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HAPplot.c
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HAPplot.c
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/********************************************************************************************
*
* Command line utility to produce CN-spectra plots
*
* Author: Gene Myers
* Date : March, 2021
*
*********************************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <dirent.h>
#include <math.h>
#include "libfastk.h"
#include "hap_plotter.h"
static char *Usage[] =
{ " [-v] [-w<double(6.0)>] [-h<double(4.5)>] [-pdf] [-T<int(4)>] [-P<dir(/tmp)>]",
" <mat>[.hap[.ktab]] <pat>[.hap[.ktab]] <asm1:dna> [<asm2:dna>] <out>"
};
static char template[16] = "._HAP.XXXX";
static int check_table(char *name, int lmer)
{ int kmer;
FILE *f;
f = fopen(name,"r");
if (f == NULL)
{ fprintf(stderr,"%s: Cannot find FastK table %s\n",Prog_Name,name);
exit (1);
}
else
{ fread(&kmer,sizeof(int),1,f);
if (lmer != 0 && kmer != lmer)
{ fprintf(stderr,"%s: Kmer (%d) of table %s != %d\n",Prog_Name,kmer,name,lmer);
exit (1);
}
fclose(f);
return (kmer);
}
}
int main(int argc, char *argv[])
{ int KMER;
int PDF;
int VERBOSE;
double XDIM, YDIM;
char *OUT;
char *MAT, *MROOT;
char *PAT, *PROOT;
char *ASM[2], *AROOT[2];
int NTHREADS;
char *SORT_PATH;
{ int i, j, k;
int flags[128];
char *eptr;
ARG_INIT("HAPpLot");
XDIM = 6.0;
YDIM = 4.5;
PDF = 0;
NTHREADS = 4;
SORT_PATH = "/tmp";
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("v")
break;
case 'h':
ARG_REAL(YDIM);
break;
case 'p':
if (strcmp("df",argv[i]+2) == 0)
PDF = 1;
else
{ fprintf(stderr,"%s: don't recognize option %s\n",Prog_Name,argv[i]);
exit (1);
}
break;
case 'w':
ARG_REAL(XDIM);
break;
case 'P':
SORT_PATH = argv[i]+2;
break;
case 'T':
ARG_POSITIVE(NTHREADS,"Number of threads")
break;
}
else
argv[j++] = argv[i];
argc = j;
VERBOSE = flags['v'];
if (argc < 5 || argc > 6)
{ fprintf(stderr,"\nUsage: %s %s\n",Prog_Name,Usage[0]);
fprintf(stderr," %*s %s\n",(int) strlen(Prog_Name),"",Usage[1]);
fprintf(stderr,"\n");
fprintf(stderr," -w: width in inches of plots\n");
fprintf(stderr," -h: height in inches of plots\n");
fprintf(stderr,"\n");
fprintf(stderr," -pdf: output .pdf (default is .png)\n");
fprintf(stderr,"\n");
fprintf(stderr," -v: verbose output to stderr\n");
fprintf(stderr," -T: number of threads to use\n");
fprintf(stderr," -P: Place all temporary files in directory -P.\n");
exit (1);
}
switch (argc)
{ case 5:
if (VERBOSE)
fprintf(stderr,"\n Single diploid assembly\n");
ASM[0] = argv[3];
ASM[1] = NULL;
break;
case 6:
if (VERBOSE)
fprintf(stderr,"\n Two haploid assemblies\n");
ASM[0] = argv[3];
ASM[1] = argv[4];
break;
default:
;
}
MAT = argv[1];
PAT = argv[2];
OUT = argv[argc-1];
}
{ char *troot, *x;
int i, j, len;
char *suffix[10] = { ".gz", ".fa", ".fq", ".fasta", ".fastq", ".db",
".dam", ".sam", ".bam", ".cram" };
char command[5000];
troot = mktemp(template);
x = PathnRoot(MAT,".ktab");
MAT = PathnRoot(x,".hap");
free(x);
x = PathnRoot(PAT,".ktab");
PAT = PathnRoot(x,".hap");
free(x);
MROOT = Root(MAT,"");
PROOT = Root(PAT,"");
KMER = check_table(Catenate(MAT,".hap",".ktab",""),0);
KMER = check_table(Catenate(PAT,".hap",".ktab",""),KMER);
for (i = 0; i < 2; i++)
{ if (ASM[i] == NULL)
continue;
for (j = 0; j < 10; j++)
{ len = strlen(ASM[i]) - strlen(suffix[j]);
if (strcmp(ASM[i]+len,suffix[j]) == 0)
ASM[i][len] = '\0';
}
AROOT[i] = Root(ASM[i],"");
if (VERBOSE)
fprintf(stderr,"\n Computing k-table and profiles for assembly %s\n",ASM[i]);
sprintf(command,"FastK -k%d -T%d -P%s -p %s",KMER,NTHREADS,SORT_PATH,ASM[i]);
system(command);
sprintf(command,"FastK -k%d -T%d -P%s -p:%s.hap %s -N%s.%s",
KMER,NTHREADS,SORT_PATH,MAT,ASM[i],AROOT[i],MROOT);
system(command);
sprintf(command,"FastK -k%d -T%d -P%s -p:%s.hap %s -N%s.%s",
KMER,NTHREADS,SORT_PATH,PAT,ASM[i],AROOT[i],PROOT);
system(command);
}
if (VERBOSE)
fprintf(stderr,"\n Creating blob table and plotting\n");
hap_plot(OUT,MAT,PAT,ASM,XDIM,YDIM,PDF,troot);
for (i = 0; i < 2; i++)
{ if (ASM[i] == NULL)
continue;
sprintf(command,"Fastrm %s %s.%s %s.%s",ASM[i],AROOT[i],MROOT,AROOT[i],PROOT);
system(command);
free(AROOT[i]);
}
free(PROOT);
free(MROOT);
free(PAT);
free(MAT);
}
Catenate(NULL,NULL,NULL,NULL);
Numbered_Suffix(NULL,0,NULL);
free(Prog_Name);
exit (0);
}