+++ /dev/null
-/* map_db.c - read a FASTA or GCG format database and generate a list
- of indices for rapid memory mapping */
-
-/* copyright (c) 1999 William R. Pearson */
-
-/* $Name: fa_34_26_5 $ - $Id: map_db.c,v 1.9 2005/09/27 15:32:58 wrp Exp $ */
-
-/* input is a libtype 1,5, or 6 sequence database */
-/* output is a BLAST2 formatdb type index file */
-
-/* format of the index file:
-
-1) map_db version number ["MP"+2 bytes]
-2) number of sequences in database [4 bytes]
-3) total length of database [8 bytes] (MP1, 4 bytes for MP0)
-4) longest sequence in database [8 bytes] (MP1, 4 bytes for MP0)
-5) list of offsets to definitions [num_seq+1] int*8 (MP1, 4 bytes for MP0)
-6) list of offsets to sequences [num_seq+1] int*8 (MP1, 4 bytes for MP1)
-7) list of flag characters for sequences [num_seq+1]bytes
- (used for GCG binary to encode 2bit or 4 bit representation)
-
- sequence files will be as defined by their format
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include "uascii.h"
-#include "ncbl2_head.h"
-
-#define GCGBIN 6
-#define LASTLIB 6
-
-int (*get_entry) ();
-
-int a_get_ent(long *, long *);
-int v_get_ent(long *, long *);
-int gcg_get_ent(long *, long *);
-int gbf_get_ent(long *, long *);
-
-void src_int4_write(FILE *, int);
-void src_int4_read(FILE *, int *);
-void src_long4_write(FILE *, long);
-void src_long4_read(FILE *, long *);
-void src_long8_write(FILE *, long);
-void src_long8_read(FILE *, long *);
-
-void newname(char *nname, char *oname, char *suff, int maxn);
-
-int (*get_ent_arr[LASTLIB+1])()={a_get_ent, gbf_get_ent, NULL, NULL, NULL,
- v_get_ent, gcg_get_ent};
-
-long openlib(char *, int);
-
-static int *sascii;
-
-main(int argc, char **argv)
-{
- FILE *libi;
- char lname[256];
- char iname[256];
- char format[4];
- char *bp;
-
- int i;
- int nlib; /* number of entries */
-
- long max_len; /* longest sequence */
- long tot_len; /* total sequence length */
-
- int n1;
-
- long f_size; /* file size from fstat() */
- int lib_size; /* current space available - may be realloc'ed */
- int lib_inc;
- int lib_type; /* 1 for protein, 0 for DNA */
- int lib_aa; /* dna=1; prot=0; */
-
- /* file offsets */
- long d_pos; /* start of description */
- long s_pos; /* start of sequence */
- long *d_pos_arr; /* array of description pointers */
- long *s_pos_arr; /* array of description pointers */
-
- lib_type = 0;
- lib_size = 200000;
- lib_inc = 100000;
-
- lib_aa = 1;
-
- while (argc > 1 && *argv[1]=='-') {
- if (strcmp(argv[1],"-n")==0) lib_aa = 0;
- argv++;
- argc--;
- }
-
- /* open the database */
- if (argc > 1) strncpy(lname, argv[1],sizeof(lname));
- else {
- fprintf(stderr," Entry library name: ");
- fgets(lname,sizeof(lname),stdin);
- if ((bp=strchr(lname,'\n'))!=NULL) *bp='\0';
- }
-
- if ((bp=strchr(lname,' '))!=NULL) {
- lib_type = atoi(bp+1);
- *bp='\0';
- }
- else lib_type = 0;
-
- if (get_ent_arr[lib_type] == NULL) {
- fprintf(stderr," cannot index file %s type %d\n",lname,lib_type);
- exit(1);
- }
-
- if (lib_type == 6) lib_aa = 0;
- if (lib_type == 1) lib_aa = 0;
-
- if (lib_aa == 1) sascii = aascii;
- else sascii = nascii;
-
- if ((f_size=openlib(lname,lib_type))==0) {
- fprintf(stderr," cannot open %s (type: %d)\n",lname,lib_type);
- exit(1);
- }
-
- /* allocate array of description pointers */
- if ((d_pos_arr=(long *)calloc(lib_size, sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate %d for desc. array\n",lib_size);
- exit(1);
- }
- /* allocate array of sequence pointers */
- if ((s_pos_arr=(long *)calloc(lib_size, sizeof(long)))==NULL) {
- fprintf(stderr," cannot allocate %d for seq. array\n",lib_size);
