105 lines
2.6 KiB
C
105 lines
2.6 KiB
C
/* genbtitle1 */
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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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#include <ctype.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, titles, accession numbers and lengths
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and writes them to an ascii file
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this file is sorted, then the next
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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 patternTITLE[] = "DEFINITION";
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char patternACCESSION[] = "ACCESSION";
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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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char accession_number[10];
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unsigned long sequence_length;
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char title[80];
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int i;
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int leftChar = 12;
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long entries_in = 0;
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long entries_out = 0;
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printf("genbtitle1 Version 1.1\n");
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if (argc != 3) {
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fprintf(stderr,"Usage: genbtitle1 filein fileout\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,"genbtitle1: 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,"genbtitle1: 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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/* let's output gathered values for last entry*/
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fprintf(ofp,"%-10.10s %-10.10s %10lu %-80.80s\n",
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entry_name,
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accession_number,
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sequence_length,
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title);
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entries_out++;
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}
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/* initialise values */
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entry_name[0] = '\0';
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accession_number[0] = '\0';
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title[0] = '\0';
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sequence_length = 0;
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entries_in++;
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strncpy(entry_name,&line[leftChar],10);
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sequence_length = atol(&line[22]);
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} else if (patmatch(line, patternTITLE) && *title=='\0'){
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for(i=0;isprint(line[leftChar+i]) && i<80;i++) title[i]=line[leftChar+i];
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for(;i<80;i++) title[i] = ' ';
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} else if (patmatch(line, patternACCESSION) && *accession_number=='\0'){
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for(i=0;isalnum(line[leftChar+i]) && i<10;i++) accession_number[i]=line[leftChar+i];
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for(;i<10;i++) accession_number[i] = ' ';
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}
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}
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if (*entry_name) {
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/* let's output gathered values for last entry*/
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fprintf(ofp,"%-10.10s %-10.10s %10lu %-80.80s\n",
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entry_name,
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accession_number,
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sequence_length,
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title);
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entries_out++;
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}
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printf(" Number of entries read = %ld\n",entries_in);
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printf(" Number of entries written = %ld\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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