int Argument_main(Argument *arg) {
register FastaDB *fdb;
register ArgumentSet *as
= ArgumentSet_create("Sequence Input Options");
gchar *query_path;
FastaComposition_Data fcd = {{0},FALSE, FALSE};
ArgumentSet_add_option(as, 'f', "fasta", "path",
"Fasta input file", NULL,
Argument_parse_string, &query_path);
ArgumentSet_add_option(as, 'i', "ignorecase", NULL,
"Ignore sequence case", "FALSE",
Argument_parse_boolean, &fcd.ignore_case);
ArgumentSet_add_option(as, 's', "separate", NULL,
"Report composition for each sequence separately", "FALSE",
Argument_parse_boolean, &fcd.report_separately);
Argument_absorb_ArgumentSet(arg, as);
Argument_process(arg, "fastacomposition",
"A utility to report sequence composition\n"
"Guy St.C. Slater. [email protected]. 2000-2003.\n", NULL);
fdb = FastaDB_open(query_path, NULL);
FastaDB_traverse(fdb, FastaDB_Mask_ID|FastaDB_Mask_SEQ,
fasta_composition_traverse_func, &fcd);
if(!fcd.report_separately)
fasta_composition_report(query_path, fcd.count, fcd.ignore_case);
FastaDB_close(fdb);
return 0;
}
int Argument_main(Argument *arg){
register FastaDB *fdb;
register ArgumentSet *as
= ArgumentSet_create("Sequence Input Options");
gchar *query_path;
gchar clip_char;
ArgumentSet_add_option(as, 'f', "fasta", "path",
"Fasta input file", NULL,
Argument_parse_string, &query_path);
ArgumentSet_add_option(as, 'c', "clip", "path",
"Clip character", "N",
Argument_parse_char, &clip_char);
Argument_absorb_ArgumentSet(arg, as);
Argument_process(arg, "fastaclip",
"A utility clip terminal Ns from fasta format sequences\n"
"Guy St.C. Slater. [email protected]. 2000-2003.\n", NULL);
fdb = FastaDB_open(query_path, NULL);
FastaDB_traverse(fdb, FastaDB_Mask_ALL,
fasta_clip_traverse_func,
GINT_TO_POINTER((gint)clip_char));
FastaDB_close(fdb);
return 0;
}
