From 417683c3d36005754c79fe8246528d6608ab48d6 Mon Sep 17 00:00:00 2001 From: Rob Pike Date: Tue, 4 Aug 2009 10:13:58 -0700 Subject: [PATCH] clean up the code a bit start a log of progress R=rsc DELTA=222 (185 added, 17 deleted, 20 changed) OCL=32701 CL=32718 --- test/bench/fasta.go | 58 ++++++-------- test/bench/fasta.out | 171 ++++++++++++++++++++++++++++++++++++++++++ test/bench/timing.log | 13 ++++ 3 files changed, 205 insertions(+), 37 deletions(-) create mode 100644 test/bench/fasta.out create mode 100644 test/bench/timing.log diff --git a/test/bench/fasta.go b/test/bench/fasta.go index ca3d56a355..fd31400c81 100644 --- a/test/bench/fasta.go +++ b/test/bench/fasta.go @@ -49,7 +49,7 @@ var out *bufio.Writer var n = flag.Int("n", 1000, "length of result") -const WIDTH = 60 +const WIDTH = 60 // Fold lines after WIDTH bytes func min(a, b int) int { if a < b { @@ -65,6 +65,7 @@ type AminoAcid struct { var lastrandom uint32 = 42 +// Random number between 0.0 and 1.0 func myrandom() float { const ( IM = 139968; @@ -77,24 +78,22 @@ func myrandom() float { } func AccumulateProbabilities(genelist []AminoAcid) { - cp := 0.0; - for i := 0; i < len(genelist); i++ { - cp += genelist[i].p; - genelist[i].p = cp; + for i := 1; i < len(genelist); i++ { + genelist[i].p += genelist[i-1].p; } } -/* This function prints the characters of the string s. When it */ -/* reaches the end of the string, it goes back to the beginning */ -/* It stops when the total number of characters printed is count. */ -/* Between each WIDTH consecutive characters it prints a newline */ -/* This function assumes that WIDTH <= strlen (s) + 1 */ +// RepeatFasta prints the characters of the byte slice s. When it +// reaches the end of the slice, it goes back to the beginning. +// It stops after generating count characters. +// After each WIDTH characters it prints a newline. +// It assumes that WIDTH <= len(s) + 1. func RepeatFasta(s []byte, count int) { pos := 0; s2 := make([]byte, len(s) + WIDTH); bytes.Copy(s2, s); bytes.Copy(s2[len(s):len(s2)], s); - for { + for count > 0 { line := min(WIDTH, count); out.Write(s2[pos:pos+line]); out.WriteByte('\n'); @@ -103,43 +102,31 @@ func RepeatFasta(s []byte, count int) { pos -= len(s); } count -= line; - if count <= 0 { - break - } } } -/* This function takes a pointer to the first element of an array */ -/* Each element of the array is a struct with a character and */ -/* a float number p between 0 and 1. */ -/* The function generates a random float number r and */ -/* finds the first array element such that p >= r. */ -/* This is a weighted random selection. */ -/* The function then prints the character of the array element. */ -/* This is done count times. */ -/* Between each WIDTH consecutive characters, the function prints a newline */ +// Each element of genelist is a struct with a character and +// a floating point number p between 0 and 1. +// RandomFasta generates a random float r and +// finds the first element such that p >= r. +// This is a weighted random selection. +// RandomFasta then prints the character of the array element. +// This sequence is repeated count times. +// Between each WIDTH consecutive characters, the function prints a newline. func RandomFasta(genelist []AminoAcid, count int) { buf := make([]byte, WIDTH + 1); - for { + for count > 0 { line := min(WIDTH, count); - pos := 0; - for { + for pos := 0; pos < line; pos++ { r := myrandom(); var i int; for i = 0; genelist[i].p < r; i++ { } buf[pos] = genelist[i].c; - pos++; - if pos >= line { - break - } } buf[line] = '\n'; out.Write(buf[0:line + 1]); count -= line; - if count <= 0 { - break - } } } @@ -177,7 +164,7 @@ func main() { AccumulateProbabilities(iub); AccumulateProbabilities(homosapiens); - alu := strings.Bytes("" + alu := strings.Bytes( "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" @@ -188,11 +175,8 @@ func main() { out.WriteString(">ONE Homo sapiens alu\n"); RepeatFasta(alu, 2 * *n); - out.Flush(); out.WriteString(">TWO IUB ambiguity codes\n"); RandomFasta(iub, 3 * *n); - out.Flush(); out.WriteString(">THREE Homo sapiens frequency\n"); RandomFasta(homosapiens, 5 * *n); - out.Flush(); } diff --git a/test/bench/fasta.out b/test/bench/fasta.out new file mode 100644 index 0000000000..f1caba0d62 --- /dev/null +++ b/test/bench/fasta.out @@ -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 diff --git a/test/bench/timing.log b/test/bench/timing.log new file mode 100644 index 0000000000..b81dcccbbf --- /dev/null +++ b/test/bench/timing.log @@ -0,0 +1,13 @@ +All tests on r45 + +Aug 3 2009 + +First version of fasta. Translation of fasta.c, fetched from + http://shootout.alioth.debian.org/u32q/benchmark.php?test=fasta&lang=gpp&id=4 + +fasta -n 25000000 + [gcc -O2 fasta.c 5.98u 0.00s 6.01r] + gccgo -O2 8.82u 0.02s 8.85r + 6g 13.50u 0.02s 13.53r + 6g -B 12.99u 0.02s 13.02r + -- 2.48.1