int main(int argc, const char *argv[])
{
int num,ret;
seq_plist l;
seqlist_init(&l);
while(1)
{
printf("pls input num:");
ret = scanf("%d",&num);
if(1 == ret)
{
if(num > 0)
seqlist_insert(l,num);
#if 1
else
seqlist_del(l,-num);
#endif
}else
break;
seqlist_show(l);
}
return 0;
}
int main(int argc, char **argv){
FILE *IN, *OUT;
seqlist_t IDs;
sequence_t *seq;
int i, keep, excl;
char *prog, *list, *f, *out, *id;
/* todo convert to uint_64 */
uint64_t n, total;
/* default values */
prog = basename(*argv);
list = NULL;
out = NULL;
OUT = stdout;
excl = keep = 0;
/* Check command line */
while ((i = getopt(argc, argv, "hl:o:x")) != -1) {
switch (i) {
case 'h':
usage(prog, EXIT_SUCCESS); break;
case 'l':
list = optarg; break;
case 'o':
out = optarg; break;
case 'x':
excl = 1; break;
default:
usage(prog, EXIT_FAILURE);
}
}
/* some files to deal with ? */
if (argc - optind < 1) { usage(prog, EXIT_FAILURE); }
/* get ids from list */
if (list != NULL) {
if ((IN = fopen(list, "r")) == NULL)
err(EXIT_FAILURE, "%s", list);
seqlist_init(&IDs);
i = seqlist_populate(&IDs, IN);
if (i == 0) errx(EXIT_FAILURE, "file: %s no identifier found", list);
if (fclose(IN) == EOF) err(EXIT_FAILURE, "%s: close failed", list);
seqlist_sort(&IDs);
}
/* open output file */
if ((out != NULL) && ((OUT = fopen(out, "w")) == NULL))
err(EXIT_FAILURE, "%s", out);
total = n = 0;
/* start filtering all argument file*/
for (i = optind; i < argc; i++) {
f = *(argv+i);
if ((IN = fopen(f, "r")) == NULL) err(EXIT_FAILURE, "%s", f);
while ((seq = sequence_parse(IN, SEQFMT_FASTA)) != NULL) {
total++;
id = seq->nam;
keep = 1;
if (list != NULL) { keep = 1 - seqlist_chk(&IDs, id); }
if (excl == 1) { keep = 1 - keep; }
if (keep == 1) { n++; sequence_print(OUT, seq, SEQFMT_FASTA); }
sequence_free(seq);
}//end while
/* check for parsing error vs EOF */
if ((feof(IN) == 0) || (total == 0)){
errx(1, "%s: unable to read sequence %d", f, total+1);
}
if (fclose(IN) == EOF) err(EXIT_FAILURE, "%s: close failed", f);
}//end for files
if ((out != NULL) && (fclose(OUT) == EOF)) err(EXIT_FAILURE, "%s", out);
if (list != NULL) seqlist_fini(&IDs);
/*display resume on stderr */
fprintf(stderr, "file %s: Extracted %"PRI_U64" from %"PRI_U64" sequences (%.2f %%)\n" ,
basename(f), n , total, (float)(n)/total*100.0);
return EXIT_SUCCESS;
}
