Refs refs;
ofstream fout;
-char refF[STRLEN], alignerFastaF[STRLEN];
+char refF[STRLEN], alignerFastaF[STRLEN], transF[STRLEN];
int polyAChoice, polyALen;
char exceptionF[STRLEN];
// always generate references for aligners, default convert all N into G
int main(int argc, char* argv[]) {
- if (argc < 4) {
- printf("USAGE : rsem-preref refFastaF polyAChoice refName [-l polyALen] [-f exceptionF] [--no-ntog] [-q]\n\n");
- printf(" refFastaF: a FASTA format file contains all reference transcripts\n");
- printf(" polyAChoice: choice for polyA tail padding.It is a number from {0,1,2}\n");
- printf(" 0: pad polyA tail\n");
- printf(" 1: do not pad polyA tail at all\n");
- printf(" 2: pad polyA tail for all references but those in exceptionF\n");
- printf(" -l: polyALen: specify the length of polyA tail you want to pad. Default is 100\n");
- printf(" -f: exceptionF: file contains a list of exception reference ids. IDs starts from 1. Must set if polyAChoice = 2\n");
- printf(" --no-ntog: do not convert N in references into G\n");
- printf(" -q: quiet\n");
- exit(-1);
- }
-
-
- polyAChoice = atoi(argv[2]);
-
- polyALen = 125;
- ntog = true;
- quiet = false;
- memset(exceptionF, 0, sizeof(exceptionF));
-
- for (int i = 4; i < argc; i++) {
- if (!strcmp(argv[i], "-l")) { polyALen = atoi(argv[i + 1]); }
- if (!strcmp(argv[i], "-f")) { strcpy(exceptionF, argv[i + 1]); }
- if (!strcmp(argv[i], "--no-ntog")) { ntog = false; }
- if (!strcmp(argv[i], "-q")) { quiet = true; }
- }
-
- verbose = !quiet;
-
- //make references
- rules = PolyARules(polyAChoice, polyALen, exceptionF);
- refs.makeRefs(argv[1], refp, rules);
- M = refs.getM();
-
- //save references
- sprintf(refF, "%s.seq", argv[3]);
- refs.saveRefs(refF);
-
- sprintf(alignerFastaF, "%s.idx.fa", argv[3]);
- fout.open(alignerFastaF);
- for (int i = 1; i <= M; i++) {
- fout<<">"<<refs.getRef(i).getName()<<endl<<(ntog ? aligner_refp.convert(refs.getRef(i).getSeq()) : refs.getRef(i).getSeq())<<endl;
- }
- fout.close();
-
- if (verbose) { printf("IDX.fa generated!\n"); }
-
- return 0;
+ if (argc < 4) {
+ printf("USAGE : rsem-preref refFastaF polyAChoice refName [-l polyALen] [-f exceptionF] [--no-ntog] [-q]\n\n");
+ printf(" refFastaF: a FASTA format file contains all reference transcripts\n");
+ printf(" polyAChoice: choice for polyA tail padding.It is a number from {0,1,2}\n");
+ printf(" 0: pad polyA tail\n");
+ printf(" 1: do not pad polyA tail at all\n");
+ printf(" 2: pad polyA tail for all references but those in exceptionF\n");
+ printf(" -l: polyALen: specify the length of polyA tail you want to pad. Default is 100\n");
+ printf(" -f: exceptionF: file contains a list of exception reference ids. IDs starts from 1. Must set if polyAChoice = 2\n");
+ printf(" --no-ntog: do not convert N in references into G\n");
+ printf(" -q: quiet\n");
+ printf(" This program will generate a file named \"refName.transcripts.fa\", which may rewrite an existing file (e.g. refFastaF).\n");
+ exit(-1);
+ }
+
+ polyAChoice = atoi(argv[2]);
+
+ polyALen = 125;
+ ntog = true;
+ quiet = false;
+ memset(exceptionF, 0, sizeof(exceptionF));
+
+ for (int i = 4; i < argc; i++) {
+ if (!strcmp(argv[i], "-l")) { polyALen = atoi(argv[i + 1]); }
+ if (!strcmp(argv[i], "-f")) { strcpy(exceptionF, argv[i + 1]); }
+ if (!strcmp(argv[i], "--no-ntog")) { ntog = false; }
+ if (!strcmp(argv[i], "-q")) { quiet = true; }
+ }
+
+ verbose = !quiet;
+
+ //make references
+ rules = PolyARules(polyAChoice, polyALen, exceptionF);
+ refs.makeRefs(argv[1], refp, rules);
+ M = refs.getM();
+
+ //save references
+ sprintf(refF, "%s.seq", argv[3]);
+ refs.saveRefs(refF);
+
+ sprintf(transF, "%s.transcripts.fa", argv[3]);
+ fout.open(transF);
+ for (int i = 1; i <= M; i++) {
+ fout<< ">"<< refs.getRef(i).getName()<< endl<< refs.getRef(i).getSeq()<< endl;
+ }
+ fout.close();
+ if (verbose) printf("%s is generated!\n", transF);
+
+ sprintf(alignerFastaF, "%s.idx.fa", argv[3]);
+ fout.open(alignerFastaF);
+ for (int i = 1; i <= M; i++) {
+ fout<<">"<<refs.getRef(i).getName()<<endl<<(ntog ? aligner_refp.convert(refs.getRef(i).getSeq()) : refs.getRef(i).getSeq())<<endl;
+ }
+ fout.close();
+ if (verbose) printf("%s is generated!\n", alignerFastaF);
+
+ return 0;
}