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retroSeekerMain.cpp
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retroSeekerMain.cpp
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/******************************************************************************
* retroSeeker: A computational software for seeking *
* the Retrotransposon/Retroelements in the net File *
* Author: Jianhua Yang *
* Email: [email protected] *
* Copyright: School of Life Sciences, Sun Yat-sen University *
* Create Date: 2023/03/18 *
*****************************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <assert.h>
#include <math.h>
#include <stdint.h>
#include <getopt.h>
#include <map>
#include <algorithm>
#include <ios>
#include <iostream>
#include <string>
#include <ostream>
#include <fstream>
#include <iomanip>
#include <locale>
#include <sstream>
#include <vector>
using namespace std;
#include "bioUtils.h"
#include "faiFile.h"
#include "bedFile.h"
#include "retroSeeker.h"
void usage(void);
char version[] = "retroSeeker version 2 [2023/6/16]\n";
int main(int argc, char **argv) {
int i = 0;
int c = 0;
char *genomeFile = NULL;
FILE *genomefp = NULL;
char *faiFile = NULL;
FILE *faifp = NULL;
char *netFile = NULL;
FILE *netfp = NULL;
char *bedFile = NULL;
FILE *bedfp = NULL;
FILE *outfp = NULL;
FILE *outfp2 = NULL;
char *outfile = NULL;
char *outfile2 = NULL;
int showVersion = 0;
int showHelp = 0;
parameter paraInfo;
if (argc == 1) {
usage();
}
const char *shortOptions = "vhVSoO:i:a:m:f:F:l:n:M:L:s:b:e:x:y:z:w:P:g:";
const struct option longOptions[] = {
{"verbose", no_argument, NULL, 'v'},
{"help", no_argument, NULL, 'h'},
{"version", no_argument, NULL, 'V'},
{"self", no_argument, NULL, 'S'},
{"output", required_argument, NULL, 'o'},
{"output2", required_argument, NULL, 'O'},
{"fa", required_argument, NULL, 'f'},
{"fai", required_argument, NULL, 'F'},
{"net", required_argument, NULL, 'n'},
{"bed", required_argument, NULL, 'b'},
{"extend", required_argument, NULL, 'e'},
{"RNA5endUp", required_argument, NULL, 'x'},
{"RNA5endDown", required_argument, NULL, 'y'},
{"RNA3endUp", required_argument, NULL, 'z'},
{"RNA3endDown", required_argument, NULL, 'w'},
{"minMatchLen", required_argument, NULL, 'm'},
{"minPolyaLen", required_argument, NULL, 'M'},
{"maxPolyaLen", required_argument, NULL, 'P'},
{"minGenebodyLen", required_argument, NULL, 'g'},
{"minLen", required_argument, NULL, 'l'},
{"maxLen", required_argument, NULL, 'L'},
{"score", required_argument, NULL, 's'},
{NULL, 0, NULL, 0 }, /* Required at end of array. */
};
paraInfo.verbose = 0;
paraInfo.extend = 30;
paraInfo.RNA5endUp = 30;
paraInfo.RNA5endDown = 30;
paraInfo.RNA3endUp = 30;
paraInfo.RNA3endDown = 30;
paraInfo.minMatchLen = 5;/*min-tsd*/
paraInfo.minPolyaLen = 5;
paraInfo.maxPolyaLen = 50;
paraInfo.minGenebodyLen = 20;
paraInfo.minLen = 50;
paraInfo.maxLen = 100000;
paraInfo.netType = 0;
paraInfo.minScore = 10;
paraInfo.bedExist = 0;
paraInfo.netExist = 0;
while ((c = getopt_long(argc, argv, shortOptions, longOptions, NULL)) >= 0) {
switch (c) {
case 'v':
paraInfo.verbose = 1;
break;
case 'h':
showHelp = 1;
break;
case 'V':
showVersion = 1;
break;
case 'S':
paraInfo.netType = 1;
break;
case 'o':
outfile = optarg;
break;
case 'O':
outfile2 = optarg;
break;
case 'f':
genomeFile = optarg;
break;
case 'F':
faiFile = optarg;
break;
case 'n':
netFile = optarg;
paraInfo.netExist = 1;
break;
case 'b':
bedFile = optarg;
paraInfo.bedExist = 1;
break;
case 'e':
paraInfo.extend = atoi(optarg);
break;
case 'x':
paraInfo.RNA5endUp = atoi(optarg);
break;
case 'y':
paraInfo.RNA5endDown = atoi(optarg);
break;
case 'z':
paraInfo.RNA3endUp = atoi(optarg);
break;
case 'w':
paraInfo.RNA3endDown = atoi(optarg);
