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agp_to_fasta.c
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agp_to_fasta.c
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/*********************************************************************************
* MIT License *
* *
* Copyright (c) 2021 Chenxi Zhou <[email protected]> *
* *
* Permission is hereby granted, free of charge, to any person obtaining a copy *
* of this software and associated documentation files (the "Software"), to deal *
* in the Software without restriction, including without limitation the rights *
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell *
* copies of the Software, and to permit persons to whom the Software is *
* furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE *
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER *
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, *
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE *
* SOFTWARE. *
*********************************************************************************/
/********************************** Revision History *****************************
* *
* 22/06/21 - Chenxi Zhou: Created *
* *
*********************************************************************************/
#include <stdlib.h>
#include <stdio.h>
#include "ketopt.h"
#include "sdict.h"
static void print_help(FILE *fp_help)
{
fprintf(fp_help, "Usage: agp_to_fasta [options] <scaffolds.agp> <contigs.fa>\n");
fprintf(fp_help, "Options:\n");
fprintf(fp_help, " -l INT line width [60]\n");
fprintf(fp_help, " -o STR output to file [stdout]\n");
}
static ko_longopt_t long_options[] = {
{ "help", ko_no_argument, 'h' },
{ 0, 0, 0 }
};
int main(int argc, char *argv[])
{
if (argc < 2) {
print_help(stderr);
return 1;
}
FILE *fo;
char *fa, *agp, *out;
int line_wd;
const char *opt_str = "o:l:h";
ketopt_t opt = KETOPT_INIT;
int c;
FILE *fp_help = stderr;
fa = agp = out = 0;
line_wd = 60;
while ((c = ketopt(&opt, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 'l') {
line_wd = atoi(opt.arg);
} else if (c == 'o') {
out = opt.arg;
} else if (c == 'h') {
fp_help = stdout;
}else if (c == '?') {
fprintf(stderr, "[E::%s] unknown option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
} else if (c == ':') {
fprintf(stderr, "[E::%s] missing option: \"%s\"\n", __func__, argv[opt.i - 1]);
return 1;
}
}
if (fp_help == stdout) {
print_help(stdout);
return 0;
}
if (argc - opt.ind < 2) {
fprintf(stderr, "[E::%s] missing input: three positional options required\n", __func__);
print_help(stderr);
return 1;
}
agp = argv[opt.ind];
fa = argv[opt.ind + 1];
fo = out == 0? stdout : fopen(out, "w");
if (fo == 0) {
fprintf(stderr, "[E::%s] cannot open fail %s for writing\n", __func__, out);
exit(EXIT_FAILURE);
}
write_fasta_file_from_agp(fa, agp, fo, line_wd);
if (out != 0)
fclose(fo);
return 0;
}