126 lines
2.5 KiB
C
126 lines
2.5 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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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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{
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fprintf(stderr,
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"usage: %s search_string %%mismatch [-case] [-match 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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{
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if(strcmp("-case",av[j]) == 0)
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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)
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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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{
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if(av[1][j] == 't')
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av[1][j] = 'u';
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if(av[1][j] == 'T')
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av[1][j] = 'U';
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}
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for(i=0;i<numseqs;i++)
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{
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if(UT)
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for(j=0;data[i].nuc[j]!='\0';j++)
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{
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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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{
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mis = 0;
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for(k=0,pos=j;k<slen && pos<data[i].length;k++,pos++)
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{
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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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{
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if(CompIUP(c,(av[1][k]|Case)) == FALSE)
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mis++;
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}
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else
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{
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if(c!=(av[1][k]|Case))
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mis++;
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}
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}
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if(k == slen && mis<=pcnt)
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{
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for(k=j;k<pos;k++)
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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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0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0x00,
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0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
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0x01,0xe,0x02,0x0d,0,0,0x04,0x0b,0,0,0x0c,0,0x03,0x0f,0,0,0,0x05,0x06,
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0x08,0x08,0x07,0x09,0x00,0xa,0,0,0,0,0,0,0,0x01,0x0e,0x02,0x0d,0,0,0x04,
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0x0b,0,0,0x0c,0,0x03,0x0f,0,0,0,0x05,0x06,0x08,0x08,0x07,0x09,0x00,0x0a,
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0,0,0,0,0x00,0
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};
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int testa,testb;
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if(a&32 != b&32)
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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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