break;
case 'm':
paraInfo.minMatchLen = atoi(optarg);
break;
case 'M':
paraInfo.minPolyaLen = atoi(optarg);
break;
case 'P':
paraInfo.maxPolyaLen = atoi(optarg);
break;
case 'g':
paraInfo.minGenebodyLen = atoi(optarg);
break;
case 'l':
paraInfo.minLen = atoi(optarg);
break;
case 'L':
paraInfo.maxLen = atoi(optarg);
break;
case 's':
paraInfo.minScore = atoi(optarg);
break;
case '?':
showHelp = 1;
break;
default:
usage();
}
}
if (showHelp) {
usage();
exit(1);
}
if (showVersion) {
fprintf(stderr, "%s", version);
exit(1);
}
if (genomeFile == NULL) {
fprintf(stderr, "Please set the --fa option\n");
exit(1);
}
genomefp = (FILE *)fopen(genomeFile, "r");
if (genomefp == NULL) {
fprintf(stderr, "ERROR: Can't open %s\n", genomeFile);
fprintf(stderr, "Please set the --fa option\n");
exit(1);
}
if (faiFile == NULL) {
fprintf(stderr, "Please set the --fai option\n");
exit(1);
}
faifp = (FILE *)fopen(faiFile, "r");
if (faifp == NULL) {
fprintf(stderr, "ERROR: Can't open %s\n", faiFile);
fprintf(stderr, "Please set the --fai option\n");
exit(1);
}
if (bedFile != NULL){
fprintf(stderr, "#Scan bed file...\n");
bedfp = (FILE *)fopen(bedFile, "r");
}
if (netFile != NULL){
fprintf(stderr, "#Scan net file...\n");
netfp = (FILE *)fopen(netFile, "r");
}
if (netFile == NULL && bedFile == NULL) {
fprintf(stderr, "ERROR: Can't open %s and %s\n", netFile, bedFile);
fprintf(stderr, "Please set the --net or --bed option\n");
exit(1);
}
if (outfile == NULL) {
outfp = stdout;
}
else {
outfp = (FILE *)fopen(outfile, "w");
if (outfp == NULL) {
fprintf(stderr, "ERROR: Can't open the output file %s\n", outfile);
usage();
}
}
if (outfile2 == NULL) {
outfp2 = stdout;
}
else {
outfp2 = (FILE *)fopen(outfile2, "w");
if (outfp2 == NULL) {
fprintf(stderr, "ERROR: Can't open the output file2 %s\n", outfile2);
usage();
}
}
searchRetroGeneInNetFile(¶Info, genomefp, faifp, netfp, outfp, bedfp, outfp2);
fflush(outfp);
fflush(outfp2);
fclose(genomefp);
fclose(faifp);
if (netFile != NULL){
fclose(netfp);
}
if (bedfp != NULL){
fclose(bedfp);
}
return 0;
}
void usage(void) {
fprintf(
stderr, "%s",
"Usage: retroSeeker [options] --fa <fasta file> --fai <fai file> --net <net file> --bed [bed file]\n\
[options]\n\
-f/--fa <file> : genome file, fasta format [Required]\n\
-F/--fai <file> : fai file of genome, you can use samtools faidx to generate [Required]\n\
-n/--net <file> : Net file, Net Format [Required]\n\
-b/--bed [file] : bed file, bed Format, scan the bed content instead of the net file [option]\n\
-o/--output <file> : main retroSeeker output file\n\
-O/--output2 <file> : output the gap and fill region (used to identified the retrogene) in the net file [option]\n\
-v/--verbose : verbose information\n\
-V/--version : retroSeeker version\n\
-h/--help : help informations\n\
-S/--self : self-chain net type. default is different normal-chain net\n\
-x/--RNA5endUp : extend length of upStream of 5'-end of the RNA direction to search tsd [default=30]\n\
-y/--RNA5endDown : extend length of dpStream of 3'-end of the RNA direction to search tsd [default=30]\n\
-z/--RNA3endUp : extend length of upStream of 5'-end of the RNA direction to search tsd [default=30]\n\
-w/--RNA3endDown : extend length of dpStream of 3'-end of the RNA direction to search tsd [default=30]\n\
-m/--minMatchLen : minimum TSD length [default>=5]\n\
-M/--minPolyaLen : minimum polya length [default>=5]\n\
-P/--maxPolyaLen : maximum polya length [default<=50]\n\
-g/--minGenebodyLen : minimum genebody length [default>=20]\n\
-l/--minLen : minimum length for retrogene [default>=50]\n\
-L/--maxLen : maximum length for retrogene [default<=100000]\n\
-s/--score : minimum score for retrogene [default>=10]\n\
");
exit(1);
}