178 lines
3.9 KiB
C
Executable file
178 lines
3.9 KiB
C
Executable file
#include <stdio.h>
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#include <malloc.h>
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#include "global_defs.h"
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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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Sequence cons; /* master alignment */
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Sequence *master; /* Current Walking sets to add */
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int cursize, maxsize = 10, ii;
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char str[2], cons_type;
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FILE *file, *consout_fp, *maskout_fp;
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int conserved_color, variable_color, partial_color, major_perc;
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if(ac == 1)
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{
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fprintf(stderr, "Usage:\n");
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fprintf(stderr,
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"%s %s\n\t%s\n\t%s\n\t%s\n\t%s\n\t%s\n\t%s\n\t%s\n",
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av[0],
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"sequence-file",
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"[-iupac] IUPAC consensus. Default",
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"[-majority percent] Majority consensus (default percent: 75)",
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"[-maskv colorv] Variable position color",
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"[-maskc colorc] Conserved position color",
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"[-maskp colorp] Partially conserved color",
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"[-consout output-consensus] Default: stdout",
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"[-maskout output-mask]");
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exit (0);
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}
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InitRecord(&cons);
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if((file = fopen(av[1],"r")) == NULL)
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{
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fprintf(stderr, "Can't open sequence-file %s.\n", av[1]);
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exit(1);
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}
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master = (Sequence*)Calloc(maxsize,sizeof(Sequence));
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cursize = 0;
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while(ReadRecord(file,&(master[cursize])) != -1)
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{
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SeqNormal(&master[cursize]);
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if(++cursize == maxsize)
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{
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maxsize *= 2;
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master = (Sequence*)
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Realloc(master, maxsize*sizeof(Sequence));
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}
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master[cursize].group_number = 99999;
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}
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fclose(file);
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cons_type = ' '; /* 'i':IUPAC, 'm':majority, 'k':mask */
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consout_fp = stdout;
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maskout_fp = NULL;
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conserved_color = 8; /* black */
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variable_color = 3; /* red */
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ii = 2;
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while(ii < ac)
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{
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if(strcmp(av[ii], "-iupac") == 0)
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{
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cons_type = 'i';
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}
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else if(strcmp(av[ii], "-majority") == 0)
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{
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cons_type = 'm';
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ii++;
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major_perc = atoi(av[ii]);
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}
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else if(strcmp(av[ii], "-maskv") == 0)
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{
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variable_color = atoi(av[++ii]);
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if(cons_type == ' ')
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cons_type = 'k';
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}
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else if(strcmp(av[ii], "-maskc") == 0)
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{
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conserved_color = atoi(av[++ii]);
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if(cons_type == ' ')
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cons_type = 'k';
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}
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else if(strcmp(av[ii], "-maskp") == 0)
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{
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partial_color = atoi(av[++ii]);
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if(cons_type == ' ')
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cons_type = 'k';
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}
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else if(strcmp(av[ii], "-consout") == 0)
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{
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if((consout_fp = fopen(av[++ii], "w")) == NULL)
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{
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fprintf(stderr, "Can't open output file %s.\n",av[ii]);
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consout_fp = stdout;
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}
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}
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else if(strcmp(av[ii], "-maskout") == 0)
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{
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if((maskout_fp = fopen(av[++ii], "w")) == NULL)
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{
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fprintf(stderr, "Can't open output file %s.\n",av[ii]);
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}
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}
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else
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{
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fprintf(stderr, "Invalid flag %s\n", av[ii]);
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}
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ii++;
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}
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if(cons_type == ' ')
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cons_type = 'i';
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if(cons_type != 'k')
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{
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if(maskout_fp != NULL)
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{
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/* Useful only when output to GDE. */
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fprintf(maskout_fp, "length:%d\n", cons.seqlen);
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fprintf(maskout_fp, "start:\n");
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}
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if((cons_type == 'i' &&
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MakeConsensus(master,cursize,&cons,0,cons_type)==FALSE) ||
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(cons_type == 'm' &&
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MajorityCons(master,cursize,&cons,0, major_perc) == FALSE))
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{
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fprintf(stderr, "Failed to make consensus.\n");
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exit(1);
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}
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WriteRecord(consout_fp, &cons, NULL, 0);
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}
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else
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{
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if(MakeScore(master,cursize,&cons,0) == FALSE)
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{
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fprintf(stderr, "Failed to make consensus.\n");
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exit(1);
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}
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/*WriteRecord(stdout, &cons, NULL, 0);
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printf("\n\n");*/
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if(maskout_fp == NULL)
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{
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maskout_fp = stdout;
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}
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fprintf(maskout_fp, "length:%d\n", cons.seqlen);
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fprintf(maskout_fp, "start:\n");
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for(ii = 0; ii < cons.seqlen; ii++)
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{
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switch(cons.c_elem[ii])
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{
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case 'F':
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fprintf(maskout_fp, "%d\n", partial_color);
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break;
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case 'E':
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fprintf(maskout_fp, "%d\n", conserved_color);
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break;
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default:
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fprintf(maskout_fp, "%d\n", variable_color);
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break;
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}
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}
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}
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fclose(consout_fp);
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fclose(maskout_fp);
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}
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