Reverse complement benchmark from computer language shootout

library/test/benchmark/reverse-complement-test-in.txt

@@ -0,0 +1,171 @@
+>ONE Homo sapiens alu
+GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA
+TCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACT
+AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG
+GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG
+CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGT
+GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA
+GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA
+TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAG
+AATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA
+GCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGT
+AATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACC
+AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTG
+GTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC
+CGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAG
+AGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTT
+TGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA
+TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCT
+GTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGG
+TTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT
+CTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG
+CGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCG
+TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTA
+CTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCG
+AGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCG
+GGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACC
+TGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAA
+TACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA
+GGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT
+GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTC
+ACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGT
+TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC
+CGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG
+CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG
+GGCGACAGAGCGAGACTCCG
+>TWO IUB ambiguity codes
+cttBtatcatatgctaKggNcataaaSatgtaaaDcDRtBggDtctttataattcBgtcg
+tactDtDagcctatttSVHtHttKtgtHMaSattgWaHKHttttagacatWatgtRgaaa
+NtactMcSMtYtcMgRtacttctWBacgaaatatagScDtttgaagacacatagtVgYgt
+cattHWtMMWcStgttaggKtSgaYaaccWStcgBttgcgaMttBYatcWtgacaYcaga
+gtaBDtRacttttcWatMttDBcatWtatcttactaBgaYtcttgttttttttYaaScYa
+HgtgttNtSatcMtcVaaaStccRcctDaataataStcYtRDSaMtDttgttSagtRRca
+tttHatSttMtWgtcgtatSSagactYaaattcaMtWatttaSgYttaRgKaRtccactt
+tattRggaMcDaWaWagttttgacatgttctacaaaRaatataataaMttcgDacgaSSt
+acaStYRctVaNMtMgtaggcKatcttttattaaaaagVWaHKYagtttttatttaacct
+tacgtVtcVaattVMBcttaMtttaStgacttagattWWacVtgWYagWVRctDattBYt
+gtttaagaagattattgacVatMaacattVctgtBSgaVtgWWggaKHaatKWcBScSWa
