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/********************************************************************************************
*
* Recreate all the .fasta files that are in a specified DAM.
*
* Author: Gene Myers
* Date : May 2014
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "DB.h"
#ifdef HIDE_FILES
#define PATHSEP "/."
#else
#define PATHSEP "/"
#endif
static char *Usage = "[-vU] [-w<int(80)>] <path:dam>";
int main(int argc, char *argv[])
{ DAZZ_DB _db, *db = &_db;
FILE *dbfile, *hdrs;
char *dbfile_name, *hdrs_name;
int nfiles;
int VERBOSE, UPPER, WIDTH;
// Process arguments
{ int i, j, k;
int flags[128];
char *eptr;
ARG_INIT("DAM2fasta")
WIDTH = 80;
j = 1;
for (i = 1; i < argc; i++)
if (argv[i][0] == '-')
switch (argv[i][1])
{ default:
ARG_FLAGS("vU")
break;
case 'w':
ARG_NON_NEGATIVE(WIDTH,"Line width")
break;
}
else
argv[j++] = argv[i];
argc = j;
UPPER = 1 + flags['U'];
VERBOSE = flags['v'];
if (argc != 2)
{ fprintf(stderr,"Usage: %s %s\n",Prog_Name,Usage);
fprintf(stderr,"\n");
fprintf(stderr," -U: Use upper case for DNA (default is lower case).\n");
fprintf(stderr," -w: Print -w bp per line (default is 80).\n");
exit (1);
}
}
// Open db
{ int status;
status = Open_DB(argv[1],db);
if (status < 0)
exit (1);
if (status == 0)
{ fprintf(stderr,"%s: Cannot be called on a .db: %s\n",Prog_Name,argv[1]);
exit (1);
}
if (db->part > 0)
{ fprintf(stderr,"%s: Cannot be called on a block: %s\n",Prog_Name,argv[1]);
exit (1);
}
}
{ char *pwd, *root;
pwd = PathTo(argv[1]);
root = Root(argv[1],".dam");
dbfile_name = Strdup(Catenate(pwd,"/",root,".dam"),"Allocating db file name");
hdrs_name = Strdup(Catenate(pwd,PATHSEP,root,".hdr"),"Allocating header file name");
dbfile = Fopen(dbfile_name,"r");
hdrs = Fopen(hdrs_name,"r");
free(pwd);
free(root);
if (dbfile_name == NULL || hdrs_name == NULL || dbfile == NULL || hdrs == NULL)
exit (1);
}
// nfiles = # of files in data base
FSCANF(dbfile,DB_NFILE,&nfiles)
// For each file do:
{ DAZZ_READ *reads;
char *read;
int f, first;
char *nstring;
nstring = Malloc(WIDTH+1,"Allocating write buffer\n");
if (nstring == NULL)
exit (1);
if (UPPER == 2)
for (f = 0; f < WIDTH; f++)
nstring[f] = 'N';
else
for (f = 0; f < WIDTH; f++)
nstring[f] = 'n';
nstring[WIDTH] = '\0';
reads = db->reads;
read = New_Read_Buffer(db);
first = 0;
for (f = 0; f < nfiles; f++)
{ int i, last, wpos;
FILE *ofile;
char prolog[MAX_NAME], fname[MAX_NAME], header[MAX_NAME];
// Scan db image file line, create .fasta file for writing
FSCANF(dbfile,DB_FDATA,&last,fname,prolog)
if (strcmp(fname,"stdout") == 0)
{ ofile = stdout;
if (VERBOSE)
{ fprintf(stderr,"Sending %d contigs to stdout ...\n",last-first);
fflush(stdout);
}
}
else
{ if ((ofile = Fopen(Catenate(".","/",fname,".fasta"),"w")) == NULL)
exit (1);
if (VERBOSE)
{ fprintf(stderr,"Creating %s.fasta ...\n",fname);
fflush(stdout);
}
}
// For the relevant range of reads, write each to the file
// recreating the original headers with the index meta-data about each read
wpos = 0;
for (i = first; i < last; i++)
{ int j, len, nlen, w;
DAZZ_READ *r;
r = reads + i;
len = r->rlen;
if (r->origin == 0)
{ if (i != first && wpos != 0)
{ fprintf(ofile,"\n");
wpos = 0;
}
FSEEKO(hdrs,r->coff,SEEK_SET)
FGETS(header,MAX_NAME,hdrs)
FPUTS(header,ofile)
}
if (r->fpulse != 0)
{ if (r->origin != 0)
nlen = r->fpulse - (reads[i-1].fpulse + reads[i-1].rlen);
else
nlen = r->fpulse;
for (j = 0; j+(w = WIDTH-wpos) <= nlen; j += w)
{ FPRINTF(ofile,"%.*s\n",w,nstring)
wpos = 0;
}
if (j < nlen)
{ FPRINTF(ofile,"%.*s",nlen-j,nstring)
if (j == 0)
wpos += nlen;
else
wpos = nlen-j;
}
}
Load_Read(db,i,read,UPPER);
for (j = 0; j+(w = WIDTH-wpos) <= len; j += w)
{ FPRINTF(ofile,"%.*s\n",w,read+j)
wpos = 0;
}
if (j < len)
{ FPRINTF(ofile,"%s",read+j)
if (j == 0)
wpos += len;
else
wpos = len-j;
}
}
if (wpos > 0)
FPRINTF(ofile,"\n")
if (ofile != stdout)
FCLOSE(ofile)
first = last;
}
free(nstring);
}
fclose(hdrs);
fclose(dbfile);
Close_DB(db);
exit (0);
}
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