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Up to 2x faster prodigal #95

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58d5f24
1)Add parameter x. 2)Remove what appears to be an error.
jaebeom-kim Aug 23, 2022
74514ca
Rapid mode
jaebeom-kim Aug 23, 2022
0920435
edit usage
jaebeom-kim Aug 23, 2022
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15 changes: 11 additions & 4 deletions dprog.c
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
coding, RBS scores, etc.
*******************************************************************************/

int dprog(struct _node *nod, int nn, struct _training *tinf, int flag) {
int dprog(struct _node *nod, int nn, struct _training *tinf, int flag, int max_node_dist, int rapid) {
int i, j, min, max_ndx = -1, path, nxt, tmp;
double max_sc = -1.0;

Expand All @@ -42,15 +42,22 @@ int dprog(struct _node *nod, int nn, struct _training *tinf, int flag) {

/* Set up distance constraints for making connections, */
/* but make exceptions for giant ORFS. */
if(i < MAX_NODE_DIST) min = 0; else min = i-MAX_NODE_DIST;
if(i < max_node_dist) min = 0; else min = i-max_node_dist;
if(nod[i].strand == -1 && nod[i].type != STOP && nod[min].ndx >=
nod[i].stop_val)
while(min >= 0 && nod[i].ndx != nod[i].stop_val) min--;
if(nod[i].strand == 1 && nod[i].type == STOP && nod[min].ndx >=
nod[i].stop_val)
while(min >= 0 && nod[i].ndx != nod[i].stop_val) min--;
if(min < MAX_NODE_DIST) min = 0;
else min = min-MAX_NODE_DIST;

/* Rapid mode is 50% faster producing the same result, */
/* when tested with E. coli genome (GCF_000008865.2). */
if(rapid){
if(min < 0) min = 0;
} else {
if(min < max_node_dist) min = 0; else min = min-max_node_dist;
}

for(j = min; j < i; j++) {
score_connection(nod, j, i, tinf, flag);
}
Expand Down
4 changes: 2 additions & 2 deletions dprog.h
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Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@

#define MAX_SAM_OVLP 60
#define MAX_OPP_OVLP 200
#define MAX_NODE_DIST 500
// #define MAX_NODE_DIST 500

int dprog(struct _node *, int, struct _training *, int);
int dprog(struct _node *, int, struct _training *, int, int, int);
void score_connection(struct _node *, int, int, struct _training *, int);
void eliminate_bad_genes(struct _node *, int, struct _training *);

Expand Down
32 changes: 22 additions & 10 deletions main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ int copy_standard_input_to_file(char *, int);
int main(int argc, char *argv[]) {

int rv, slen, nn, ng, i, ipath, *gc_frame, do_training, output, max_phase;
int closed, do_mask, nmask, force_nonsd, user_tt, is_meta, num_seq, quiet;
int closed, do_mask, nmask, force_nonsd, user_tt, is_meta, num_seq, quiet, max_node_dist, rapid;
int piped, max_slen, fnum;
double max_score, gc, low, high;
unsigned char *seq, *rseq, *useq;
Expand Down Expand Up @@ -87,7 +87,7 @@ int main(int argc, char *argv[]) {
memset(meta[i].tinf, 0, sizeof(struct _training));
}
nn = 0; slen = 0; ipath = 0; ng = 0; nmask = 0;
user_tt = 0; is_meta = 0; num_seq = 0; quiet = 0;
user_tt = 0; is_meta = 0; num_seq = 0; quiet = 0; max_node_dist = 500; rapid = 0;
max_phase = 0; max_score = -100.0;
train_file = NULL; do_training = 0;
start_file = NULL; trans_file = NULL; nuc_file = NULL;
Expand All @@ -113,15 +113,17 @@ int main(int argc, char *argv[]) {