- exit(1);
- }
-
- /* allocate array of sequence flags */
-
- nlib = 0; tot_len=0; max_len=-1;
- while ((n1=get_entry(&d_pos, &s_pos)) > 0) {
- d_pos_arr[nlib] = d_pos;
- s_pos_arr[nlib] = s_pos;
- nlib++;
- tot_len += n1;
- if (n1 > max_len) max_len = n1;
- if (nlib >= lib_size) { /* too many entries */
- lib_size += lib_inc;
- if ((d_pos_arr=(long *)realloc(d_pos_arr,lib_size*sizeof(long)))==NULL) {
- fprintf(stderr," cannot realloc allocate %d for desc.. array\n",
- lib_size);
- exit(1);
- }
- if ((s_pos_arr=(long *)realloc(s_pos_arr,lib_size*sizeof(long)))==NULL) {
- fprintf(stderr," cannot realloc allocate %d for seq. array\n",
- lib_size);
- exit(1);
- }
- }
- }
-
- d_pos_arr[nlib]= d_pos; /* put in the end of the file */
- s_pos_arr[nlib]=0;
-
- /* all the information is in, write it out */
-
- newname(iname,lname,"xin",sizeof(iname));
-
- if ((libi=fopen(iname,"w"))==NULL) {
- fprintf(stderr," cannot open %s for writing\n",iname);
- exit(1);
- }
-
- /* write out format version */
- format[0]='M';
- format[1]='P';
-#ifdef BIG_LIB64
- format[2]= 1; /* format 1 for 8-byte offsets */
-#else
- format[2]='\0'; /* format '\0' for original 4-byte */
-#endif
-
- format[3]=lib_type;
- fwrite(format,4,sizeof(char),libi);
-
- /* write out sequence type */
- src_int4_write(libi, lib_aa);
-
- /* write out file fstat as integrity check */
-#ifdef BIG_LIB64
- src_long8_write(libi, f_size);
-#else
- src_int4_write(libi, f_size);
-#endif
-
- /* write out num_seq */
- src_int4_write(libi, nlib);
-
-#ifdef BIG_LIB64
- /* write out tot_len, max_len */
- src_long8_write(libi, tot_len);
-#else
- src_int4_write(libi, tot_len);
-#endif
- src_int4_write(libi, max_len);
-
-#ifdef BIG_LIB64
- for (i=0; i<=nlib; i++) src_long8_write(libi,d_pos_arr[i]);
- for (i=0; i<=nlib; i++) src_long8_write(libi,s_pos_arr[i]);
-#else
- for (i=0; i<=nlib; i++) src_int4_write(libi,d_pos_arr[i]);
- for (i=0; i<=nlib; i++) src_int4_write(libi,s_pos_arr[i]);
-#endif
-
- fclose(libi);
-
-#ifdef BIG_LIB64
- fprintf(stderr," wrote %d sequences (tot=%ld, max=%ld) to %s\n",
- nlib,tot_len,max_len,iname);
-#else
- fprintf(stderr," wrote %d sequences (tot=%ld, max=%ld) to %s\n",
- nlib,tot_len,max_len,iname);
-#endif
-}
-
-
-FILE *libf=NULL;
-long lpos;
-
-#define MAXLINE 4096
-char lline[MAXLINE+1];
-
-long
-openlib(char *lname, int lib_type)
-{
- long f_size;
- struct stat stat_buf;
-
- if (stat(lname,&stat_buf)<0) {
- fprintf(stderr," cannot stat library: %s\n",lname);
- return 0;
- }
-
- if ((libf=fopen(lname,"r"))==NULL) {
- fprintf(stderr," cannot open library: %s (type: %d)\n",
- lname, lib_type);
- return 0;
- }
-
- f_size = stat_buf.st_size;
-
- get_entry = get_ent_arr[lib_type];
-
- lpos = ftell(libf);
- if (fgets(lline,MAXLINE,libf)==NULL) return 0;
- return f_size;
-}
-
-int
-a_get_ent(long *d_pos, long *s_pos)
-{
- register char *cp;
- register int *ap, n1;
-
- ap = sascii;
-
- while (lline[0]!='>' && lline[0]!=';') {
- lpos = ftell(libf);
- if (fgets(lline,sizeof(lline),libf)==NULL) {
- *d_pos = lpos;
- return 0;
- }
- }
-
- *d_pos = lpos;
-
- /* make certain we have the end of the line */
- while (strchr((char *)lline,'\n')==NULL) {
- if (fgets(lline,sizeof(lline),libf)==NULL) break;
- }
-
- *s_pos = ftell(libf);
- lline[0]='\0';
- n1 = 0;
- while (fgets(lline,sizeof(lline),libf)!=NULL) {
- if (lline[0]=='>') break;
- if (lline[0]==';') {
- if (strchr(lline,'\n')==NULL) {
- fprintf(stderr," excessive continuation\n%s",lline);
- return -1;
- }
- }
-
- for (cp=lline; *cp; ) if (ap[*cp++]<NA) n1++;
- lpos = ftell(libf);
- }
- return n1;
-}
-
-int
-v_get_ent(long *d_pos, long *s_pos)
-{
