/test/data/bridging_reads.r.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @read1:2
2
+ AGGCCGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGC
3
+ +
4
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
5
+ @read2:2
6
+ GGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGT
7
+ +
8
+ ggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
9
+ @read3:2
10
+ CGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTAT
11
+ +
12
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
13
+ @read4:2
14
+ ACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGCTAAG
15
+ +
16
+ ggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
17
+ @read5:2
18
+ GGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGC
19
+ +
20
+ gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
data/test/data/sorghum_transcript.fa ADDED
@@ -0,0 +1,4 @@
1
+ >Sb02g000720.1a
2
+ CCCCAACCCTCCTCTTCTCCCTCCCCTGACTGGAGAGAGAGAACCTGAACCTTCCCGAGAGGATAGATAGGGGGGACGGAAGGCACCCGCATCGAGGAAACCAAAAGAGAGGCAATCTCTAGAACCCTCTCTTCCACCTCCCTCTCTCCCTCCCGCGCCGATCCATTCCATTCCATTCCAACTCAATCCCCCCCCACCCAGCCCAAACAATGGCGTCGGACGGGAGCGGCGTGGTGACGGTGTACGGGAACAACGGCGCAGCCCTTCTGGAACCCTCAAAGCAGCCCAAGTCGGCGACTTTCTCCGTCAAGGTCGGCCTCGCGCAGATGCTCCGTGGCGGGGTCATCATGGACGTCGTCACCCCGGAACAAGCCCGCATCGCGGAGGAAGCCGGCGCCTGCGCCGTCATGGCGCTGGAGCGCGTCCCCGCCGACATCCGCTCGCAGGGCGGCGTGGCGCGGATGTCCGACCCGGGCCTCATCCGCGACATCAAGCGCGCCGTCACCATCCCCGTCATGGCCAAAGCGCGCATCGGCCACTTCGTCGAGGCGCAGATCCTCGAGGCCGTCGGCGTCGACTACGTCGACGAGAGCGAGGTCCTCACACCCGCCGACGACGCGCACCACATCAACAAGCACAACTTCCGTGTCCCCTTCGTCTGTGGCTGCCGTGACCTTGGTGAGGCGCTCCGGAGGGTCCGTGAGGGCGCCGCCATGATCCGCACCAAGGGGG
3
+ >Sb02g000720.1b
4
+ AGGCCGGGACCGGCAACATCGTCGAGGCCGTCAGGCATGTGCGGTCCGTCATGGGCGATGTCCGTGCGCTCCGGAACATGGATGATGATGAGGTGTTCGCGTATGCTAAGCGCATCGCCGCGCCGTATGATTTGGTGATGCAGACCAAGCAGCTGGGCCGCCTCCCTGTTGTGCAGTTCGCGGCCGGGGGTGTGGCCACGCCTGCTGATGCCGCGCTCATGATGCAGCTTGGGTGCGACGGCGTCTTCGTCGGCTCGGGAATCTTCAAGAGTGGCGACCCTGCTCGCCGCGCGCGTGCCATCGTTCAGGCTGTCACCCACTACAGCGACCCTACCATCCTCGCCGACGTCAGCGCCGGACTCGGGGAGGCCATGGTCGGCATCAACCTCAACGACCCTAAGGTCGAGCGATACGCCGCCAGATCCGAGTGAACAACCCTATCCGCTCCACCATCGTCATCTTCTCTCATATATTTGTATCACCCATCCATCCATCTGCCTTCGATATGCATCTCCACTCCGCCGGCTTCATCCTTCTCTTCTTAATAATTTTTGCATTACAAACAGTAGCTTATTTTGTCTCATGTCTCTCCATCAGTAATAACGGGACTGAATCAATGGTAAGAAATCAAAGCGTATGGTACTATGCAGAACCTCTTTATTTTTGTGTCCTCTTATTAGCTACTGTATTAAGTTAGACTAGGCTCCCCTGGTTTATCATGTACTCAATCAAATGTTGAACGGTTTGTATGTCTGTCGCTCTGCCAGCCCTGCTTATGGCTTATGAATGATGAATCAATGAATGAATCACATGTTCTTCATCC
data/test/data/tiny.sam ADDED
@@ -0,0 +1,4 @@
1
+ @HD VN:1.0 SO:unsorted
2
+ @SQ SN:NM_014620 LN:2300
3
+ @PG ID:bowtie2 PN:bowtie2 VN:2.2.3 CL:"/Users/rds45/.rvm/gems/ruby-2.0.0-p247/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -p 8 -X 350 --quiet --seed 1337 -x transcripts --passthrough -1 /Users/rds45/code/eXpress/sample_data/reads_1.fastq -2 /Users/rds45/code/eXpress/sample_data/reads_2.fastq"