+accRVacacaaactaccScattRatatKVtactatatttHttaagtttSKtRtacaaagt
+RDttcaaaaWgcacatWaDgtDKacgaacaattacaRNWaatHtttStgttattaaMtgt
+tgDcgtMgcatBtgcttcgcgaDWgagctgcgaggggVtaaScNatttacttaatgacag
+cccccacatYScaMgtaggtYaNgttctgaMaacNaMRaacaaacaKctacatagYWctg
+ttWaaataaaataRattagHacacaagcgKatacBttRttaagtatttccgatctHSaat
+actcNttMaagtattMtgRtgaMgcataatHcMtaBSaRattagttgatHtMttaaKagg
+YtaaBataSaVatactWtataVWgKgttaaaacagtgcgRatatacatVtHRtVYataSa
+KtWaStVcNKHKttactatccctcatgWHatWaRcttactaggatctataDtDHBttata
+aaaHgtacVtagaYttYaKcctattcttcttaataNDaaggaaaDYgcggctaaWSctBa
+aNtgctggMBaKctaMVKagBaactaWaDaMaccYVtNtaHtVWtKgRtcaaNtYaNacg
+gtttNattgVtttctgtBaWgtaattcaagtcaVWtactNggattctttaYtaaagccgc
+tcttagHVggaYtgtNcDaVagctctctKgacgtatagYcctRYHDtgBattDaaDgccK
+tcHaaStttMcctagtattgcRgWBaVatHaaaataYtgtttagMDMRtaataaggatMt
+ttctWgtNtgtgaaaaMaatatRtttMtDgHHtgtcattttcWattRSHcVagaagtacg
+ggtaKVattKYagactNaatgtttgKMMgYNtcccgSKttctaStatatNVataYHgtNa
+BKRgNacaactgatttcctttaNcgatttctctataScaHtataRagtcRVttacDSDtt
+aRtSatacHgtSKacYagttMHtWataggatgactNtatSaNctataVtttRNKtgRacc
+tttYtatgttactttttcctttaaacatacaHactMacacggtWataMtBVacRaSaatc
+cgtaBVttccagccBcttaRKtgtgcctttttRtgtcagcRttKtaaacKtaaatctcac
+aattgcaNtSBaaccgggttattaaBcKatDagttactcttcattVtttHaaggctKKga
+tacatcBggScagtVcacattttgaHaDSgHatRMaHWggtatatRgccDttcgtatcga
+aacaHtaagttaRatgaVacttagattVKtaaYttaaatcaNatccRttRRaMScNaaaD
+gttVHWgtcHaaHgacVaWtgttScactaagSgttatcttagggDtaccagWattWtRtg
+ttHWHacgattBtgVcaYatcggttgagKcWtKKcaVtgaYgWctgYggVctgtHgaNcV
+taBtWaaYatcDRaaRtSctgaHaYRttagatMatgcatttNattaDttaattgttctaa
+ccctcccctagaWBtttHtBccttagaVaatMcBHagaVcWcagBVttcBtaYMccagat
+gaaaaHctctaacgttagNWRtcggattNatcRaNHttcagtKttttgWatWttcSaNgg
+gaWtactKKMaacatKatacNattgctWtatctaVgagctatgtRaHtYcWcttagccaa
+tYttWttaWSSttaHcaaaaagVacVgtaVaRMgattaVcDactttcHHggHRtgNcctt
+tYatcatKgctcctctatVcaaaaKaaaagtatatctgMtWtaaaacaStttMtcgactt
+taSatcgDataaactaaacaagtaaVctaggaSccaatMVtaaSKNVattttgHccatca
+cBVctgcaVatVttRtactgtVcaattHgtaaattaaattttYtatattaaRSgYtgBag
+aHSBDgtagcacRHtYcBgtcacttacactaYcgctWtattgSHtSatcataaatataHt
+cgtYaaMNgBaatttaRgaMaatatttBtttaaaHHKaatctgatWatYaacttMctctt
+ttVctagctDaaagtaVaKaKRtaacBgtatccaaccactHHaagaagaaggaNaaatBW
+attccgStaMSaMatBttgcatgRSacgttVVtaaDMtcSgVatWcaSatcttttVatag
+ttactttacgatcaccNtaDVgSRcgVcgtgaacgaNtaNatatagtHtMgtHcMtagaa
+attBgtataRaaaacaYKgtRccYtatgaagtaataKgtaaMttgaaRVatgcagaKStc
+tHNaaatctBBtcttaYaBWHgtVtgacagcaRcataWctcaBcYacYgatDgtDHccta
+>THREE Homo sapiens frequency
+aacacttcaccaggtatcgtgaaggctcaagattacccagagaacctttgcaatataaga
+atatgtatgcagcattaccctaagtaattatattctttttctgactcaaagtgacaagcc
+ctagtgtatattaaatcggtatatttgggaaattcctcaaactatcctaatcaggtagcc
+atgaaagtgatcaaaaaagttcgtacttataccatacatgaattctggccaagtaaaaaa
+tagattgcgcaaaattcgtaccttaagtctctcgccaagatattaggatcctattactca
