/* Reads the thermodynamic parameters if the thermodynamic alignment
tag was set to 1 */
static void
read_thermodynamic_parameters()
{
thal_results o;
/* if the path to the parameter files did not change,
we do not want to read again */
if (thermodynamic_path_changed == 0) return;
/* check that the path to the parameters folder was given */
if (thermodynamic_params_path == NULL) {
#ifdef OS_WIN
/* in windows check for .\\primer3_config */
struct stat st;
if ((stat(".\\primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
thermodynamic_params_path =
(char*) malloc(strlen(".\\primer3_config\\") * sizeof(char) + 1);
if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
strcpy(thermodynamic_params_path, ".\\primer3_config\\");
} else {
/* no default directory found */
return;
}
#else
/* in linux, check for ./primer3_config and /opt/primer3_config */
struct stat st;
if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
thermodynamic_params_path =
(char*) malloc(strlen("./primer3_config/") * sizeof(char) + 1);
if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
strcpy(thermodynamic_params_path, "./primer3_config/");
} else if ((stat("/opt/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
thermodynamic_params_path =
(char*) malloc(strlen("/opt/primer3_config/") * sizeof(char) + 1);
if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
strcpy(thermodynamic_params_path, "/opt/primer3_config/");
} else {
/* no default directory found */
return;
}
#endif
}
/* read in the thermodynamic parameters */
if (get_thermodynamic_values(thermodynamic_params_path, &o)) {
fprintf(stderr, "%s\n", o.msg);
exit(-1);
}
/* mark that the last given path was used for reading the parameters */
thermodynamic_path_changed = 0;
}
static PyObject*
loadThermoParams(PyObject *self, PyObject *args) {
/* This loads the thermodynamic parameters from the parameter files
* found at the provided path and should only need to be called once
* prior to running thermodynamic calculations. Returns boolean indicating
* success.
*/
char *param_path=NULL;
thal_results thalres;
if (!PyArg_ParseTuple(args, "s", ¶m_path)) {
return NULL;
}
if (get_thermodynamic_values(param_path, &thalres)){
PyErr_SetString(PyExc_IOError, thalres.msg);
return NULL;
} else {
Py_RETURN_TRUE;
}
}
/* Beginning of main */
int main(int argc, char** argv)
{
const char* usage;
int tmp_ret;
thal_args a;
thal_results o;
set_thal_default_args(&a);
a.temponly=0; /* by default print only melting temperature,
do not draw structure or print any additional parameters */
if(a.debug == 0) {
#undef DEBUG
} else {
#define DEBUG
}
usage = "USAGE: %s OPTIONS oligo\n"
"-mv monovalent_conc - concentration of monovalent cations in mM, by default 50 mM\n"
"\n"
"-dv divalent_conc - concentration of divalent cations in mM, by default 0 mM\n"
"\n"
"-n dNTP_conc - concentration of deoxynycleotide triphosphate in mM, by default 0 mM\n"
"\n"
"-d dna_conc - concentration of DNA strands in nM, by default 50 nM\n"
"\n"
"-a mode - alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)\n"
"\n"
"-t temp - temperature at which duplex is calculated, by default 37C\n"
"\n"
"-r - causes the alignment NOT to be displayed on stderr, _only_ Tm is printed\n"
"\n"
"-maxloop size - the maximum size of secondary structures loops.\n"
" Default is 30 (this is maximum allowed length, currently).\n"
"\n"
"-path <path> - the path to the thermodynamic parameter files\n"
"\n"
"-s1 DNA_oligomer\n"
"\n"
"-s2 DNA_oligomer\n"
"\n";
if(argc < 2) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
return -1;
}
/* BEGIN: READ the INPUT */
for(i = 1; i < argc; ++i) {
if (!strncmp("-mv", argv[i], 3)) { /* conc of monovalent cations */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
a.mv = strtod(argv[i+1], &endptr);
if ('\0' != *endptr || a.mv < 0.0) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
i++;
} else if (!strncmp("-dv", argv[i], 3)) { /* conc of divalent cations */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
a.dv = strtod(argv[i+1], &endptr);
if('\0' != *endptr || a.dv < 0.0) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
i++;
} else if (!strcmp("-path", argv[i])) {
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
path = (char*)argv[i+1];
i++;
