/*--------------------------------------------------------------------------*/
int main(int argc, char *argv[]){
struct RNAalifold_args_info args_info;
unsigned int input_type;
char ffname[FILENAME_MAX_LENGTH], gfname[FILENAME_MAX_LENGTH], fname[FILENAME_MAX_LENGTH];
char *input_string, *string, *structure, *cstruc, *ParamFile, *ns_bases, *c;
int n_seq, i, length, sym, r, noPS, with_sci;
int endgaps, mis, circular, doAlnPS, doColor, doMEA, n_back, eval_energy, pf, istty;
double min_en, real_en, sfact, MEAgamma, bppmThreshold, betaScale;
char *AS[MAX_NUM_NAMES]; /* aligned sequences */
char *names[MAX_NUM_NAMES]; /* sequence names */
FILE *clust_file = stdin;
pf_paramT *pf_parameters;
model_detailsT md;
fname[0] = ffname[0] = gfname[0] = '\0';
string = structure = cstruc = ParamFile = ns_bases = NULL;
pf_parameters = NULL;
endgaps = mis = pf = circular = doAlnPS = doColor = n_back = eval_energy = oldAliEn = doMEA = ribo = noPS = 0;
do_backtrack = 1;
dangles = 2;
gquad = 0;
sfact = 1.07;
bppmThreshold = 1e-6;
MEAgamma = 1.0;
betaScale = 1.;
with_sci = 0;
set_model_details(&md);
/*
#############################################
# check the command line prameters
#############################################
*/
if(RNAalifold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* temperature */
if(args_info.temp_given) temperature = args_info.temp_arg;
/* structure constraint */
if(args_info.constraint_given) fold_constrained=1;
/* do not take special tetra loop energies into account */
if(args_info.noTetra_given) md.special_hp = tetra_loop=0;
/* set dangle model */
if(args_info.dangles_given){
if((args_info.dangles_arg != 0) && (args_info.dangles_arg != 2))
warn_user("required dangle model not implemented, falling back to default dangles=2");
else
md.dangles = dangles=args_info.dangles_arg;
}
/* do not allow weak pairs */
if(args_info.noLP_given) md.noLP = noLonelyPairs = 1;
/* do not allow wobble pairs (GU) */
if(args_info.noGU_given) md.noGU = noGU = 1;
/* do not allow weak closing pairs (AU,GU) */
if(args_info.noClosingGU_given) md.noGUclosure = no_closingGU = 1;
/* gquadruplex support */
if(args_info.gquad_given) md.gquad = gquad = 1;
/* sci computation */
if(args_info.sci_given) with_sci = 1;
/* do not convert DNA nucleotide "T" to appropriate RNA "U" */
/* set energy model */
if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
/* take another energy parameter set */
if(args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
/* Allow other pairs in addition to the usual AU,GC,and GU pairs */
if(args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
/* set pf scaling factor */
if(args_info.pfScale_given) sfact = args_info.pfScale_arg;
/* assume RNA sequence to be circular */
if(args_info.circ_given) circular=1;
/* do not produce postscript output */
if(args_info.noPS_given) noPS = 1;
/* partition function settings */
if(args_info.partfunc_given){
pf = 1;
if(args_info.partfunc_arg != -1)
do_backtrack = args_info.partfunc_arg;
}
/* MEA (maximum expected accuracy) settings */
if(args_info.MEA_given){
pf = doMEA = 1;
if(args_info.MEA_arg != -1)
MEAgamma = args_info.MEA_arg;
}
if(args_info.betaScale_given) betaScale = args_info.betaScale_arg;
/* set the bppm threshold for the dotplot */
if(args_info.bppmThreshold_given)
bppmThreshold = MIN2(1., MAX2(0.,args_info.bppmThreshold_arg));
/* set cfactor */
if(args_info.cfactor_given) cv_fact = args_info.cfactor_arg;
/* set nfactor */
if(args_info.nfactor_given) nc_fact = args_info.nfactor_arg;
if(args_info.endgaps_given) endgaps = 1;
if(args_info.mis_given) mis = 1;
if(args_info.color_given) doColor=1;
if(args_info.aln_given) doAlnPS=1;
if(args_info.old_given) oldAliEn = 1;
if(args_info.stochBT_given){
n_back = args_info.stochBT_arg;
do_backtrack = 0;
pf = 1;
init_rand();
}
if(args_info.stochBT_en_given){
n_back = args_info.stochBT_en_arg;