+tatcgtgtttttctttattgccgccatccccggagtatctcacccatccttctcttaaag
+gcctaatattacctatgcaaataaacatatattgttgaaaattgagaacctgatcgtgat
+tcttatgtgtaccatatgtatagtaatcacgcgactatatagtgctttagtatcgcccgt
+gggtgagtgaatattctgggctagcgtgagatagtttcttgtcctaatatttttcagatc
+gaatagcttctatttttgtgtttattgacatatgtcgaaactccttactcagtgaaagtc
+atgaccagatccacgaacaatcttcggaatcagtctcgttttacggcggaatcttgagtc
+taacttatatcccgtcgcttactttctaacaccccttatgtatttttaaaattacgttta
+ttcgaacgtacttggcggaagcgttattttttgaagtaagttacattgggcagactcttg
+acattttcgatacgactttctttcatccatcacaggactcgttcgtattgatatcagaag
+ctcgtgatgattagttgtcttctttaccaatactttgaggcctattctgcgaaatttttg
+ttgccctgcgaacttcacataccaaggaacacctcgcaacatgccttcatatccatcgtt
+cattgtaattcttacacaatgaatcctaagtaattacatccctgcgtaaaagatggtagg
+ggcactgaggatatattaccaagcatttagttatgagtaatcagcaatgtttcttgtatt
+aagttctctaaaatagttacatcgtaatgttatctcgggttccgcgaataaacgagatag
+attcattatatatggccctaagcaaaaacctcctcgtattctgttggtaattagaatcac
+acaatacgggttgagatattaattatttgtagtacgaagagatataaaaagatgaacaat
+tactcaagtcaagatgtatacgggatttataataaaaatcgggtagagatctgctttgca
+attcagacgtgccactaaatcgtaatatgtcgcgttacatcagaaagggtaactattatt
+aattaataaagggcttaatcactacatattagatcttatccgatagtcttatctattcgt
+tgtatttttaagcggttctaattcagtcattatatcagtgctccgagttctttattattg
+ttttaaggatgacaaaatgcctcttgttataacgctgggagaagcagactaagagtcgga
+gcagttggtagaatgaggctgcaaaagacggtctcgacgaatggacagactttactaaac
+caatgaaagacagaagtagagcaaagtctgaagtggtatcagcttaattatgacaaccct
+taatacttccctttcgccgaatactggcgtggaaaggttttaaaagtcgaagtagttaga
+ggcatctctcgctcataaataggtagactactcgcaatccaatgtgactatgtaatactg
+ggaacatcagtccgcgatgcagcgtgtttatcaaccgtccccactcgcctggggagacat
+gagaccacccccgtggggattattagtccgcagtaatcgactcttgacaatccttttcga
+ttatgtcatagcaatttacgacagttcagcgaagtgactactcggcgaaatggtattact
+aaagcattcgaacccacatgaatgtgattcttggcaatttctaatccactaaagcttttc
+cgttgaatctggttgtagatatttatataagttcactaattaagatcacggtagtatatt
+gatagtgatgtctttgcaagaggttggccgaggaatttacggattctctattgatacaat
+ttgtctggcttataactcttaaggctgaaccaggcgtttttagacgacttgatcagctgt
+tagaatggtttggactccctctttcatgtcagtaacatttcagccgttattgttacgata
+tgcttgaacaatattgatctaccacacacccatagtatattttataggtcatgctgttac
+ctacgagcatggtattccacttcccattcaatgagtattcaacatcactagcctcagaga
+tgatgacccacctctaataacgtcacgttgcggccatgtgaaacctgaacttgagtagac
+gatatcaagcgctttaaattgcatataacatttgagggtaaagctaagcggatgctttat
+ataatcaatactcaataataagatttgattgcattttagagttatgacacgacatagttc
+actaacgagttactattcccagatctagactgaagtactgatcgagacgatccttacgtc
+gatgatcgttagttatcgacttaggtcgggtctctagcggtattggtacttaaccggaca
+ctatactaataacccatgatcaaagcataacagaatacagacgataatttcgccaacata
+tatgtacagaccccaagcatgagaagctcattgaaagctatcattgaagtcccgctcaca
+atgtgtcttttccagacggtttaactggttcccgggagtcctggagtttcgacttacata
+aatggaaacaatgtattttgctaatttatctatagcgtcatttggaccaatacagaatat
+tatgttgcctagtaatccactataacccgcaagtgctgatagaaaatttttagacgattt