/* Parse the command line arguments */
for(i = 1; i < argc; i++) {
if(i == argc-1 && (strcmp(argv[i], "-t") == 0 || strcmp(argv[i], "-T") == 0
|| strcmp(argv[i], "-a") == 0 || strcmp(argv[i], "-A") == 0 ||
if(i == argc-1 &&
(strcmp(argv[i], "-t") == 0 || strcmp(argv[i], "-T") == 0 ||
strcmp(argv[i], "-a") == 0 || strcmp(argv[i], "-A") == 0 ||
strcmp(argv[i], "-g") == 0 || strcmp(argv[i], "-g") == 0 ||
strcmp(argv[i], "-f") == 0 || strcmp(argv[i], "-F") == 0 ||
strcmp(argv[i], "-s") == 0 || strcmp(argv[i], "-S") == 0 ||
strcmp(argv[i], "-i") == 0 || strcmp(argv[i], "-I") == 0 ||
strcmp(argv[i], "-o") == 0 || strcmp(argv[i], "-O") == 0 ||
strcmp(argv[i], "-p") == 0 || strcmp(argv[i], "-P") == 0))
usage("-a/-f/-g/-i/-o/-p/-s options require parameters.");
strcmp(argv[i], "-p") == 0 || strcmp(argv[i], "-P") == 0 ||
strcmp(argv[i], "-x") == 0 || strcmp(argv[i], "-X") == 0 ))
usage("-a/-f/-g/-i/-o/-p/-s/-x options require parameters.");
else if(strcmp(argv[i], "-c") == 0 || strcmp(argv[i], "-C") == 0)
closed = 1;
else if(strcmp(argv[i], "-q") == 0 || strcmp(argv[i], "-Q") == 0)
Expand Down Expand Up @@ -189,6 +191,12 @@ int main(int argc, char *argv[]) {
else usage("Invalid output format specified.");
i++;
}
else if(strcmp(argv[i], "-x") == 0 || strcmp(argv[i], "-X") == 0) {
max_node_dist = atoi(argv[i+1]);
i++;
}
else if(strcmp(argv[i], "-r") == 0 || strcmp(argv[i], "-R") == 0)
rapid = 1;
else usage("Unknown option.");
}

Expand Down Expand Up @@ -382,7 +390,7 @@ int main(int argc, char *argv[]) {
fprintf(stderr, "Building initial set of genes to train from...");
}
record_overlapping_starts(nodes, nn, &tinf, 0);
ipath = dprog(nodes, nn, &tinf, 0);
ipath = dprog(nodes, nn, &tinf, 0, max_node_dist, rapid);
if(quiet == 0) {
fprintf(stderr, "done!\n");
}
Expand Down Expand Up @@ -514,7 +522,7 @@ int main(int argc, char *argv[]) {
write_start_file(start_ptr, nodes, nn, &tinf, num_seq, slen, 0, NULL,
VERSION, cur_header);
record_overlapping_starts(nodes, nn, &tinf, 1);
ipath = dprog(nodes, nn, &tinf, 1);
ipath = dprog(nodes, nn, &tinf, 1, max_node_dist, rapid);
eliminate_bad_genes(nodes, ipath, &tinf);
ng = add_genes(genes, nodes, ipath);
tweak_final_starts(genes, ng, nodes, nn, &tinf);
Expand Down Expand Up @@ -555,7 +563,7 @@ int main(int argc, char *argv[]) {
reset_node_scores(nodes, nn);
score_nodes(seq, rseq, slen, nodes, nn, meta[i].tinf, closed, is_meta);
record_overlapping_starts(nodes, nn, meta[i].tinf, 1);
ipath = dprog(nodes, nn, meta[i].tinf, 1);
ipath = dprog(nodes, nn, meta[i].tinf, 1, max_node_dist, rapid);
if(nodes[ipath].score > max_score) {
max_phase = i;
max_score = nodes[ipath].score;
Expand Down Expand Up @@ -645,7 +653,7 @@ void usage(char *msg) {
fprintf(stderr, " [-g tr_table] [-h] [-i input_file] [-m]");
fprintf(stderr, " [-n] [-o output_file]\n");
fprintf(stderr, " [-p mode] [-q] [-s start_file]");
fprintf(stderr, " [-t training_file] [-v]\n");
fprintf(stderr, " [-t training_file] [-x] [-r] [-v]\n");
fprintf(stderr, "\nDo 'prodigal -h' for more information.\n\n");
exit(15);
}
Expand Down Expand Up @@ -684,6 +692,10 @@ void help() {
fprintf(stderr, " -t: Write a training file (if none exists); ");
fprintf(stderr, "otherwise, read and use\n");
fprintf(stderr, " the specified training file.\n");
fprintf(stderr, " -x: Specify the number of neighbor nodes to score connection.");
fprintf(stderr, " Default is 500.\n");
fprintf(stderr, " -r: Rapid mode. When tested with the E. coli genome, ");
fprintf(stderr, "the same result was obtained in 2/3 of the original time.");
fprintf(stderr, " -v: Print version number and exit.\n\n");
exit(0);
}
Expand Down