do_backtrack = 0;
pf = 1;
eval_energy = 1;
init_rand();
}
if(args_info.ribosum_file_given){
RibosumFile = strdup(args_info.ribosum_file_arg);
ribo = 1;
}
if(args_info.ribosum_scoring_given){
RibosumFile = NULL;
ribo = 1;
}
if(args_info.layout_type_given)
rna_plot_type = args_info.layout_type_arg;
/* alignment file name given as unnamed option? */
if(args_info.inputs_num == 1){
clust_file = fopen(args_info.inputs[0], "r");
if (clust_file == NULL) {
fprintf(stderr, "can't open %s\n", args_info.inputs[0]);
}
}
/* free allocated memory of command line data structure */
RNAalifold_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if(circular && gquad){
nrerror("G-Quadruplex support is currently not available for circular RNA structures");
}
make_pair_matrix();
if (circular && noLonelyPairs)
warn_user("depending on the origin of the circular sequence, "
"some structures may be missed when using --noLP\n"
"Try rotating your sequence a few times\n");
if (ParamFile != NULL) read_parameter_file(ParamFile);
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1; c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
/*
########################################################
# handle user input from 'stdin' if necessary
########################################################
*/
if(fold_constrained){
if(istty){
print_tty_constraint_full();
print_tty_input_seq_str("");
}
input_type = get_input_line(&input_string, VRNA_INPUT_NOSKIP_COMMENTS);
if(input_type & VRNA_INPUT_QUIT){ return 0;}
else if((input_type & VRNA_INPUT_MISC) && (strlen(input_string) > 0)){
cstruc = strdup(input_string);
free(input_string);
}
else warn_user("constraints missing");
}
if (istty && (clust_file == stdin))
print_tty_input_seq_str("Input aligned sequences in clustalw or stockholm format\n(enter a line starting with \"//\" to indicate the end of your input)");
n_seq = read_clustal(clust_file, AS, names);
if (n_seq==0) nrerror("no sequences found");
if (clust_file != stdin) fclose(clust_file);
/*
########################################################
# done with 'stdin' handling, now init everything properly
########################################################
*/
length = (int) strlen(AS[0]);
structure = (char *)space((unsigned) length+1);
if(fold_constrained && cstruc != NULL)
strncpy(structure, cstruc, length);
if (endgaps)
for (i=0; i<n_seq; i++) mark_endgaps(AS[i], '~');
/*
########################################################
# begin actual calculations
########################################################
*/
if (circular) {
int i;
double s = 0;
min_en = circalifold((const char **)AS, structure);
for (i=0; AS[i]!=NULL; i++)
s += energy_of_circ_structure(AS[i], structure, -1);
real_en = s/i;
} else {
float *ens = (float *)space(2*sizeof(float));
min_en = alifold((const char **)AS, structure);
if(md.gquad)
energy_of_ali_gquad_structure((const char **)AS, structure, n_seq, ens);
else
energy_of_alistruct((const char **)AS, structure, n_seq, ens);
real_en = ens[0];
free(ens);
}
string = (mis) ? consens_mis((const char **) AS) : consensus((const char **) AS);
printf("%s\n%s", string, structure);
if(istty){
if(with_sci){
float sci = min_en;
float e_mean = 0;
for (i=0; AS[i]!=NULL; i++){
char *seq = get_ungapped_sequence(AS[i]);
char *str = (char *)space(sizeof(char) * (strlen(seq) + 1));
e_mean += fold(seq, str);
free(seq);
free(str);
}
e_mean /= i;
sci /= e_mean;
printf( "\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)"
"\n SCI = %2.4f\n",
min_en, real_en, min_en-real_en, sci);
} else
printf("\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)\n",
min_en, real_en, min_en - real_en);
} else {
if(with_sci){
float sci = min_en;
float e_mean = 0;
for (i=0; AS[i]!=NULL; i++){
char *seq = get_ungapped_sequence(AS[i]);
char *str = (char *)space(sizeof(char) * (strlen(seq) + 1));
e_mean += fold(seq, str);