+ataaatgccccaagtatccctcccgtgaatcctccgttatactaattagtattcgttcat
+acgtataccgcgcatatatgaacatttggcgataaggcgcgtgaattgttacgtgacaga
+gatagcagtttcttgtgatatggttaacagacgtacatgaagggaaactttatatctata
+gtgatgcttccgtagaaataccgccactggtctgccaatgatgaagtatgtagctttagg
+tttgtactatgaggctttcgtttgtttgcagagtataacagttgcgagtgaaaaaccgac
+gaatttatactaatacgctttcactattggctacaaaatagggaagagtttcaatcatga
+gagggagtatatggatgctttgtagctaaaggtagaacgtatgtatatgctgccgttcat
+tcttgaaagatacataagcgataagttacgacaattataagcaacatccctaccttcgta
+acgatttcactgttactgcgcttgaaatacactatggggctattggcggagagaagcaga
+tcgcgccgagcatatacgagacctataatgttgatgatagagaaggcgtctgaattgata
+catcgaagtacactttctttcgtagtatctctcgtcctctttctatctccggacacaaga
+attaagttatatatatagagtcttaccaatcatgttgaatcctgattctcagagttcttt
+ggcgggccttgtgatgactgagaaacaatgcaatattgctccaaatttcctaagcaaatt
+ctcggttatgttatgttatcagcaaagcgttacgttatgttatttaaatctggaatgacg
+gagcgaagttcttatgtcggtgtgggaataattcttttgaagacagcactccttaaataa
+tatcgctccgtgtttgtatttatcgaatgggtctgtaaccttgcacaagcaaatcggtgg
+tgtatatatcggataacaattaatacgatgttcatagtgacagtatactgatcgagtcct
+ctaaagtcaattacctcacttaacaatctcattgatgttgtgtcattcccggtatcgccc
+gtagtatgtgctctgattgaccgagtgtgaaccaaggaacatctactaatgcctttgtta
+ggtaagatctctctgaattccttcgtgccaacttaaaacattatcaaaatttcttctact
+tggattaactacttttacgagcatggcaaattcccctgtggaagacggttcattattatc
+ggaaaccttatagaaattgcgtgttgactgaaattagatttttattgtaagagttgcatc
+tttgcgattcctctggtctagcttccaatgaacagtcctcccttctattcgacatcgggt
+ccttcgtacatgtctttgcgatgtaataattaggttcggagtgtggccttaatgggtgca
+actaggaatacaacgcaaatttgctgacatgatagcaaatcggtatgccggcaccaaaac
+gtgctccttgcttagcttgtgaatgagactcagtagttaaataaatccatatctgcaatc
+gattccacaggtattgtccactatctttgaactactctaagagatacaagcttagctgag
+accgaggtgtatatgactacgctgatatctgtaaggtaccaatgcaggcaaagtatgcga
+gaagctaataccggctgtttccagctttataagattaaaatttggctgtcctggcggcct
+cagaattgttctatcgtaatcagttggttcattaattagctaagtacgaggtacaactta
+tctgtcccagaacagctccacaagtttttttacagccgaaacccctgtgtgaatcttaat
+atccaagcgcgttatctgattagagtttacaactcagtattttatcagtacgttttgttt
+ccaacattacccggtatgacaaaatgacgccacgtgtcgaataatggtctgaccaatgta
+ggaagtgaaaagataaatat

library/test/benchmark/reverse-complement-test-out.txt

@@ -0,0 +1,171 @@
+>ONE Homo sapiens alu
+CGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAC
+CTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA
+GGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT
+GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAA
+AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTC
+TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGG
+GTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACC
+ACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG
+GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA
+CAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT
+GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTC
+TCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAAT
+TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCT
+GACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA
+CCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGC
+GCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCC
+TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTA
+GTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT
+CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCT
+TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTC
+ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG
+GGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGT
+TTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG
+CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAG
+TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCG
+CCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC
+GCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG
+CCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC
+TGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCG
+CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCA
+AGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCC
+CGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTC
+GAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC
+GTGAGCCACCGCGCCCGGCC
+>TWO IUB ambiguity codes
+TAGGDHACHATCRGTRGVTGAGWTATGYTGCTGTCABACDWVTRTAAGAVVAGATTTNDA
+GASMTCTGCATBYTTCAAKTTACMTATTACTTCATARGGYACMRTGTTTTYTATACVAAT
+TTCTAKGDACKADACTATATNTANTCGTTCACGBCGYSCBHTANGGTGATCGTAAAGTAA
+CTATBAAAAGATSTGWATBCSGAKHTTABBAACGTSYCATGCAAVATKTSKTASCGGAAT
+WVATTTNTCCTTCTTCTTDDAGTGGTTGGATACVGTTAYMTMTBTACTTTHAGCTAGBAA
+AAGAGKAAGTTRATWATCAGATTMDDTTTAAAVAAATATTKTCYTAAATTVCNKTTRACG
+ADTATATTTATGATSADSCAATAWAGCGRTAGTGTAAGTGACVGRADYGTGCTACHVSDT
+CTVCARCSYTTAATATARAAAATTTAATTTACDAATTGBACAGTAYAABATBTGCAGBVG
+TGATGGDCAAAATBNMSTTABKATTGGSTCCTAGBTTACTTGTTTAGTTTATHCGATSTA
+AAGTCGAKAAASTGTTTTAWAKCAGATATACTTTTMTTTTGBATAGAGGAGCMATGATRA
+AAGGNCAYDCCDDGAAAGTHGBTAATCKYTBTACBGTBCTTTTTGDTAASSWTAAWAARA
+TTGGCTAAGWGRADTYACATAGCTCBTAGATAWAGCAATNGTATMATGTTKMMAGTAWTC
+CCNTSGAAWATWCAAAAMACTGAADNTYGATNAATCCGAYWNCTAACGTTAGAGDTTTTC
+ATCTGGKRTAVGAABVCTGWGBTCTDVGKATTBTCTAAGGVADAAAVWTCTAGGGGAGGG
+TTAGAACAATTAAHTAATNAAATGCATKATCTAAYRTDTCAGSAYTTYHGATRTTWAVTA
+BGNTCDACAGBCCRCAGWCRTCABTGMMAWGMCTCAACCGATRTGBCAVAATCGTDWDAA
+CAYAWAATWCTGGTAHCCCTAAGATAACSCTTAGTGSAACAWTBGTCDTTDGACWDBAAC
+HTTTNGSKTYYAAYGGATNTGATTTAARTTAMBAATCTAAGTBTCATYTAACTTADTGTT
+TCGATACGAAHGGCYATATACCWDTKYATDCSHTDTCAAAATGTGBACTGSCCVGATGTA
+TCMMAGCCTTDAAABAATGAAGAGTAACTHATMGVTTAATAACCCGGTTVSANTGCAATT
+GTGAGATTTAMGTTTAMAAYGCTGACAYAAAAAGGCACAMYTAAGVGGCTGGAABVTACG
+GATTSTYGTBVAKTATWACCGTGTKAGTDTGTATGTTTAAAGGAAAAAGTAACATARAAA
+GGTYCAMNYAAABTATAGNTSATANAGTCATCCTATWADKAACTRGTMSACDGTATSAYT
+AAHSHGTAABYGACTYTATADTGSTATAGAGAAATCGNTAAAGGAAATCAGTTGTNCYMV
