--- /dev/null
+>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
set -e
. $GOROOT/src/Make.$GOARCH
+mode=run
+case X"$1" in
+X-test)
+ mode=test
+ shift
+esac
+
gc() {
$GC $1.go; $LD $1.$O
}
$GC -B $1.go; $LD $1.$O
}
+runonly() {
+ if [ $mode = run ]
+ then
+ "$@"
+ fi
+}
+
+
+
run() {
+ if [ $mode = test ]
+ then
+ if echo $1 | grep -q '^gc '
+ then
+ $1 # compile the program
+ program=$(echo $1 | sed 's/gc //')
+ shift
+ echo $program
+ $1 <fasta-1000.out > /tmp/$$
+ case $program in
+ chameneosredux)
+ # exact numbers may vary but non-numbers should match
+ grep -v '[0-9]' /tmp/$$ > /tmp/$$x
+ grep -v '[0-9]' chameneosredux.txt > /tmp/$$y
+ cmp /tmp/$$x /tmp/$$y
+ rm -f /tmp/$$ /tmp/$$x /tmp/$$y
+ ;;
+ *)
+ cmp /tmp/$$ $program.txt
+ rm -f /tmp/$$
+ esac
+ fi
+ return
+ fi
echo -n ' '$1' '
$1
shift
}
fasta() {
- echo 'fasta -n 25000000'
+ runonly echo 'fasta -n 25000000'
run 'gcc -O2 fasta.c' a.out 25000000
#run 'gccgo -O2 fasta.go' a.out -n 25000000 #commented out until WriteString is in bufio
run 'gc fasta' $O.out -n 25000000
}
revcomp() {
- gcc -O2 fasta.c
- a.out 25000000 > x
- echo 'reverse-complement < output-of-fasta-25000000'
+ runonly gcc -O2 fasta.c
+ runonly a.out 25000000 > x
+ runonly echo 'reverse-complement < output-of-fasta-25000000'
run 'gcc -O2 reverse-complement.c' a.out < x
run 'gccgo -O2 reverse-complement.go' a.out < x
run 'gc reverse-complement' $O.out < x
}
nbody() {
- echo 'nbody -n 50000000'
+ runonly echo 'nbody -n 50000000'
run 'gcc -O2 nbody.c' a.out 50000000
run 'gccgo -O2 nbody.go' a.out -n 50000000
run 'gc nbody' $O.out -n 50000000
}
binarytree() {
- echo 'binary-tree 15 # too slow to use 20'
+ runonly echo 'binary-tree 15 # too slow to use 20'
run 'gcc -O2 binary-tree.c -lm' a.out 15
run 'gccgo -O2 binary-tree.go' a.out -n 15
run 'gccgo -O2 binary-tree-freelist.go' $O.out -n 15
}
fannkuch() {
- echo 'fannkuch 12'
+ runonly echo 'fannkuch 12'
run 'gcc -O2 fannkuch.c' a.out 12
run 'gccgo -O2 fannkuch.go' a.out -n 12
run 'gc fannkuch' $O.out -n 12
}
regexdna() {
- gcc -O2 fasta.c
- a.out 100000 > x
- echo 'regex-dna 100000'
+ runonly gcc -O2 fasta.c
+ runonly a.out 100000 > x
+ runonly echo 'regex-dna 100000'
run 'gcc -O2 regex-dna.c -lpcre' a.out <x
# run 'gccgo -O2 regex-dna.go' a.out <x # pages badly; don't run
run 'gc regex-dna' $O.out <x
}
spectralnorm() {
- echo 'spectral-norm 5500'
+ runonly echo 'spectral-norm 5500'
run 'gcc -O2 spectral-norm.c -lm' a.out 5500
run 'gccgo -O2 spectral-norm.go' a.out -n 5500
run 'gc spectral-norm' $O.out -n 5500
}
knucleotide() {
- gcc -O2 fasta.c
- a.out 1000000 > x # should be using 25000000
- echo 'k-nucleotide 1000000'
+ runonly gcc -O2 fasta.c
+ runonly a.out 1000000 > x # should be using 25000000
+ runonly echo 'k-nucleotide 1000000'
run 'gcc -O2 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include k-nucleotide.c -lglib-2.0' a.out <x
run 'gccgo -O2 k-nucleotide.go' a.out <x # warning: pages badly!
run 'gc k-nucleotide' $O.out <x
}
mandelbrot() {
- echo 'mandelbrot 16000'
+ runonly echo 'mandelbrot 16000'
run 'gcc -O2 mandelbrot.c' a.out 16000
run 'gccgo -O2 mandelbrot.go' a.out -n 16000
run 'gc mandelbrot' $O.out -n 16000
}
meteor() {
- echo 'meteor 16000'
+ runonly echo 'meteor 16000'
run 'gcc -O2 meteor-contest.c' a.out
run 'gccgo -O2 meteor-contest.go' a.out
run 'gc meteor-contest' $O.out
}
pidigits() {
- echo 'pidigits 10000'
+ runonly echo 'pidigits 10000'
run 'gcc -O2 pidigits.c -lgmp' a.out 10000
# run 'gccgo -O2 pidigits.go' a.out -n 10000 # uncomment when gccgo library updated
run 'gc pidigits' $O.out -n 10000
}
threadring() {
- echo 'threadring 50000000'
+ runonly echo 'threadring 50000000'
run 'gcc -O2 threadring.c -lpthread' a.out 50000000
run 'gccgo -O2 threadring.go' a.out -n 50000000
run 'gc threadring' $O.out -n 50000000
}
chameneos() {
- echo 'chameneos 6000000'
+ runonly echo 'chameneos 6000000'
run 'gcc -O2 chameneosredux.c -lpthread' a.out 6000000
# run 'gccgo -O2 chameneosredux.go' a.out -n 6000000 # doesn't support the non-forward-decl variant
run 'gc chameneosredux' $O.out -n 6000000
for i in $run
do
$i
- echo
+ runonly echo
done