list_db.c

序列对齐 Compare a protein sequence to a protein sequence database or a DNA sequence to a DNA sequenc

/* list_db.c - report values from map_db.c  */

/* copyright (c) 1999 William R. Pearson */

/* 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]
4)  longest sequence in database    [8 bytes]
5) list of offsets to definitions  [num_seq+1] int*8
6) list of offsets to sequences    [num_seq+1] int*8
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 "uascii.h"
#include "ncbl2_head.h"

void src_int4_write(FILE *, int);
void src_int4_read(FILE *, int *);
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);

main(int argc, char **argv)
{
  FILE *libi;
  char lname[256];
  char iname[256];
  char format[4];
  char *bp;

  int i;
  int d_pos;	/* start of description */
  int s_pos;	/* start of sequence */
  int attr;	/* sequence attribute */
  int lib_aa;	/* 0 => DNA, 1 => protein */
  int nlib;	/* number of entries */
  long f_size;
  long max_len;	/* longest sequence */
  long tot_len;	/* total sequence length */
  int n1;
  
  int lib_size;	/* current space available - may be realloc'ed */
  int lib_inc;
  int lib_type; /* 1 for protein, 0 for DNA */
  int lib_dna;	/* dna=1; prot=0; */
  long *d_pos_arr;	/* array of description pointers */
  long *s_pos_arr;	/* array of description pointers */
  char *attr_arr;	/* array of attribute chars */

  int mm64_flag;

  lib_type = 0;
  lib_dna = 0;

  /* 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;

  newname(iname,lname,"xin",sizeof(iname));

  if ((libi=fopen(iname,"r"))==NULL) {
    fprintf(stderr," cannot open %s\n",iname);
    exit(1);
  }

  fread(format,1,sizeof(format),libi);
  printf("%c%c%d %d\n",format[0],format[1],format[2],format[3]);
  mm64_flag = (format[2]==1);

  src_int4_read(libi,&lib_aa);

  if (mm64_flag) src_long8_read(libi,&f_size);
  else src_long4_read(libi,&f_size);

  src_int4_read(libi,&nlib);

  if (mm64_flag) {
    src_long8_read(libi,&tot_len);
    src_long8_read(libi,&max_len);
  }
  else {
    src_long4_read(libi,&tot_len);
    src_long4_read(libi,&max_len);
  }

  printf(" %d entries; tot: %ld; max: %ld\n",nlib,tot_len,max_len);

  /* allocate array of description pointers */
  if ((d_pos_arr=(long *)calloc(nlib+1, sizeof(long)))==NULL) {
    fprintf(stderr," cannot allocate %d for desc. array\n",nlib+1);
    exit(1);
  }
  /* allocate array of sequence pointers */
  if ((s_pos_arr=(long *)calloc(nlib+1, sizeof(long)))==NULL) {
    fprintf(stderr," cannot allocate %d for seq. array\n",nlib+1);
    exit(1);
  }
  if ((attr_arr=(char *)calloc(nlib+1, sizeof(char)))==NULL) {
    fprintf(stderr," cannot allocate %d for attr. array\n",nlib+1);
    exit(1);
  }
  
  if (mm64_flag) {
    for (i=0; i<=nlib; i++) src_long8_read(libi,&d_pos_arr[i]);
    for (i=0; i<=nlib; i++) src_long8_read(libi,&s_pos_arr[i]);
  }
  else {
    for (i=0; i<=nlib; i++) src_long4_read(libi,&d_pos_arr[i]);
    for (i=0; i<=nlib; i++) src_long4_read(libi,&s_pos_arr[i]);
  }

  fread(attr_arr,nlib+1,sizeof(char),libi);
  fclose(libi);

  printf("header\tseq\n");

  for (i=0; i<nlib; i++) printf("%ld\t%ld\n",d_pos_arr[i],s_pos_arr[i]);
}

void src_int4_read(FILE *fd,  int *val)
{
  int tval;
#ifdef IS_BIG_ENDIAN
  fread(&tval,(size_t)4,(size_t)1,fd);
  *val = tval;
#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_long4_read(FILE *fd,  long *val)
{
  int tval;
#ifdef IS_BIG_ENDIAN
  fread(&tval,(size_t)4,(size_t)1,fd);
  *val = tval;
#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_long8_read(FILE *fd,  long *val)
{
#ifdef IS_BIG_ENDIAN
  fread((char *)val,(size_t)8,(size_t)1,fd);
#else
  unsigned char b[8];

  fread((char *)&b[0],(size_t)1,(size_t)8,fd);
  *val = 0;
  *val = (int)
    ((((((((int)b[0]<<8)+(int)b[1]<<8)+(int)b[2]<<8)+(int)b[3]<<8)+
		(int)b[4]<<8)+(int)b[5]<<8)+(int)b[6]<<8)+(int)b[7];
#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
newname(char *nname, char *oname, char *suff, int maxn)
{
  strncpy(nname,oname,maxn-1);
  strncat(nname,".",1);
  strncat(nname,suff,maxn-strlen(nname));
}