+TNACDRTATBNATATASTAGAAMSCGGGANRCKKMCAAACATTNAGTCTRMAATBMTACC
+CGTACTTCTBGDSYAATWGAAAATGACADDCHAKAAAYATATTKTTTTCACANACWAGAA
+AKATCCTTATTAYKHKCTAAACARTATTTTDATBTVWCYGCAATACTAGGKAAASTTDGA
+MGGCHTTHAATVCAHDRYAGGRCTATACGTCMAGAGAGCTBTHGNACARTCCBDCTAAGA
+GCGGCTTTARTAAAGAATCCNAGTAWBTGACTTGAATTACWTVACAGAAABCAATNAAAC
+CGTNTRANTTGAYCMAWBADTANABRGGTKTHTWTAGTTVCTMBKTAGMTVKCCAGCANT
+TVAGSWTTAGCCGCRHTTTCCTTHNTATTAAGAAGAATAGGMTRAARTCTABGTACDTTT
+TATAAVDHAHTATAGATCCTAGTAAGYTWATDWCATGAGGGATAGTAAMDMNGBASTWAM
+TSTATRBAYDABATGTATATYCGCACTGTTTTAACMCWBTATAWAGTATBTSTATVTTAR
+CCTMTTAAKADATCAACTAATYTSVTAKGDATTATGCKTCAYCAKAATACTTKAANGAGT
+ATTSDAGATCGGAAATACTTAAYAAVGTATMCGCTTGTGTDCTAATYTATTTTATTTWAA
+CAGWRCTATGTAGMTGTTTGTTYKTNGTTKTCAGAACNTRACCTACKTGSRATGTGGGGG
+CTGTCATTAAGTAAATNGSTTABCCCCTCGCAGCTCWHTCGCGAAGCAVATGCKACGHCA
+ACAKTTAATAACASAAADATTWNYTGTAATTGTTCGTMHACHTWATGTGCWTTTTGAAHY
+ACTTTGTAYAMSAAACTTAADAAATATAGTABMATATYAATGSGGTAGTTTGTGTBYGGT
+TWSGSVGWMATTDMTCCWWCABTCSVACAGBAATGTTKATBGTCAATAATCTTCTTAAAC
+ARVAATHAGYBWCTRWCABGTWWAATCTAAGTCASTAAAKTAAGVKBAATTBGABACGTA
+AGGTTAAATAAAAACTRMDTWBCTTTTTAATAAAAGATMGCCTACKAKNTBAGYRASTGT
+ASSTCGTHCGAAKTTATTATATTYTTTGTAGAACATGTCAAAACTWTWTHGKTCCYAATA
+AAGTGGAYTMCYTAARCSTAAATWAKTGAATTTRAGTCTSSATACGACWAKAASATDAAA
+TGYYACTSAACAAHAKTSHYARGASTATTATTHAGGYGGASTTTBGAKGATSANAACACD
+TRGSTTRAAAAAAAACAAGARTCVTAGTAAGATAWATGVHAAKATWGAAAAGTYAHVTAC
+TCTGRTGTCAWGATRVAAKTCGCAAVCGASWGGTTRTCSAMCCTAACASGWKKAWDAATG
+ACRCBACTATGTGTCTTCAAAHGSCTATATTTCGTVWAGAAGTAYCKGARAKSGKAGTAN
+TTTCYACATWATGTCTAAAADMDTWCAATSTKDACAMAADADBSAAATAGGCTHAHAGTA
+CGACVGAATTATAAAGAHCCVAYHGHTTTACATSTTTATGNCCMTAGCATATGATAVAAG
+>THREE Homo sapiens frequency
+ATATTTATCTTTTCACTTCCTACATTGGTCAGACCATTATTCGACACGTGGCGTCATTTT
+GTCATACCGGGTAATGTTGGAAACAAAACGTACTGATAAAATACTGAGTTGTAAACTCTA
+ATCAGATAACGCGCTTGGATATTAAGATTCACACAGGGGTTTCGGCTGTAAAAAAACTTG
+TGGAGCTGTTCTGGGACAGATAAGTTGTACCTCGTACTTAGCTAATTAATGAACCAACTG
+ATTACGATAGAACAATTCTGAGGCCGCCAGGACAGCCAAATTTTAATCTTATAAAGCTGG
+AAACAGCCGGTATTAGCTTCTCGCATACTTTGCCTGCATTGGTACCTTACAGATATCAGC
+GTAGTCATATACACCTCGGTCTCAGCTAAGCTTGTATCTCTTAGAGTAGTTCAAAGATAG
+TGGACAATACCTGTGGAATCGATTGCAGATATGGATTTATTTAACTACTGAGTCTCATTC
+ACAAGCTAAGCAAGGAGCACGTTTTGGTGCCGGCATACCGATTTGCTATCATGTCAGCAA
+ATTTGCGTTGTATTCCTAGTTGCACCCATTAAGGCCACACTCCGAACCTAATTATTACAT
+CGCAAAGACATGTACGAAGGACCCGATGTCGAATAGAAGGGAGGACTGTTCATTGGAAGC
+TAGACCAGAGGAATCGCAAAGATGCAACTCTTACAATAAAAATCTAATTTCAGTCAACAC
+GCAATTTCTATAAGGTTTCCGATAATAATGAACCGTCTTCCACAGGGGAATTTGCCATGC
+TCGTAAAAGTAGTTAATCCAAGTAGAAGAAATTTTGATAATGTTTTAAGTTGGCACGAAG
+GAATTCAGAGAGATCTTACCTAACAAAGGCATTAGTAGATGTTCCTTGGTTCACACTCGG
+TCAATCAGAGCACATACTACGGGCGATACCGGGAATGACACAACATCAATGAGATTGTTA
+AGTGAGGTAATTGACTTTAGAGGACTCGATCAGTATACTGTCACTATGAACATCGTATTA
+ATTGTTATCCGATATATACACCACCGATTTGCTTGTGCAAGGTTACAGACCCATTCGATA