} else if (!strncmp("-s1", argv[i], 3)) { /* first sequence in 5'->3' direction */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
oligo1 = (const unsigned char*)argv[i+1];
i++;
} else if (!strncmp("-s2", argv[i], 3)) { /* second sequence in 5'->3' direction */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
oligo2 = (const unsigned char*)argv[i+1];
i++;
} else if (!strncmp("-a", argv[i], 2)) { /* annealing type END1, END2, ANY, considered only when duplexis;
by default ANY */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
if(strcmp(argv[i+1],"END1")==0) {
a.type = thal_end1;
} else if(strcmp(argv[i+1],"END2")==0) {
a.type = thal_end2;
} else if(strcmp(argv[i+1],"HAIRPIN")==0) {
a.type = thal_hairpin;
a.dimer = 0;
} else {
a.type = thal_any; /* ANY */
}
i++;
} else if (!strncmp("-d", argv[i], 2)) { /* dna conc */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
a.dna_conc = strtod(argv[i+1], &endptr);
if('\0' != *endptr || a.dna_conc < 0 || a.dna_conc == 0) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
i++;
} else if (!strncmp("-r", argv[i], 2)) { /* only temp is calculated */
a.temponly = 1;
} else if (!strncmp("-t", argv[i], 2)) { /* temperature at which sec str are calculated */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
a.temp = strtod(argv[i+1], &endptr) + ABSOLUTE_ZERO;
if('\0' != *endptr) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
i++;
} else if (!strncmp("-n", argv[i], 2)) { /* concentration of dNTPs */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
a.dntp = strtod(argv[i+1], &endptr);
if('\0' != *endptr || a.dntp < 0.0) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
i++;
} else if (!strncmp("-maxloop", argv[i], 8)) { /* maximum size of loop calculated;
this value can not be larger than 30 */
if(argv[i+1]==NULL) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
a.maxLoop = (int) (strtod(argv[i+1], &endptr));
if(a.maxLoop > MAX_LOOP ) {
a.maxLoop = MAX_LOOP;
#ifdef DEBUG
fputs("Warning: the maximum size of secondary structures loop is set to default (30)\n", stderr);
#endif
} else if(a.maxLoop < MIN_LOOP) {
a.maxLoop = MIN_LOOP;
#ifdef DEBUG
fputs("Warning: the maximum size of secondary structures loop was set to minimum size of allowed loop length (0)\n", stderr);
#endif
}
if('\0' != *endptr || a.maxLoop < 0) {
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
}
i++;
} else if(!strncmp("-", argv[i], 1)) { /* Unknown option. */
#ifdef DEBUG
fprintf(stderr, usage, argv[0]);
#endif
exit(-1);
} else {
break;
}
}
/* END reading INPUT */
/* check the input correctness */
if(a.dimer!=0 && (oligo2==NULL || oligo1==NULL)) { /* if user wants to calculate structure
of dimer then two sequences must be defined*/
fprintf(stderr, usage, argv[0]);
exit(-1);
}
if(a.dimer==0 && (oligo2==NULL && oligo1==NULL)) { /* if user wants to calculate structure
of monomer then only one sequence must be defined */
fprintf(stderr, usage, argv[0]);
exit(-1);
}
/* read thermodynamic parameters */
if (path == NULL) {
/* check for the default paths */
struct stat st;
#ifdef OS_WIN
if ((stat(".\\primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
tmp_ret = get_thermodynamic_values(".\\primer3_config\\", &o);
} else {
/* no default directory found, error */
fprintf(stderr, "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\n");
exit(-1);
}
#else
if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
tmp_ret = get_thermodynamic_values("./primer3_config/", &o);
} else if ((stat("/opt/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
tmp_ret = get_thermodynamic_values("/opt/primer3_config/", &o);
} else {
/* no default directory found, error */
fprintf(stderr, "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\n");
exit(-1);
}
#endif
} else tmp_ret = get_thermodynamic_values(path, &o);
if (tmp_ret) {
fprintf(stderr, "%s\n", o.msg);
exit(-1);
}
/* execute thermodynamical alignemnt */
if(a.dimer==0 && oligo1!=NULL){
thal(oligo1,oligo1,&a,&o);
} else if(a.dimer==0 && oligo1==NULL && oligo2!=NULL) {
thal(oligo2,oligo2,&a,&o);
} else {
thal(oligo1,oligo2,&a,&o);
}
/* encountered error during thermodynamical calc */
if (o.temp == THAL_ERROR_SCORE) {
tmp_ret = fprintf(stderr, "Error: %s\n", o.msg);
exit(-1);
}
if(a.temponly==1)
printf("%f\n",o.temp);
/* cleanup */
destroy_thal_structures();
return EXIT_SUCCESS;
}