4
+ 2:NM_014620:1094:172 99 NM_014620 1095 1 50M = 1217 172 ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:0 YT:Z:CP
data/test/helper.rb CHANGED
@@ -7,10 +7,41 @@ SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[
7
7
  ]
8
8
  SimpleCov.start
9
9
 
10
- require 'test/unit'
10
+ require 'minitest/autorun'
11
11
  begin; require 'turn/autorun'; rescue LoadError; end
12
- require 'shoulda-context'
12
+ require 'shoulda/context'
13
13
  require 'transrate'
14
14
 
15
15
  Turn.config.format = :pretty
16
16
  Turn.config.trace = 5
17
+
18
+ # fake CRBBlast class
19
+ class CRBHelper
20
+
21
+ attr_accessor :target_is_prot, :hash
22
+ def initialize t
23
+ @target_is_prot = t
24
+ end
25
+
26
+ def reciprocals
27
+ return @hash
28
+ end
29
+
30
+ end
31
+
32
+ # rake Hit class
33
+ class HitHelper
34
+
35
+ attr_accessor :query, :target, :qstart, :qend, :tstart, :tend, :qlen, :tlen
36
+ def initialize query, target, qstart, qend, tstart, tend, qlen, tlen
37
+ @query = query
38
+ @target = target
39
+ @qstart = qstart
40
+ @tstart = tstart
41
+ @tend = tend
42
+ @qend = qend
43
+ @qlen = qlen
44
+ @tlen = tlen
45
+ end
46
+
47
+ end
data/test/test_bowtie.rb ADDED
@@ -0,0 +1,54 @@
1
+ #!/usr/bin/env ruby
2
+
3
+ require 'helper'
4
+ require 'tmpdir'
5
+
6
+ class TestBowtie < Test::Unit::TestCase
7
+
8
+ context "bowtie" do
9
+
10
+ setup do
11
+ @reference = File.join(File.dirname(__FILE__), 'data',
12
+ 'sorghum_transcript.fa')
13
+ @left = File.join(File.dirname(__FILE__), 'data', '150uncovered.l.fq')
14
+ @right = File.join(File.dirname(__FILE__), 'data', '150uncovered.r.fq')
15
+ @mapper = Transrate::Bowtie2.new
16
+ end
17
+
18
+ should "build index" do
19
+ Dir.mktmpdir do |tmpdir|
20
+ Dir.chdir tmpdir do
21
+ @mapper.build_index @reference
22
+ assert File.exist?("sorghum_transcript.1.bt2")
23
+ end
24
+ end
25
+ end
26
+
27
+ should "build index and map reads" do
28
+ Dir.mktmpdir do |tmpdir|
29
+ Dir.chdir tmpdir do
30
+ @mapper.build_index @reference
31
+ left = File.basename(@left)
32
+ right = File.basename(@right)
33
+ index = File.basename(@mapper.index_name)
34
+ @mapper.map_reads(@reference, @left, @right)
35
+ sam = @mapper.sam
36
+ assert File.exist?("#{sam}"), "sam file doesn't exist"
37
+ cmd = "grep -v \"^@\" #{sam} | wc -l "
38
+ line_in_sam_file = `#{cmd}`.chomp.to_i
39
+ assert_equal 424, line_in_sam_file
40
+ end
41
+ end
42
+ end
43
+
44
+ should "raise error when no index built" do
45
+ Dir.mktmpdir do |tmpdir|
46
+ Dir.chdir tmpdir do
47
+ assert_raise Transrate::Bowtie2Error do
48
+ @mapper.map_reads(@reference, @left, @right)
49
+ end
50
+ end
51
+ end
52
+ end
53
+ end
54
+ end