- register char *cp;
- register int *ap;
- int n1;
-
- ap = sascii;
-
- /* check for seq_id line */
- while (lline[0]!='>' && lline[0]!=';') {
- lpos = ftell(libf);
- if (fgets(lline,sizeof(lline),libf)==NULL) {
- *d_pos = lpos;
- return 0;
- }
- }
- *d_pos = lpos;
-
- /* get the description line */
- if (fgets(lline,sizeof(lline),libf)==NULL) return 0;
- /* make certain we have the end of the line */
- while (strchr((char *)lline,'\n')==NULL) {
- if (fgets(lline,sizeof(lline),libf)==NULL) break;
- }
-
- *s_pos = ftell(libf);
- lline[0]='\0';
- n1 = 0;
- while (fgets(lline,sizeof(lline),libf)!=NULL) {
- if (lline[0]=='>') break;
-
- for (cp=lline; *cp; ) if (ap[*cp++]<NA) n1++;
- lpos = ftell(libf);
- }
- return n1;
-}
-
-static char gcg_type[10];
-static long gcg_len;
-static int gcg_bton[4]={2,4,1,3};
-
-int
-gcg_get_ent(long *d_pos, long *s_pos)
-{
- register char *cp;
- register int *ap;
- char libstr[20], dummy[20];
- char gcg_date[6];
- int r_block;
- int n1;
-
- /* check for seq_id line */
- while (lline[0]!='>') {
- lpos = ftell(libf);
- if (fgets(lline,sizeof(lline),libf)==NULL) {
- *d_pos = lpos;
- return 0;
- }
- }
- *d_pos = lpos;
-
- /* get the encoding/sequence length info */
-
- sscanf(&lline[4],"%s %s %s %s %ld",
- libstr,gcg_date,gcg_type,dummy,&gcg_len);
-
- /* get the description line */
- if (fgets(lline,MAXLINE,libf)==NULL) return;
-
- *s_pos = ftell(libf);
- /* seek to the end of the sequence; +1 to jump over newline */
- if (gcg_type[0]=='2') {
- r_block = (gcg_len+3)/4;
- fseek(libf,r_block+1,SEEK_CUR);
- }
- else fseek(libf,gcg_len+1,SEEK_CUR);
-
- lpos = ftell(libf);
- fgets(lline,MAXLINE,libf);
-
- return gcg_len;
-}
-
-int
-gbf_get_ent(long *d_pos, long *s_pos)
-{
- int n1;
- char *cp;
- register int *ap;
-
-#if !defined(TFAST)
- ap = sascii;
-#else
- ap = nascii;
-#endif
-
- while (lline[0]!='L' || lline[1]!='O' ||
- strncmp(lline,"LOCUS",5)) { /* find LOCUS */
- lpos = ftell(libf);
- if (fgets(lline,MAXLINE,libf)==NULL) return (-1);
- }
- *d_pos=lpos;
-
- while (lline[0]!='O' || lline[1]!='R' ||
- strncmp(lline,"ORIGIN",6)) { /* find ORIGIN */
- if (fgets(lline,MAXLINE,libf)==NULL) return (-1);
- }
- *s_pos = ftell(libf);
-
- lline[0]='\0';
- n1=0;
- while (fgets(lline,MAXLINE,libf)!=NULL) {
- if (lline[0]=='/') break;
- for (cp=lline; *cp; ) if (ap[*cp++]<NA) n1++;
- }
- lpos = ftell(libf);
- fgets(lline,MAXLINE,libf);
-
- return n1;
-}
-
-void src_int4_read(FILE *fd, int *val)
-{
-#ifdef IS_BIG_ENDIAN
- fread((char *)val,(size_t)4,(size_t)1,fd);
-#else
- unsigned char b[4];
-
- fread((char *)&b[0],(size_t)1,(size_t)4,fd);
- *val = 0;
- *val = (int)((int)((int)(b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8)
- +(int)b[3];
-#endif
-}
-
-void src_int4_write(FILE *fd, int val)
-{
-#ifdef IS_BIG_ENDIAN
- fwrite(&val,(size_t)4,(size_t)1,fd);
-#else
- unsigned char b[4];
-
- b[3] = val & 255;
- b[2] = (val=val>>8)&255;
- b[1] = (val=val>>8)&255;
- b[0] = (val=val>>8)&255;
-
- fwrite(b,(size_t)1,(size_t)4,fd);
-#endif
-}
-
-void src_long8_write(FILE *fd, long val)
-{
-#ifdef IS_BIG_ENDIAN
- fwrite(&val,(size_t)8,(size_t)1,fd);
-#else
- unsigned char b[8];
-
- b[7] = val & 255;
- b[6] = (val=val>>8)&255;
- b[5] = (val=val>>8)&255;
- b[4] = (val=val>>8)&255;
- b[3] = (val=val>>8)&255;
- b[2] = (val=val>>8)&255;
- b[1] = (val=val>>8)&255;
- b[0] = (val=val>>8)&255;
-
- fwrite(b,(size_t)1,(size_t)8,fd);
-#endif
-}
-
-void
-newname(char *nname, char *oname, char *suff, int maxn)
-{
- strncpy(nname,oname,maxn-1);
- strncat(nname,".",1);
- strncat(nname,suff,maxn-strlen(nname));
-}
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