+AATACAAACACGGAGCGATATTATTTAAGGAGTGCTGTCTTCAAAAGAATTATTCCCACA
+CCGACATAAGAACTTCGCTCCGTCATTCCAGATTTAAATAACATAACGTAACGCTTTGCT
+GATAACATAACATAACCGAGAATTTGCTTAGGAAATTTGGAGCAATATTGCATTGTTTCT
+CAGTCATCACAAGGCCCGCCAAAGAACTCTGAGAATCAGGATTCAACATGATTGGTAAGA
+CTCTATATATATAACTTAATTCTTGTGTCCGGAGATAGAAAGAGGACGAGAGATACTACG
+AAAGAAAGTGTACTTCGATGTATCAATTCAGACGCCTTCTCTATCATCAACATTATAGGT
+CTCGTATATGCTCGGCGCGATCTGCTTCTCTCCGCCAATAGCCCCATAGTGTATTTCAAG
+CGCAGTAACAGTGAAATCGTTACGAAGGTAGGGATGTTGCTTATAATTGTCGTAACTTAT
+CGCTTATGTATCTTTCAAGAATGAACGGCAGCATATACATACGTTCTACCTTTAGCTACA
+AAGCATCCATATACTCCCTCTCATGATTGAAACTCTTCCCTATTTTGTAGCCAATAGTGA
+AAGCGTATTAGTATAAATTCGTCGGTTTTTCACTCGCAACTGTTATACTCTGCAAACAAA
+CGAAAGCCTCATAGTACAAACCTAAAGCTACATACTTCATCATTGGCAGACCAGTGGCGG
+TATTTCTACGGAAGCATCACTATAGATATAAAGTTTCCCTTCATGTACGTCTGTTAACCA
+TATCACAAGAAACTGCTATCTCTGTCACGTAACAATTCACGCGCCTTATCGCCAAATGTT
+CATATATGCGCGGTATACGTATGAACGAATACTAATTAGTATAACGGAGGATTCACGGGA
+GGGATACTTGGGGCATTTATAAATCGTCTAAAAATTTTCTATCAGCACTTGCGGGTTATA
+GTGGATTACTAGGCAACATAATATTCTGTATTGGTCCAAATGACGCTATAGATAAATTAG
+CAAAATACATTGTTTCCATTTATGTAAGTCGAAACTCCAGGACTCCCGGGAACCAGTTAA
+ACCGTCTGGAAAAGACACATTGTGAGCGGGACTTCAATGATAGCTTTCAATGAGCTTCTC
+ATGCTTGGGGTCTGTACATATATGTTGGCGAAATTATCGTCTGTATTCTGTTATGCTTTG
+ATCATGGGTTATTAGTATAGTGTCCGGTTAAGTACCAATACCGCTAGAGACCCGACCTAA
+GTCGATAACTAACGATCATCGACGTAAGGATCGTCTCGATCAGTACTTCAGTCTAGATCT
+GGGAATAGTAACTCGTTAGTGAACTATGTCGTGTCATAACTCTAAAATGCAATCAAATCT
+TATTATTGAGTATTGATTATATAAAGCATCCGCTTAGCTTTACCCTCAAATGTTATATGC
+AATTTAAAGCGCTTGATATCGTCTACTCAAGTTCAGGTTTCACATGGCCGCAACGTGACG
+TTATTAGAGGTGGGTCATCATCTCTGAGGCTAGTGATGTTGAATACTCATTGAATGGGAA
+GTGGAATACCATGCTCGTAGGTAACAGCATGACCTATAAAATATACTATGGGTGTGTGGT
+AGATCAATATTGTTCAAGCATATCGTAACAATAACGGCTGAAATGTTACTGACATGAAAG
+AGGGAGTCCAAACCATTCTAACAGCTGATCAAGTCGTCTAAAAACGCCTGGTTCAGCCTT
+AAGAGTTATAAGCCAGACAAATTGTATCAATAGAGAATCCGTAAATTCCTCGGCCAACCT
+CTTGCAAAGACATCACTATCAATATACTACCGTGATCTTAATTAGTGAACTTATATAAAT
+ATCTACAACCAGATTCAACGGAAAAGCTTTAGTGGATTAGAAATTGCCAAGAATCACATT
+CATGTGGGTTCGAATGCTTTAGTAATACCATTTCGCCGAGTAGTCACTTCGCTGAACTGT
+CGTAAATTGCTATGACATAATCGAAAAGGATTGTCAAGAGTCGATTACTGCGGACTAATA
+ATCCCCACGGGGGTGGTCTCATGTCTCCCCAGGCGAGTGGGGACGGTTGATAAACACGCT
+GCATCGCGGACTGATGTTCCCAGTATTACATAGTCACATTGGATTGCGAGTAGTCTACCT
+ATTTATGAGCGAGAGATGCCTCTAACTACTTCGACTTTTAAAACCTTTCCACGCCAGTAT
+TCGGCGAAAGGGAAGTATTAAGGGTTGTCATAATTAAGCTGATACCACTTCAGACTTTGC
+TCTACTTCTGTCTTTCATTGGTTTAGTAAAGTCTGTCCATTCGTCGAGACCGTCTTTTGC
+AGCCTCATTCTACCAACTGCTCCGACTCTTAGTCTGCTTCTCCCAGCGTTATAACAAGAG
+GCATTTTGTCATCCTTAAAACAATAATAAAGAACTCGGAGCACTGATATAATGACTGAAT
+TAGAACCGCTTAAAAATACAACGAATAGATAAGACTATCGGATAAGATCTAATATGTAGT
+GATTAAGCCCTTTATTAATTAATAATAGTTACCCTTTCTGATGTAACGCGACATATTACG
+ATTTAGTGGCACGTCTGAATTGCAAAGCAGATCTCTACCCGATTTTTATTATAAATCCCG
+TATACATCTTGACTTGAGTAATTGTTCATCTTTTTATATCTCTTCGTACTACAAATAATT
