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@alexpreynolds
Last active Mar 28, 2021
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Take reverse-complement of DNA string passed in via standard input
#include <stdlib.h>
#include <stdio.h>
/*
basemap[] works by storing a very small array that maps a base to
its complement, by dereferencing the array with the ASCII char's
decimal value as the index
(int) 'A' = 65;
(int) 'C' = 67;
(int) 'G' = 71;
(int) 'T' = 84;
(int) 'a' = 97;
(int) 'c' = 99;
(int) 'g' = 103;
(int) 't' = 116;
(int) 'N' = 78;
(int) 'U' = 85;
(int) 'u' = 117;
etc.
for example: basemap['A'] => basemap[65] => 'T' etc.
*/
static const unsigned char basemap[256] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
96, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127,
128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143,
144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175,
176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191,
192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223,
224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255
};
int
main(int argc, const char** argv)
{
char* line = NULL;
size_t len = 0;
ssize_t read;
while ((read = getline(&line, &len, stdin)) != -1) {
for (int idx = read - 2; idx >= 0; --idx) {
fprintf(stdout, "%c", basemap[(int)line[idx]]);
}
fprintf(stdout, "\n");
}
if (line) {
free(line);
line = NULL;
}
return EXIT_SUCCESS;
}
@alexpreynolds
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alexpreynolds commented Dec 4, 2015

To compile on POSIX-compatible setups:

$ gcc -Wall rc.c -o rc

On older compilers, you may need to enter something like:

$ gcc -Wall -std=gnu99 rc.c -o rc

To run, e.g.:

$ echo -e 'ATTCG\nTTCCA\nGGGAT\nNNaTT' | ./rc
CGAAT
TGGAA
ATCCC
AAtNN

@alexpreynolds
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alexpreynolds commented Apr 6, 2018

Updated basemap[] to include IUPAC degenerate base mappings.

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