+++ /dev/null
-/* May, June 1987 - modified for rapid read of database
-
- copyright (c) 1987,1988,1989,1992,1995,2000 William R. Pearson
-
- This is one of three alternative files that can be used to
- read a database. The three files are nxgetaa.c, nmgetaa.c, and
- mmgetaa.c.
-
- nxgetaa.c contains the original code for reading databases, and
- is still used for Mac and PC versions of fasta33 (which do not
- use mmap).
-
- nmgetaa.c and mmgetaa.c are used together. nmgetaa.c provides
- the same functions as nxgetaa.c if memory mapping is not used,
- mmgetaa.c provides the database reading functions if memory
- mapping is used. The decision to use memory mapping is made on
- a file-by-file basis.
-
- June 2, 1987 - added TFASTA
- March 30, 1988 - combined ffgetaa, fgetgb;
- April 8, 1988 - added PIRLIB format for unix
- Feb 4, 1989 - added universal subroutines for libraries
- December, 1995 - added range option file.name:1-1000
- Feb 22, 2002 - fix to allow "plain" text file queries
-
- getnt.c associated subroutines for matching sequences */
-
-/* $Name: fa_34_26_5 $ - $Id: getseq.c,v 1.13 2006/10/05 18:22:07 wrp Exp $ */
-
-/*
- 8-April-88
- The compile time #define PIRLIB allows this routine to be used
- to read protein and DNA sequence libraries in the NBRF/PIR
- VAX/VMS library format. That is:
-
- >P1;LCBO
- This is a line of description
- GTYH ... the sequence starts on this line
-
- This may ease conversion from UWGCG format libraries. It
- has not been extensively tested.
-
- In addition, sequence libraries with a '>' in the 4th position
- are recognized as NBRF format libraries for consistency with
- UWGCG
-*/
-
-/* Nov 12, 1987 - this version checks to see if the sequence
- is DNA or protein by asking whether > 85% is A, C, G, T
-
- May 5, 1988 - modify the DNA/PROTEIN checker by re-reading
- DNA sequences in order to check for 'U'.
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "defs.h"
-#include "structs.h"
-
-#ifndef SFCHAR
-#define SFCHAR ':'
-#endif
-
-#ifdef VMS
-#define PIRLIB
-#endif
-
-#define XTERNAL
-#include "uascii.h"
-#include "upam.h"
-#undef XTERNAL
-
-#define YES 1
-#define NO 0
-#define MAXLINE 512
-
-#ifndef min
-#define min(x,y) ((x) > (y) ? (y) : (x))
-#endif
-
-#ifdef SUPERFAMNUM
-extern int nsfnum; /* number of superfamily numbers */
-extern int sfnum[]; /* superfamily number from types 0 and 5 */
-extern int nsfnum_n;
-extern int sfnum_n[];
-#endif
-
-#define NO_FORMAT 0
-#define FASTA_FORMAT 1
-#define GCG_FORMAT 2
-
-static int seq_format=NO_FORMAT;
-static char seq_title[200];
-
-int scanseq(unsigned char *, int, char *);
-void sf_sort(int *, int);
-extern void init_ascii(int is_ext, int *sascii, int is_dna);
-
-/* getseq - get a query sequence, possibly re-reading to set type
- returns - length of query sequence or error = 0
-
- char *filen - name of file to be opened
- char *seq - destination for query sequence
- int maxs - maximum length of query
- char libstr[20] - short description (locus or acc)
- int *dnaseq - -1 => use scanseq to determine sequence type
- 0 => must be protein
