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/*******************************************************************************************
*
* Synthetic DNA shotgun sequence generator
* Generate a fake genome of size genlen*1Mb long, that has an AT-bias of -b.
* The -r parameter seeds the random number generator for the generation of the genome
* so that one can reproducbile produce the same underlying genome to sample from. If
* missing, then the job id of the invocation seeds the generator. The sequence is
* sent to the standard output in .fasta format.
*
* Author: Gene Myers
* Date : April 2016
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <math.h>
static char *Usage = "<genlen:double> [-U] [-b<double(.5)>] [-w<int(80)>] [-r<int>]";
static int GENOME; // -g option * 1Mbp
static double BIAS; // -b option
static int HASR = 0; // -r option is set?
static int SEED; // -r option
static int WIDTH; // -w option
static int UPPER; // -U option
static char *Prog_Name;
// Generate a random DNA sequence of length *len* with an AT-bias of BIAS.
// Uppercase letters if UPPER is set, lowercase otherwise.
static char *random_genome(int len)
{ static char *seq = NULL;
static double x, PRA, PRC, PRG;
int i;
if (seq == NULL)
{ PRA = BIAS/2.;
PRC = (1.-BIAS)/2. + PRA;
PRG = (1.-BIAS)/2. + PRC;
if ((seq = (char *) malloc(WIDTH+1)) == NULL)
{ fprintf(stderr,"%s: Allocating genome sequence\n",Prog_Name);
exit (1);
}
}
if (UPPER)
for (i = 0; i < len; i++)
{ x = drand48();
if (x < PRC)
if (x < PRA)
seq[i] = 'A';
else
seq[i] = 'C';
else
if (x < PRG)
seq[i] = 'G';
else
seq[i] = 'T';
}
else
for (i = 0; i < len; i++)
{ x = drand48();
if (x < PRC)
if (x < PRA)
seq[i] = 'a';
else
seq[i] = 'c';
else
if (x < PRG)
seq[i] = 'g';
else
seq[i] = 't';
}
seq[len] = '\0';
return (seq);
}
int main(int argc, char *argv[])
{ int i, j;
char *eptr;
double glen;
// Process command arguments
//
// Usage: <GenomeLen:double> [-b<double(.5)>] [-r<int>]
Prog_Name = strdup("rangen");
WIDTH = 80;
BIAS = .5;
HASR = 0;
UPPER = 0;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
fprintf(stderr,"%s: %s is an illegal option\n",Prog_Name,argv[i]);
exit (1);
case 'U':
if (argv[i][2] != '\0')
{ fprintf(stderr,"%s: %s is an illegal option\n",Prog_Name,argv[i]);
exit (1);
}
UPPER = 1;
break;
case 'b':
BIAS = strtod(argv[i]+2,&eptr);
if (*eptr != '\0' || argv[i][2] == '\0')
{ fprintf(stderr,"%s: -%c '%s' argument is not a real number\n",
Prog_Name,argv[i][1],argv[i]+2);
exit (1);
}
if (BIAS < 0. || BIAS > 1.)
{ fprintf(stderr,"%s: AT-bias must be in [0,1] (%g)\n",Prog_Name,BIAS);
exit (1);
}
break;
case 'r':
SEED = strtol(argv[i]+2,&eptr,10);
HASR = 1;
if (*eptr != '\0' || argv[i][2] == '\0')
{ fprintf(stderr,"%s: -r argument is not an integer\n",Prog_Name);
exit (1);
}
break;
case 'w':
WIDTH = strtol(argv[i]+2,&eptr,10);
if (*eptr != '\0' || argv[i][2] == '\0')
{ fprintf(stderr,"%s: -w '%s' argument is not an integer\n",Prog_Name,argv[i]+2);
exit (1);
}
if (WIDTH < 0)
{ fprintf(stderr,"%s: Line width must be non-negative (%d)\n",Prog_Name,WIDTH);
exit (1);
}
break;
}
else
argv[j++] = argv[i];
argc = j;
if (argc != 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
fprintf(stderr,"\n");
fprintf(stderr," -r: Random number generator seed (default is process id).\n");
fprintf(stderr," -b: AT vs GC ratio or bias.\n");
fprintf(stderr," -w: Print -w bp per line (default is 80).\n");
fprintf(stderr," -U: Output sequence in upper case (default is lower case).\n");
exit (1);
}
glen = strtod(argv[1],&eptr);
if (*eptr != '\0')
{ fprintf(stderr,"%s: genome length is not a real number\n",Prog_Name);
exit (1);
}
if (glen < 0.)
{ fprintf(stderr,"%s: Genome length must be positive (%g)\n",Prog_Name,glen);
exit (1);
}
GENOME = (int) (glen*1000000.);
// Set up random number generator
if (HASR)
srand48(SEED);
else
srand48(getpid());
// Generate the sequence line at a time where all lines have width WDITH, save the last.
fprintf(stdout,">random len=%d bias=%g\n",GENOME,BIAS);
for (j = 0; j+WIDTH < GENOME; j += WIDTH)
fprintf(stdout,"%s\n",random_genome(WIDTH));
if (j < GENOME)
fprintf(stdout,"%s\n",random_genome(GENOME-j));
exit (0);
}
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