83 lines
2.0 KiB
C
83 lines
2.0 KiB
C
/* genbentryname1 */
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#define MAXLINE 81 /* maximum input line length*/
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/* program to create index for genbank library in embl cdrom form */
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/* this one gets the entry names and offsets and writes them to an ascii file
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this file is sorted, then the next program converts the sorted file to binary
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and adds the header */
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char patternENTRY[] = "LOCUS";
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char patternSEQUENCE[] = "ORIGIN";
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#define patmatch(L,P) (strncmp((L),(P),strlen(P))==0)
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int main(int argc, char *argv[])
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{
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FILE *ifp;
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FILE *ofp;
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char line[MAXLINE];
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char entry_name[10];
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long entry_offset = 0;
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long sequence_offset = 0;
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long entries_in = 0;
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long entries_out = 0;
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int leftChar = 12;
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printf("genbentryname1 Version 1.0\n");
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if (argc != 4) {
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fprintf(stderr,"Usage: genbentryname1 filein fileout division\n");
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exit(2);
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}
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if ((ifp = fopen(argv[1],"r")) == NULL) {
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fprintf(stderr,"genbentryname1: Cannot open input file %s\n",argv[1]);
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exit(1);
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}
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if ((ofp = fopen(argv[2],"w")) == NULL) {
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fprintf(stderr,"genbentryname1: Cannot open output file %s\n",argv[2]);
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exit(1);
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}
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entry_name[0]='\0';
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while (fgets(line,MAXLINE,ifp)!=NULL){
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if (patmatch(line, patternENTRY)){
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if (*entry_name)
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printf("No sequence for entry %-10.10s\n",entry_name);
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strncpy(entry_name,&line[leftChar],10);
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entry_offset = ftell(ifp) - strlen(line);
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entries_in++;
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} else if (patmatch(line, patternSEQUENCE) && *entry_name) {
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fgets(line, MAXLINE, ifp);
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sequence_offset = ftell(ifp) - strlen(line) + 10;
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/* 10 = magic offset to first character of sequence */
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fprintf(ofp,"%-10.10s %10d %10d %-5.5s\n",entry_name,entry_offset,sequence_offset,argv[3]);
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entries_out++;
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entry_name[0]='\0';
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}
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}
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printf(" Number of entries read = %d\n",entries_in);
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printf(" Number of entries written = %d\n\n",entries_out);
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fclose(ifp);
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fclose(ofp);
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return 0;
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}
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