- 1 => must be DNA
- long *sq0off - offset into query specified by query_file:1001-2000
-*/
-
-int
-getseq(char *filen, int *qascii, unsigned char *seq, int maxs, char *libstr, long *sq0off)
-{
- FILE *fptr;
- char line[512],*bp, *bp1, *bpn, *tp;
- int i, rn, n;
- int ic;
- int sstart, sstop, sset=0;
- int llen, l_offset;
-#ifdef SUPERFAMNUM
- static char tline[MAXLINE];
-#endif
-
- seq_title[0]='\0';
- libstr[0]='\0';
-
- sstart = sstop = -1;
-#ifndef DOS
- if ((bp=strchr(filen,':'))!=NULL && *(bp+1)!='\0') {
-#else
- if ((bp=strchr(filen+3,':'))!=NULL && *(bp+1)!='\0') {
-#endif
- *bp='\0';
- if (*(bp+1)=='-') {
- sstart = 0;
- sscanf(bp+2,"%d",&sstop);
- }
- else {
- sscanf(bp+1,"%d-%d",&sstart,&sstop);
- sstart--;
- if (sstop <= 0 ) sstop = BIGNUM;
- }
- sset=1;
- }
- else {
- sstart = 0;
- sstop = BIGNUM;
- }
-
- /* check for input from stdin */
- if (strcmp(filen,"-") && strcmp(filen,"@")) {
- if ((fptr=fopen(filen,"r"))==NULL) {
- fprintf(stderr," could not open %s\n",filen);
- return 0;
- }
- }
- else {
- fptr = stdin;
- }
- rn = n=0;
-
- while(fgets(line,sizeof(line),fptr)!=NULL) {
-#ifdef PIRLIB
- if (line[0]=='>'&& (line[3]==';'||line[3]=='>'))
- fgets(line,sizeof(line),fptr);
- else
-#endif
- l_offset = 0;
- if (line[0]=='>') {
- seq_format = FASTA_FORMAT;
-#ifdef SUPERFAMNUM
- sfnum[nsfnum=0]= sfnum_n[nsfnum_n=0]=0;
- strncpy(tline,line+1,sizeof(tline));
- tline[sizeof(tline)-1]='\0';
-
- if ((bp=strchr(tline,' ')) && (bp=strchr(bp+1,SFCHAR))) {
- if ((bp1=strchr(bp+1,SFCHAR))==NULL) {
- fprintf(stderr," second %c missing: %s\n",SFCHAR,tline);
- }
- else {
- if ((bpn=strchr(bp+1,NSFCHAR))!=NULL) *bpn = '\0';
- *bp1 = '\0';
- i = 0;
- if ((tp = strtok(bp+1," \t"))!=NULL) {
- sfnum[i++] = atoi(tp);
- while ((tp = strtok((char *)NULL," \t")) != (char *)NULL) {
- if (isdigit(*tp)) sfnum[i++] = atoi(tp);
- if (i>=9) break;
- }
- }
- sfnum[nsfnum=i]= 0;
- if (nsfnum>1) sf_sort(sfnum,nsfnum);
- else {
- if (nsfnum < 1) fprintf(stderr," found | but no sfnum: %s\n",libstr);
- }
- if (bpn != NULL) {
- tp = strtok(bpn+1," \t");
- sfnum_n[0]=atoi(tp);
- i = 1;
- while ((tp=strtok(NULL," \t"))!=NULL) {
- sfnum_n[i++] = atoi(tp);
- if (i >= 10) {
- fprintf(stderr,
- " error - too many negative superfamilies: %d\n %s\n",
- i,tline);
- break;
- }
- }
- sfnum_n[nsfnum_n=i]=0;
- sf_sort(sfnum_n,nsfnum_n);
- }
- }
- }
- else {
- sfnum[nsfnum = 0] = 0;
- sfnum_n[nsfnum_n = 0] = 0;
- }
-#endif
- if ((bp=(char *)strchr(line,'\n'))!=NULL) *bp='\0';
- strncpy(seq_title,line+1,sizeof(seq_title));
- seq_title[sizeof(seq_title)-1]='\0';
- if ((bp=(char *)strchr(line,' '))!=NULL) *bp='\0';
- strncpy(libstr,line+1,12);
- libstr[12]='\0';
- }
- else if (seq_format==NO_FORMAT && strcmp(line,"..")==0) {
- seq_format = GCG_FORMAT;
-/*
- if (*dnaseq != 1) qascii['*'] = qascii['X'];
-*/
- l_offset = 10;
- llen = strlen(line);
- while (strncmp(&line[llen-3],"..\n",(size_t)3) != 0) {
- if (fgets(line,sizeof(line),fptr)==NULL) return 0;
- llen = strlen(line);
- }
- bp = strtok(line," \t");
-/*
- if ((bp=(char *)strchr(line,' '))!=NULL) *bp='\0';
