source code
// The Computer Language Benchmarks Game
// https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
//
// Contributed by Ian Osgood
var last = 42, A = 3877, C = 29573, M = 139968;
function rand(max) {
last = (last * A + C) % M;
return max * last / M;
}
var ALU =
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
var IUB = {
a:0.27, c:0.12, g:0.12, t:0.27,
B:0.02, D:0.02, H:0.02, K:0.02,
M:0.02, N:0.02, R:0.02, S:0.02,
V:0.02, W:0.02, Y:0.02
}
var HomoSap = {
a: 0.3029549426680,
c: 0.1979883004921,
g: 0.1975473066391,
t: 0.3015094502008
}
function makeCumulative(table) {
var last = null;
for (var c in table) {
if (last) table[c] += table[last];
last = c;
}
}
function fastaRepeat(n, seq) {
var seqi = 0, lenOut = 60;
while (n>0) {
if (n<lenOut) lenOut = n;
if (seqi + lenOut < seq.length) {
console.log( seq.substring(seqi, seqi+lenOut) );
seqi += lenOut;
} else {
var s = seq.substring(seqi);
seqi = lenOut - s.length;
console.log( s + seq.substring(0, seqi) );
}
n -= lenOut;
}
}
function fastaRandom(n, table) {
var line = new Array(60);
makeCumulative(table);
while (n>0) {
if (n<line.length) line = new Array(n);
for (var i=0; i<line.length; i++) {
var r = rand(1);
for (var c in table) {
if (r < table[c]) {
line[i] = c;
break;
}
}
}
console.log( line.join('') );
n -= line.length;
}
}
var n = +process.argv[2];
console.log(">ONE Homo sapiens alu")
fastaRepeat(2*n, ALU)
console.log(">TWO IUB ambiguity codes")
fastaRandom(3*n, IUB)
console.log(">THREE Homo sapiens frequency")
fastaRandom(5*n, HomoSap)
notes, command-line, and program output
NOTES:
64-bit Ubuntu quad core
Version 4.6.2
node.js v17.8.0
Wed, 23 Mar 2022 21:00:21 GMT
MAKE:
mv fasta.typescript fasta.ts
/opt/src/node-v17.8.0/bin/tsc --target es2022 --strict --noEmitOnError --removeComments fasta.ts
fasta.ts(8,15): error TS7006: Parameter 'max' implicitly has an 'any' type.
fasta.ts(36,25): error TS7006: Parameter 'table' implicitly has an 'any' type.
fasta.ts(44,22): error TS7006: Parameter 'n' implicitly has an 'any' type.
fasta.ts(44,25): error TS7006: Parameter 'seq' implicitly has an 'any' type.
fasta.ts(60,22): error TS7006: Parameter 'n' implicitly has an 'any' type.
fasta.ts(60,25): error TS7006: Parameter 'table' implicitly has an 'any' type.
make: [/home/dunham/all-benchmarksgame/2000-benchmarksgame/nanobench/makefiles/u64q.programs.Makefile:429: fasta.typescript_run] Error 1 (ignored)
4.18s to complete and log all make actions
COMMAND LINE:
/opt/src/node-v17.8.0/bin/node --use_strict fasta.js 250000
PROGRAM FAILED
PROGRAM OUTPUT:
node:internal/modules/cjs/loader:936
throw err;
^
Error: Cannot find module '/home/dunham/all-benchmarksgame/benchmarksgame_i53330/fasta/tmp/fasta.js'
at Function.Module._resolveFilename (node:internal/modules/cjs/loader:933:15)
at Function.Module._load (node:internal/modules/cjs/loader:778:27)
at Function.executeUserEntryPoint [as runMain] (node:internal/modules/run_main:77:12)
at node:internal/main/run_main_module:17:47 {
code: 'MODULE_NOT_FOUND',
requireStack: []
}
Node.js v17.8.0