mirror of
https://github.com/c3lang/c3c.git
synced 2026-02-27 12:01:16 +00:00
106 lines
2.0 KiB
C
106 lines
2.0 KiB
C
module fasta;
|
|
import std::io;
|
|
import libc;
|
|
|
|
const IM = 139968;
|
|
const IA = 3877;
|
|
const IC = 29573;
|
|
const SEED = 42;
|
|
|
|
uint seed = SEED;
|
|
|
|
fn float fasta_rand(float max_val)
|
|
{
|
|
seed = (seed * IA + IC) % IM;
|
|
return max_val * seed / IM;
|
|
}
|
|
|
|
private String alu =
|
|
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"
|
|
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"
|
|
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"
|
|
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"
|
|
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"
|
|
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"
|
|
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
|
|
|
|
|
|
String iub = "acgtBDHKMNRSVWY";
|
|
double[] iub_p = {
|
|
0.27,
|
|
0.12,
|
|
0.12,
|
|
0.27,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02,
|
|
0.02 };
|
|
|
|
String homosapiens = "acgt";
|
|
double[] homosapiens_p = {
|
|
0.3029549426680,
|
|
0.1979883004921,
|
|
0.1975473066391,
|
|
0.3015094502008
|
|
};
|
|
|
|
const LINELEN = 60;
|
|
|
|
// slowest character-at-a-time output
|
|
fn void repeat_fasta(String seq, int n)
|
|
{
|
|
usz len = seq.len;
|
|
int i = void;
|
|
for (i = 0; i < n; i++)
|
|
{
|
|
io::putchar(seq[i % len]);
|
|
if (i % LINELEN == LINELEN - 1) io::putchar('\n');
|
|
}
|
|
if (i % LINELEN != 0) io::putchar('\n');
|
|
}
|
|
|
|
fn void random_fasta(String symb, double[] probability, int n)
|
|
{
|
|
assert(symb.len == probability.len);
|
|
int len = probability.len;
|
|
int i = void;
|
|
for (i = 0; i < n; i++)
|
|
{
|
|
double v = fasta_rand(1.0);
|
|
/* slowest idiomatic linear lookup. Fast if len is short though. */
|
|
int j = void;
|
|
for (j = 0; j < len - 1; j++)
|
|
{
|
|
v -= probability[j];
|
|
if (v < 0) break;
|
|
}
|
|
io::putchar(symb[j]);
|
|
if (i % LINELEN == LINELEN - 1) io::putchar('\n');
|
|
}
|
|
if (i % LINELEN != 0) io::putchar('\n');
|
|
}
|
|
|
|
fn int main(int argc, char **argv)
|
|
{
|
|
int n = 1000;
|
|
if (argc > 1) n = libc::atoi(argv[1]);
|
|
|
|
io::printf(">ONE Homo sapiens alu\n");
|
|
repeat_fasta(alu, n * 2);
|
|
|
|
io::printf(">TWO IUB ambiguity codes\n");
|
|
random_fasta(iub, iub_p, n * 3);
|
|
|
|
io::printf(">THREE Homo sapiens frequency\n");
|
|
random_fasta(homosapiens, homosapiens_p, n * 5);
|
|
|
|
return 0;
|
|
}
|