free(seq);
free(str);
}
e_mean /= i;
sci /= e_mean;
printf(" (%6.2f = %6.2f + %6.2f) [%2.4f]\n", min_en, real_en, min_en-real_en, sci);
}
else
printf(" (%6.2f = %6.2f + %6.2f) \n", min_en, real_en, min_en-real_en );
}
strcpy(ffname, "alirna.ps");
strcpy(gfname, "alirna.g");
if (!noPS) {
char **A;
A = annote(structure, (const char**) AS);
if(md.gquad){
if (doColor)
(void) PS_rna_plot_a_gquad(string, structure, ffname, A[0], A[1]);
else
(void) PS_rna_plot_a_gquad(string, structure, ffname, NULL, A[1]);
} else {
if (doColor)
(void) PS_rna_plot_a(string, structure, ffname, A[0], A[1]);
else
(void) PS_rna_plot_a(string, structure, ffname, NULL, A[1]);
}
free(A[0]); free(A[1]); free(A);
}
if (doAlnPS)
PS_color_aln(structure, "aln.ps", (const char const **) AS, (const char const **) names);
/* free mfe arrays */
free_alifold_arrays();
if (pf) {
float energy, kT;
char * mfe_struc;
mfe_struc = strdup(structure);
kT = (betaScale*((temperature+K0)*GASCONST))/1000.; /* in Kcal */
pf_scale = exp(-(sfact*min_en)/kT/length);
if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
fflush(stdout);
if (cstruc!=NULL) strncpy(structure, cstruc, length+1);
pf_parameters = get_boltzmann_factors_ali(n_seq, temperature, betaScale, md, pf_scale);
energy = alipf_fold_par((const char **)AS, structure, NULL, pf_parameters, do_backtrack, fold_constrained, circular);
if (n_back>0) {
/*stochastic sampling*/
for (i=0; i<n_back; i++) {
char *s;
double prob=1.;
s = alipbacktrack(&prob);
printf("%s ", s);
if (eval_energy ) printf("%6g %.2f ",prob, -1*(kT*log(prob)-energy));
printf("\n");
free(s);
}
}
if (do_backtrack) {
printf("%s", structure);
if (!istty) printf(" [%6.2f]\n", energy);
else printf("\n");
}
if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", energy);
printf(" frequency of mfe structure in ensemble %g\n",
exp((energy-min_en)/kT));
if (do_backtrack) {
FILE *aliout;
cpair *cp;
char *cent;
double dist;
FLT_OR_DBL *probs = export_ali_bppm();
plist *pl, *mfel;
assign_plist_from_pr(&pl, probs, length, bppmThreshold);
assign_plist_from_db(&mfel, mfe_struc, 0.95*0.95);
if (!circular){
float *ens;
cent = get_centroid_struct_pr(length, &dist, probs);
ens=(float *)space(2*sizeof(float));
energy_of_alistruct((const char **)AS, cent, n_seq, ens);
/*cent_en = energy_of_struct(string, cent);*/ /*ali*/
printf("%s %6.2f {%6.2f + %6.2f}\n",cent,ens[0]-ens[1],ens[0],(-1)*ens[1]);
free(cent);
free(ens);
}
if(doMEA){
float mea, *ens;
plist *pl2;
assign_plist_from_pr(&pl2, probs, length, 1e-4/(1+MEAgamma));
mea = MEA(pl2, structure, MEAgamma);
ens = (float *)space(2*sizeof(float));
if(circular)
energy_of_alistruct((const char **)AS, structure, n_seq, ens);
else
ens[0] = energy_of_structure(string, structure, 0);
printf("%s {%6.2f MEA=%.2f}\n", structure, ens[0], mea);
free(ens);
free(pl2);
}
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_ali.out");
} else strcpy(ffname, "alifold.out");
aliout = fopen(ffname, "w");
if (!aliout) {
fprintf(stderr, "can't open %s skipping output\n", ffname);
} else {
print_aliout(AS, pl, bppmThreshold, n_seq, mfe_struc, aliout);
}
fclose(aliout);
if (fname[0]!='\0') {
strcpy(ffname, fname);
strcat(ffname, "_dp.ps");
} else strcpy(ffname, "alidot.ps");
cp = make_color_pinfo(AS,pl, bppmThreshold, n_seq, mfel);
(void) PS_color_dot_plot(string, cp, ffname);
free(cp);
free(pl);
free(mfel);
}
free(mfe_struc);
free_alipf_arrays();
free(pf_parameters);
}
if (cstruc!=NULL) free(cstruc);
(void) fflush(stdout);
free(string);
free(structure);
for (i=0; AS[i]; i++) {
free(AS[i]); free(names[i]);
}
return 0;
}
int main(int argc, char *argv[]){
struct RNALalifold_args_info args_info;
char *string, *structure, *ParamFile, *ns_bases, *c;
char ffname[80], gfname[80], fname[80];
int n_seq, i, length, sym, r, maxdist;
int mis, pf, istty;
float cutoff;
double min_en, real_en, sfact;
