131 lines
3.1 KiB
C
131 lines
3.1 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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FILE *file;
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int i,j,k,color,numseqs,numenzymes,nextpos,len;
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char enzymes[80][80],dummy[80];
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if(ac<3)
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{
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fprintf(stderr,"Usage: %s enzyme_file seq_file\n",av[0]);
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exit(-1);
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}
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file = fopen(av[2],"r");
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if(file == NULL)
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exit(-1);
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numseqs = ReadFlat(file,data,10000);
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file = fopen(av[1],"r");
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if(file == NULL)
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exit(-1);
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for(numenzymes = 0;
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fscanf(file,"%s %s",enzymes[numenzymes],dummy)>0;
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numenzymes++);
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for(i=0;i<numseqs;i++)
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{
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/*
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if(numseqs>1)
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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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if(numseqs>1)
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printf("nodash:\n");
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printf("start:\n");
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for(j=0;j<data[i].length;)
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{
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for(;data[i].nuc[j] == '-' && j<data[i].length;)
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{
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printf("8\n");
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j++;
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}
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if((nextpos = FindNext(data[i].nuc,j,enzymes,numenzymes
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,&len,&color)) != -1)
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{
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for(k=j;k<nextpos;k++)
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printf("8\n");
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for(k=j+nextpos;k<j+nextpos+len;k++)
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printf("%d\n",color);
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j=nextpos+len;
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}
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else
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for(;j<data[i].length;j++)
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printf("8\n");
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}
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}
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exit(0);
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}
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FindNext(target,offset,enzymes,numenzymes,match_len,color)
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char *target,enzymes[][80];
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int numenzymes,*match_len,*color;
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{
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int i,j,k,closest,len1,dif,flag = FALSE;
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closest = strlen(target);
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*match_len = 0;
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for(k=0;k<numenzymes;k++)
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{
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dif = (strlen(target)) - (len1 = strlen(enzymes[k])) +1;
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if(len1>0)
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for(flag = FALSE,j=offset;j<dif && flag == FALSE;j++)
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{
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flag = TRUE;
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for(i=0;i<len1 && flag;i++)
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{
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flag = Comp(enzymes[k][i],target[i+j])?
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TRUE:FALSE;
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}
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}
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if(j-1<closest)
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{
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closest = j-1;
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*color = k%6+1;
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*match_len = strlen(enzymes[k]);
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}
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}
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if(closest + *match_len < strlen(target))
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return(closest);
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else
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return(-1);
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}
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Comp(a,b)
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char a,b;
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{
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static int CtoB[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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0x08,0x08,0x07,0,0x09,0xa,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,0,0,0,0x05,0x06,0x08,0x08,0x07,0,0x09,0x0a,
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0,0,0,0,0x00,0
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};
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static int BtoC[128] =
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{
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'-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
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'~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
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'-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
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'~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
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'-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
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'~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
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'-','A','C','M','G','R','S','V','T','W','Y','H','K','D','B','N',
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'~','a','c','m','g','r','s','v','t','w','y','h','k','d','b','n',
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};
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return ((CtoB[a]) & (CtoB[b]));
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}
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