+AATATCTCAACCCGTATTGTGTGATTCTAATTACCAACAGAATACGAGGAGGTTTTTGCT
+TAGGGCCATATATAATGAATCTATCTCGTTTATTCGCGGAACCCGAGATAACATTACGAT
+GTAACTATTTTAGAGAACTTAATACAAGAAACATTGCTGATTACTCATAACTAAATGCTT
+GGTAATATATCCTCAGTGCCCCTACCATCTTTTACGCAGGGATGTAATTACTTAGGATTC
+ATTGTGTAAGAATTACAATGAACGATGGATATGAAGGCATGTTGCGAGGTGTTCCTTGGT
+ATGTGAAGTTCGCAGGGCAACAAAAATTTCGCAGAATAGGCCTCAAAGTATTGGTAAAGA
+AGACAACTAATCATCACGAGCTTCTGATATCAATACGAACGAGTCCTGTGATGGATGAAA
+GAAAGTCGTATCGAAAATGTCAAGAGTCTGCCCAATGTAACTTACTTCAAAAAATAACGC
+TTCCGCCAAGTACGTTCGAATAAACGTAATTTTAAAAATACATAAGGGGTGTTAGAAAGT
+AAGCGACGGGATATAAGTTAGACTCAAGATTCCGCCGTAAAACGAGACTGATTCCGAAGA
+TTGTTCGTGGATCTGGTCATGACTTTCACTGAGTAAGGAGTTTCGACATATGTCAATAAA
+CACAAAAATAGAAGCTATTCGATCTGAAAAATATTAGGACAAGAAACTATCTCACGCTAG
+CCCAGAATATTCACTCACCCACGGGCGATACTAAAGCACTATATAGTCGCGTGATTACTA
+TACATATGGTACACATAAGAATCACGATCAGGTTCTCAATTTTCAACAATATATGTTTAT
+TTGCATAGGTAATATTAGGCCTTTAAGAGAAGGATGGGTGAGATACTCCGGGGATGGCGG
+CAATAAAGAAAAACACGATATGAGTAATAGGATCCTAATATCTTGGCGAGAGACTTAAGG
+TACGAATTTTGCGCAATCTATTTTTTACTTGGCCAGAATTCATGTATGGTATAAGTACGA
+ACTTTTTTGATCACTTTCATGGCTACCTGATTAGGATAGTTTGAGGAATTTCCCAAATAT
+ACCGATTTAATATACACTAGGGCTTGTCACTTTGAGTCAGAAAAAGAATATAATTACTTA
+GGGTAATGCTGCATACATATTCTTATATTGCAAAGGTTCTCTGGGTAATCTTGAGCCTTC
+ACGATACCTGGTGAAGTGTT

library/test/benchmark/reverse-complement.factor

@@ -0,0 +1,59 @@
+IN: temporary
+USING: compiler hashtables io kernel math math namespaces
+sequences strings vectors words words ;
+
+! Instead of a variable, we define an inline word which pushes
+! the hash on the stack, for performance.
+DEFER: trans-hash
+
+[
+    26 [ CHAR: A + dup set ] each
+    26 [ CHAR: a + dup set ] each
+
+    "TGCAAKYRMBDHV"
+    "ACGTUMRYKVHDB"
+    2dup
+    [ set ] 2each
+    [ ch>lower set ] 2each
+] make-hash
+
+\ trans-hash swap unit define-compound
+\ trans-hash t "inline" set-word-prop
+
+: translate-seq ( seq -- sbuf )
+    [
+        2000000 <sbuf> building set
+        <reversed> [ <reversed> % ] each
+        building get dup [ trans-hash hash ] inject
+    ] with-scope ;
+
+SYMBOL: out
+
+: seg ( sbuf n -- str )
+    60 * dup 60 + pick length min rot <slice> >string ;
+
+: show-seq ( seq -- )
+    translate-seq dup length 59 + 60 /i
+    [ seg out get stream-print ] each-with ;
+
+: clear-seq ( seq -- ) 0 swap set-length ;
+
+: do-line ( seq line -- seq )
+    dup first ">;" memq? [
+        over show-seq out get stream-print dup clear-seq
+    ] [
+        over push
+    ] if ;
+
+: (reverse-complement) ( seq -- )
+    readln [ do-line (reverse-complement) ] [ show-seq ] if* ;
+
+: reverse-complement ( infile outfile -- )
+    <file-writer> [
+        stdio get out set
+        <file-reader> [
+            500000 <vector> (reverse-complement)
+        ] with-stream
+    ] with-stream ;
+
+{ translate-seq seg clear-seq } [ compile ] each