char *AS[MAX_NUM_NAMES]; /* aligned sequences */
char *names[MAX_NUM_NAMES]; /* sequence names */
FILE *clust_file = stdin;
string = structure = ParamFile = ns_bases = NULL;
mis = pf = 0;
maxdist = 70;
do_backtrack = 1;
dangles = 2;
sfact = 1.07;
cutoff = 0.0005;
/*
#############################################
# check the command line parameters
#############################################
*/
if(RNALalifold_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* temperature */
if(args_info.temp_given) temperature = args_info.temp_arg;
/* structure constraint */
if(args_info.noTetra_given) tetra_loop=0;
/* set dangle model */
if(args_info.dangles_given) dangles = args_info.dangles_arg;
/* do not allow weak pairs */
if(args_info.noLP_given) noLonelyPairs = 1;
/* do not allow wobble pairs (GU) */
if(args_info.noGU_given) noGU = 1;
/* do not allow weak closing pairs (AU,GU) */
if(args_info.noClosingGU_given) no_closingGU = 1;
/* set energy model */
if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
/* take another energy parameter set */
if(args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
/* Allow other pairs in addition to the usual AU,GC,and GU pairs */
if(args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
/* set pf scaling factor */
if(args_info.pfScale_given) sfact = args_info.pfScale_arg;
/* partition function settings */
if(args_info.partfunc_given){
pf = 1;
if(args_info.partfunc_arg != -1)
do_backtrack = args_info.partfunc_arg;
}
/* set cfactor */
if(args_info.cfactor_given) cv_fact = args_info.cfactor_arg;
/* set nfactor */
if(args_info.nfactor_given) nc_fact = args_info.nfactor_arg;
/* set the maximum base pair span */
if(args_info.span_given) maxdist = args_info.span_arg;
/* set the pair probability cutoff */
if(args_info.cutoff_given) cutoff = args_info.cutoff_arg;
/* calculate most informative sequence */
if(args_info.mis_given) mis = 1;
/* check unnamed options a.k.a. filename of input alignment */
if(args_info.inputs_num == 1){
clust_file = fopen(args_info.inputs[0], "r");
if(clust_file == NULL){
fprintf(stderr, "can't open %s\n", args_info.inputs[0]);
}
}
else{
RNALalifold_cmdline_parser_print_help();
exit(1);
}
/* free allocated memory of command line data structure */
RNALalifold_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if (ParamFile != NULL)
read_parameter_file(ParamFile);
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1; c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
if (istty && (clust_file == stdin)) {
print_tty_input_seq_str("Input aligned sequences in clustalw format");
}
n_seq = read_clustal(clust_file, AS, names);
if (clust_file != stdin) fclose(clust_file);
if (n_seq==0)
nrerror("no sequences found");
length = (int) strlen(AS[0]);
if (length<maxdist) {
fprintf(stderr, "Alignment length < window size: setting L=%d\n",length);
maxdist=length;
}
structure = (char *) space((unsigned) length+1);
/*
#############################################
# begin calculations
#############################################
*/
update_fold_params();
if(!pf)
min_en = aliLfold(AS, structure, maxdist);
{
eos_debug=-1; /* shut off warnings about nonstandard pairs */
/* for (i=0; AS[i]!=NULL; i++)
s += energy_of_struct(AS[i], structure);
real_en = s/i;*/
}
string = (mis) ? consens_mis((const char **) AS) : consensus((const char **) AS);
printf("%s\n%s\n", string, structure);
/* if (istty)
printf("\n minimum free energy = %6.2f kcal/mol (%6.2f + %6.2f)\n",
min_en, real_en, min_en - real_en);
else
printf(" (%6.2f = %6.2f + %6.2f) \n", min_en, real_en, min_en-real_en );
*/
strcpy(ffname, "alirna.ps");
strcpy(gfname, "alirna.g");
/* if (length<=2500) {
char *A;
A = annote(structure, (const char**) AS);
(void) PS_rna_plot_a(string, structure, ffname, NULL, A);
free(A);
} else
fprintf(stderr,"INFO: structure too long, not doing xy_plot\n");
*/
