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/********************************************************************************************
*
* Recreate all the .fasta files that have been loaded into a specified database.
*
* Author: Gene Myers
* Date : May 2014
*
********************************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "DB.h"
static char *Usage = "[-vU] [-w<int(80)>] <path:db>";
int main(int argc, char *argv[])
{ DAZZ_DB _db, *db = &_db;
FILE *dbfile;
char *dbfile_name;
int VERBOSE, UPPER, WIDTH;
// Process arguments
{ int i, j, k;
int flags[128];
char *eptr;
ARG_INIT("DB2fasta")
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, and db stub file
{ int status;
char *pwd, *root;
status = Open_DB(argv[1],db);
if (status < 0)
exit (1);
if (status == 1)
{ fprintf(stderr,"%s: Cannot be called on a .dam index: %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);
}
pwd = PathTo(argv[1]);
root = Root(argv[1],".db");
dbfile_name = Strdup(Catenate(pwd,"/",root,".db"),"Allocating db file name");
dbfile = Fopen(dbfile_name,"r");
free(pwd);
free(root);
if (dbfile_name == NULL || dbfile == NULL)
exit (1);
}
// For each cell do:
{ DAZZ_READ *reads;
char lname[MAX_NAME];
FILE *ofile = NULL;
int f, first, last, ofirst, nfiles;
char *read;
FSCANF(dbfile,DB_NFILE,&nfiles)
reads = db->reads;
read = New_Read_Buffer(db);
first = ofirst = 0;
for (f = 0; f < nfiles; f++)
{ int i;
char prolog[MAX_NAME], fname[MAX_NAME];
// Scan db image file line, create .fasta file for writing
FSCANF(dbfile,DB_FDATA,&last,fname,prolog)
if (f == 0 || strcmp(fname,lname) != 0)
{ if (f > 0)
{ if (ofile == stdout)
{ fprintf(stderr," %d reads\n",first-ofirst);
fflush(stderr);
}
else
FCLOSE(ofile)
}
if (strcmp(fname,"stdout") == 0)
{ ofile = stdout;
ofirst = first;
if (VERBOSE)
{ fprintf(stderr,"Sending to stdout ...");
fflush(stdout);
}
}
else
{ if ((ofile = Fopen(Catenate(".","/",fname,".fasta"),"w")) == NULL)
exit (1);
if (VERBOSE)
{ fprintf(stderr,"Creating %s.fasta ...\n",fname);
fflush(stdout);
}
}
strcpy(lname,fname);
}
// For the relevant range of reads, write each to the file
// recreating the original headers with the index meta-data about each read
for (i = first; i < last; i++)
{ int j, len;
int flags, qv;
DAZZ_READ *r;
r = reads + i;
len = r->rlen;
flags = r->flags;
qv = (flags & DB_QV);
FPRINTF(ofile,">%s/%d/%d_%d",prolog,r->origin,r->fpulse,r->fpulse+len)
if (qv > 0)
FPRINTF(ofile," RQ=0.%3d",qv)
FPRINTF(ofile,"\n")
Load_Read(db,i,read,UPPER);
for (j = 0; j+WIDTH < len; j += WIDTH)
FPRINTF(ofile,"%.*s\n",WIDTH,read+j)
if (j < len)
FPRINTF(ofile,"%s\n",read+j)
}
first = last;
}
if (f > 0)
{ if (ofile == stdout)
{ fprintf(stderr," %d reads\n",first-ofirst);
fflush(stderr);
}
else
FCLOSE(ofile)
}
}
fclose(dbfile);
Close_DB(db);
exit (0);
}
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