86 lines
1.7 KiB
C
86 lines
1.7 KiB
C
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#include "Flatio.c"
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#define MAX(a,b) ((a)>(b)?(a):(b))
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/*
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* Varpos.c- An extremely simple program for showing which positions
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* are varying in an alignment. Use this as a model for other
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* external functions.
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*
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* Read in a flat file alignment, pass back an alignment color
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* mask.
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*
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* Copyright 1991/1992 Steven Smith, Harvard Genome lab.
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*
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*/
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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 i,j,k,numseqs,rev = FALSE;
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int maxlen = -99999,
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score = 0,
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minoffset = 99999;
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char ch;
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if(ac>2)
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{
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fprintf(stderr,"Usage %s [-rev]<gde_flat_file>gde_color_mask\n", av[0]);
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exit(1);
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}
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if(ac == 2)
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if(strcmp(av[1],"-rev") == 0)
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rev = TRUE;
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numseqs = ReadFlat(stdin,data,10000);
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if(numseqs == 0)
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exit(1);
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for(j=0;j<numseqs;j++)
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{
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if(data[j].length+data[j].offset > maxlen)
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maxlen = data[j].length+data[j].offset;
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if(data[j].offset < minoffset)
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minoffset = data[j].offset;
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}
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printf("length:%d\n",maxlen);
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printf("offset:%d\n",minoffset);
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printf("start:\n");
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for(j=0;j<maxlen;j++)
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{
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int a=0,c=0,g=0,u=0;
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for(k=0;k<numseqs;k++)
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if(data[k].length+data[k].offset > j)
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{
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if(j>data[k].offset)
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ch=data[k].nuc[j-data[k].offset] | 32;
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else
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ch = '-';
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if(ch=='a')a++;
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if(ch=='c')c++;
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if(ch=='g')g++;
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if(ch=='u')u++;
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if(ch=='t')u++;
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}
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score=MAX(a,c);
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score=MAX(score,g);
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score=MAX(score,u);
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if(a+c+g+u)
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{
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if(rev)
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score=(score*6/(a+c+g+u)+8);
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else
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score=((8-score*6/(a+c+g+u))+8);
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}
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else
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score=8;
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printf("%d\n",score);
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}
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exit(0);
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}
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