114 lines
2.9 KiB
C
114 lines
2.9 KiB
C
/*
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* Copyright 1991 Steven Smith at the Harvard Genome Lab.
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* All rights reserved.
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*/
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#include "Flatio.c"
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int main(ac, av)
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int ac;
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char **av;
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{
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struct data_format data[10000];
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int Match = 2, Mismatch = 8;
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int i, j, k, l, numseqs, mis, Case = 32;
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int slen, pcnt, pos;
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int UT = FALSE;
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char c;
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if (ac < 3) {
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fprintf(stderr,
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"usage: %s search_string %%mismatch [-case] [-match "
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"color] [-mismatch color]\n",
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av[0]);
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fprintf(stderr, " [-u=t]\n");
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exit(0);
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}
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for (j = 3; j < ac; j++) {
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if (strcmp("-case", av[j]) == 0) Case = 0;
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if (strcmp("-match", av[j]) == 0)
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sscanf(av[j + 1], "%d", &Match);
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if (strcmp("-u=t", av[j]) == 0) UT = TRUE;
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if (strcmp("-mismatch", av[j]) == 0)
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sscanf(av[j + 1], "%d", &Mismatch);
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}
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numseqs = ReadFlat(stdin, data, 10000);
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slen = strlen(av[1]);
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sscanf(av[2], "%d", &pcnt);
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pcnt *= slen;
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pcnt /= 100;
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if (UT)
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for (j = 0; j <= strlen(av[1]); j++) {
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if (av[1][j] == 't') av[1][j] = 'u';
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if (av[1][j] == 'T') av[1][j] = 'U';
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}
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for (i = 0; i < numseqs; i++) {
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if (UT)
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for (j = 0; data[i].nuc[j] != '\0'; j++) {
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if (data[i].nuc[j] == 't')
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data[i].nuc[j] = 'u';
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else if (data[i].nuc[j] == 'T')
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data[i].nuc[j] = 'U';
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}
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printf("name:%s\n", data[i].name);
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printf("length:%d\n", strlen(data[i].nuc));
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printf("start:\n");
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for (j = 0; j < data[i].length; j++) {
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mis = 0;
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for (k = 0, pos = j; k < slen && pos < data[i].length;
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k++, pos++) {
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c = data[i].nuc[pos];
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for (; (c == ' ' || c == '-' || c == '~') &&
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pos < data[i].length;)
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c = data[i].nuc[++pos];
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c |= Case;
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if (data[i].type == '#') {
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if (CompIUP(c, (av[1][k] | Case)) ==
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FALSE)
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mis++;
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}
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else {
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if (c != (av[1][k] | Case)) mis++;
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}
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}
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if (k == slen && mis <= pcnt) {
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for (k = j; k < pos; k++) printf("%d\n", Match);
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j = pos - 1;
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}
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else
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printf("%d\n", Mismatch);
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}
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}
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exit(0);
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}
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int CompIUP(a, b)
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char a, b;
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{
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static int tmatr[16] = {'-', 'a', 'c', 'm', 'g', 'r', 's', 'v',
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't', 'w', 'y', 'h', 'k', 'd', 'b', 'n'};
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static int matr[128] = {
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0x00, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0x01,
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0xe, 0x02, 0x0d, 0, 0, 0x04, 0x0b, 0, 0, 0x0c, 0,
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0x03, 0x0f, 0, 0, 0, 0x05, 0x06, 0x08, 0x08, 0x07, 0x09,
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0x00, 0xa, 0, 0, 0, 0, 0, 0, 0, 0x01, 0x0e,
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0x02, 0x0d, 0, 0, 0x04, 0x0b, 0, 0, 0x0c, 0, 0x03,
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0x0f, 0, 0, 0, 0x05, 0x06, 0x08, 0x08, 0x07, 0x09, 0x00,
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0x0a, 0, 0, 0, 0, 0x00, 0};
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int testa, testb;
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if (a & 32 != b & 32) return (FALSE);
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testa = matr[(int)a];
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testb = matr[(int)b];
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return (testa & testb);
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}
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