- else if ((bp=(char *)strchr(line,'\n'))!=NULL) *bp='\0';
-*/
- if (bp!=NULL) strncpy(libstr,bp,12);
- else strncpy(libstr,filen,12);
- libstr[12]='\0';
- if (fgets(line,sizeof(line),fptr)==NULL) return 0;
- }
- else {
- if (libstr[0]=='\0') strncpy(libstr,filen,12);
- libstr[12]='\0';
- }
-
- if (seq_format==GCG_FORMAT && strlen(line)<l_offset) continue;
-
- if (line[0]!='>'&& line[0]!=';') {
- for (i=l_offset; (n<maxs && rn < sstop)&&
- ((ic=qascii[line[i]&AAMASK])<EL); i++)
- if (ic<NA && ++rn > sstart) seq[n++]= ic;
- if (ic == ES || rn > sstop) break;
- }
- }
-
- if (n==maxs) {
- fprintf(stderr," sequence may be truncated %d %d\n",n,maxs);
- fflush(stderr);
- }
- if ((bp=strchr(libstr,'\n'))!=NULL) *bp = '\0';
- if ((bp=strchr(libstr,'\r'))!=NULL) *bp = '\0';
- seq[n]= EOSEQ;
-
-
- if (seq_format !=GCG_FORMAT)
- while(fgets(line,sizeof(line),fptr)!=NULL) {
-#ifdef PIRLIB
- if (line[0]=='>'&& (line[3]==';'||line[3]=='>'))
- fgets(line,sizeof(line),fptr);
- else
-#endif
- if (line[0]!='>'&& line[0]!=';') {
- for (i=0; (n<maxs && rn < sstop)&&
- ((ic=qascii[line[i]&AAMASK])<EL); i++)
- if (ic<NA && ++rn > sstart ) seq[n++]= ic;
- if (ic == ES || rn > sstop) break;
- }
- }
- else {
- llen = strlen(line);
- while (strncmp(&line[llen-3],"..\n",(size_t)3) != 0) {
- if (fgets(line,sizeof(line),fptr)==NULL) return 0;
- llen = strlen(line);
- }
- while (fgets(line,sizeof(line),fptr)!=NULL) {
- if (strlen(line)<l_offset) continue;
- for (i=l_offset; (n<maxs && rn < sstop) &&
- ((ic=qascii[line[i]&AAMASK])<EL); i++)
- if (ic<NA && ++rn > sstart ) seq[n++]= ic;
- if (ic == ES || rn > sstop ) break;
- }
- }
-
- if (n==maxs) {
- fprintf(stderr," sequence may be truncated %d %d\n",n,maxs);
- fflush(stderr);
- }
- seq[n]= EOSEQ;
-
- if (fptr!=stdin) fclose(fptr);
-
- if (sset==1) {
- sstart++;
- filen[strlen(filen)]=':';
- if (*sq0off==1 || sstart>=1) *sq0off = sstart;
- }
-
- return n;
-}
-
-int
-gettitle(char *filen, char *title, int len) {
- FILE *fptr;
- char line[512];
- char *bp;
- int sset;
-#ifdef WIN32
- char *strpbrk();
-#endif
-
- sset = 0;
-
- if (strncmp(filen,"-",1)==0 || strncmp(filen,"@",1)==0) {
- strncpy(title,seq_title,len);
- title[len-1]='\0';
- return (int)strlen(title);
- }
-
- if ((bp=strchr(filen,':'))!=NULL) { *bp='\0'; sset=1;}
-
-
- if ((fptr=fopen(filen,"r"))==NULL) {
- fprintf(stderr," file %s was not found\n",filen);
- fflush(stderr);
- return 0;
- }
-
- if (sset==1) filen[strlen(filen)]=':';
-
- while(fgets(line,sizeof(line),fptr)!=NULL) {
- if (line[0]=='>'|| line[0]==';') goto found;
- }
- fclose(fptr);
- title[0]='\0';
- return 0;
-
- found:
-
-#ifdef PIRLIB
- if (line[0]=='>'&&(line[3]==';'||line[3]=='>')) {
- if ((bp = strchr(line,'\n'))!=NULL) *bp='\0';
- ll=strlen(line); line[ll++]=' '; line[ll]='\0';
- fgets(&line[ll],sizeof(line)-ll,fptr);
- }
-#endif
-
-#ifdef WIN32
- bp = strpbrk(line,"\n\r");
-#else
- bp = strchr(line,'\n');
-#endif
- if (bp!=NULL) *bp = 0;
- strncpy(title,line,len);
- title[len-1]='\0';
- fclose(fptr);
- return strlen(title);
-}
-
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