/* {*/ /* free mfe arrays but preserve base_pair for PS_dot_plot */
/* struct bond *bp;
bp = base_pair; base_pair = space(16);
free_alifold_arrays(); / * frees base_pair * /
base_pair = bp;
}*/
if (pf) {
double energy, kT;
plist *pl;
char * mfe_struc;
mfe_struc = strdup(structure);
kT = (temperature+273.15)*1.98717/1000.; /* in Kcal */
pf_scale = -1;/*exp(-(sfact*min_en)/kT/length);*/
if (length>2000) fprintf(stderr, "scaling factor %f\n", pf_scale);
fflush(stdout);
/* init_alipf_fold(length); */
/* energy = alipfW_fold(AS, structure, &pl, maxdist, cutoff); */
if (do_backtrack) {
printf("%s", structure);
/*if (!istty) printf(" [%6.2f]\n", energy);
else */
printf("\n");
}
/*if ((istty)||(!do_backtrack))
printf(" free energy of ensemble = %6.2f kcal/mol\n", energy);
useless!!*/
/* printf(" frequency of mfe structure in ensemble %g\n",
exp((energy-min_en)/kT));*/
if (do_backtrack) {
FILE *aliout;
cpair *cp;
strcpy(ffname, "alifold.out");
aliout = fopen(ffname, "w");
if (!aliout) {
fprintf(stderr, "can't open %s skipping output\n", ffname);
} else {
fprintf(aliout, "%d sequence; length of alignment %d\n",
n_seq, length);
fprintf(aliout, "alifold output\n");
fprintf(aliout, "%s\n", structure);
}
strcpy(ffname, "alidotL.ps");
cp = make_color_pinfo2(AS,pl,n_seq);
(void) PS_color_dot_plot_turn(string, cp, ffname, maxdist);
free(cp);
}
free(mfe_struc);
free(pl);
}
free(base_pair);
(void) fflush(stdout);
free(string);
free(structure);
for (i=0; AS[i]; i++) {
free(AS[i]); free(names[i]);
}
return 0;
}
int main(int argc, char *argv[])
{
char *AS1[MAX_NUM_NAMES], *AS2[MAX_NUM_NAMES],
*names1[MAX_NUM_NAMES], *names2[MAX_NUM_NAMES];
char fname[13];
char *ParamFile=NULL;
int i, r, n_seq, n_seq2;
double deltaf;
double kT, sfact=1.07;
int pf=0, istty, delta=-1;
int noconv=0;
duplexT mfe, *subopt;
FILE *file1=NULL, *file2=NULL; /* input alignments */
for (i=1; i<argc; i++) {
if (argv[i][0]=='-')
switch ( argv[i][1] )
{
case 'T': if (argv[i][2]!='\0') usage();
if(i==argc-1) usage();
r=sscanf(argv[++i], "%lf", &temperature);
if (!r) usage();
break;
case 'p':
fprintf(stderr, "partition function folding not yet implemented\n");
usage();
pf=1;
if (argv[i][2]!='\0')
(void) sscanf(argv[i]+2, "%d", &do_backtrack);
break;
case 'n':
if ( strcmp(argv[i], "-noGU")==0) noGU=1;
if ( strcmp(argv[i], "-noCloseGU")==0) no_closingGU=1;
if ( strcmp(argv[i], "-noLP")==0) noLonelyPairs=1;
if ( strcmp(argv[i], "-noconv")==0) noconv=1;
break;
case '4':
tetra_loop=0;
break;
case 'e':
if (i>=argc-1) usage();
r=sscanf(argv[++i], "%lf", &deltaf);
if (r!=1) usage();
delta = (int) (0.1+deltaf*100);
break;
case 's': subopt_sorted=1;
break;
case 'd': dangles=0;
if (argv[i][2]!='\0') {
r=sscanf(argv[i]+2, "%d", &dangles);
if (r!=1) usage();
}
break;
case 'P':
if (i==argc-1) usage();
ParamFile = argv[++i];
break;
default: usage();
}
else { /* doesn't start with '-' should be filename */
if (i>argc-1) usage();
file1 = fopen(argv[i], "r");
if (file1 == NULL) {
fprintf(stderr, "can't open %s\n", argv[i]);
usage();
}
file2 = fopen(argv[++i], "r");
if (file1 == NULL) {
fprintf(stderr, "can't open %s\n", argv[i]);
usage();
}
}
}
if (!(file1 && file2)) {
fprintf(stderr, "No input files");
usage();
}
if (ParamFile != NULL)
read_parameter_file(ParamFile);
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
n_seq = read_clustal(file1, AS1, names1);
n_seq2 = read_clustal(file2, AS2, names2);
fclose(file1); fclose(file2);
if (n_seq != n_seq2) nrerror("unequal number of seqs in alignments");
update_fold_params();
if (delta>=0) {
duplexT *sub;
subopt = aliduplex_subopt(AS1, AS2, delta, 5);
for (sub=subopt; sub->i >0; sub++) {
print_struc(sub);
free(sub->structure);
}
free(subopt);
} else {
mfe = aliduplexfold(AS1, AS2);
print_struc(&mfe);
free(mfe.structure);
}
for (i=0; AS1[i]; i++) {
free(AS1[i]); free(names1[i]);
free(AS2[i]); free(names2[i]);
}
return 0;
}
