int main( int argc, char *argv[] ) {
//This function will calculate the all structures within a fixed
//range of the "algorithmic" mfe. The algorithmic mfe is the
//minimum free energy of a structure, ignoring symmetry corrections.
//The output is a list of the structures, including the difference
//from the algorithmic mfe, followed by the symmetry factor and the
//corrected energies, after adjusting for symmetries. The list is
//sorted by the corrected energies.
char seq[ MAXSEQLENGTH];
int seqNum[ MAXSEQLENGTH+1];
int isNicked[ MAXSEQLENGTH];
int nNicks = 0;
int nicks[MAXSTRANDS];
int nickIndex;
int **etaN;
int complexity = 3;
int length, tmpLength;
float gap = -1;
int i;
int vs;
char outFile[MAXLINE];
int inputFileSpecified;
FILE *fp;
dnaStructures mfeStructs = {NULL, 0, 0, 0, NAD_INFINITY};
//this struct will store
//all the structures within the given range
char inputFile[ MAXLINE];
strcpy( inputFile, "");
inputFileSpecified = ReadCommandLineNPK( argc, argv, inputFile);
if(NupackShowHelp) {
printf("Usage: subopt [OPTIONS] PREFIX\n");
printf("Calculate and store all structures within the specified energy gap\n");
printf("of the MFE structure.\n");
printf("Example: subopt -multi -T 25 -material dna example\n");
PrintNupackThermoHelp();
PrintNupackUtilitiesHelp();
exit(1);
}
if( !inputFileSpecified ) {
printf("Enter output file prefix: ");
scanf("%s", inputFile);
strcat(inputFile,".in"); // Here, .in is just a placeholder
}
if( !inputFileSpecified ||
!ReadInputFile( inputFile, seq, &vs, &gap, NULL, NULL) ) {
if (inputFileSpecified==0) getUserInput( seq, &vs, &gap, NULL);
else abort();
}
strncpy(outFile,inputFile,strlen(inputFile)-3);
outFile[strlen(inputFile)-3] = '\0';
strcat(outFile,".subopt");
header( argc, argv, "subopt", outFile);
printInputs( argc, argv, seq, vs, &gap, NULL, outFile);
// Add newline for stylistic reasons
fp = fopen(outFile,"a");
fprintf(fp,"\n");
fclose(fp);
if( !DO_PSEUDOKNOTS ) {
complexity = 3;
}
else {
complexity = 5;
}
tmpLength = length = strlen( seq);
convertSeq(seq, seqNum, tmpLength);
mfeFullWithSym_SubOpt( seqNum, tmpLength, &mfeStructs, complexity,
DNARNACOUNT, DANGLETYPE,
TEMP_K - ZERO_C_IN_KELVIN,
vs, (DBL_TYPE) gap, 0, SODIUM_CONC, MAGNESIUM_CONC,
USE_LONG_HELIX_FOR_SALT_CORRECTION);
//the rest is for printing purposes
for( i = 0; i < tmpLength; i++) {
isNicked[i] = 0;
if( seq[i] == '+') {
length--;
isNicked[ i - nNicks++ -1] = 1;
}
}
//initialize nicks
for( i = 0; i < MAXSTRANDS; i++) {
nicks[i] = -1;
}
nickIndex = 0;
for( i = 0; i < length; i++) {
if( isNicked[i])
nicks[ nickIndex++] = i;
}
//overkill, but convenient
etaN = (int**) malloc( (length*(length+1)/2 + (length+1))*sizeof( int*));
InitEtaN( etaN, nicks, length);
PrintDnaStructures( &mfeStructs, etaN, nicks, vs, outFile);
clearDnaStructures( &mfeStructs);
return 0;
}
int main( int argc, char *argv[] ) {
char seqChar[MAXSEQLENGTH];
int seqNum[MAXSEQLENGTH+1];
DBL_TYPE pf;
int complexity = 3;
int length, tmpLength;
char inputFile[ MAXLINE];
int vs;
char sampleFile[MAXLINE];
//permAvgPairs stores the expected value of each
//class of base pairs, grouped by permutation or complex, respectively
int inputFileSpecified;
FILE *F_sample = NULL; // ppairs file
int index;
strcpy( inputFile, "");
nupack_sample = 1;
nupack_num_samples = 10;
struct timeval rand_time;
gettimeofday(&rand_time,0);
nupack_random_seed = (rand_time.tv_sec)*1000000 + rand_time.tv_usec;
inputFileSpecified = ReadCommandLineNPK( argc, argv, inputFile);
if(NupackShowHelp) {
printf("Usage: sample [OPTIONS] PREFIX\n");
printf("Randomly sample unpseudoknotted structures from the equilibrium distribution\n");
printf("Example: sample -multi -T 25 -material dna -samples 100 example\n");
PrintNupackThermoHelp();
PrintNupackUtilitiesHelp();
exit(1);
}
if( !inputFileSpecified ) {
printf("Enter output file prefix: ");
scanf("%s", inputFile);
strcat(inputFile,".in"); // Here, .in is just a placeholder
}
if(!inputFileSpecified ||
!ReadInputFile( inputFile, seqChar, &vs, NULL, NULL, NULL) ) {
if (inputFileSpecified==0) getUserInput( seqChar, &vs, NULL, NULL);
else abort();
}
strncpy(sampleFile,inputFile,strlen(inputFile)-3);
sampleFile[strlen(inputFile)-3] = '\0';
strcat(sampleFile,".sample");
header( argc, argv, "sample", sampleFile);
printInputs( argc, argv, seqChar, vs, NULL, NULL,sampleFile);
tmpLength = length = strlen( seqChar);
convertSeq(seqChar, seqNum, tmpLength);
int ns1,ns2;
getSequenceLength(seqChar, &ns1);
getSequenceLengthInt(seqNum, &ns2);
init_genrand(nupack_random_seed);
pairPr = NULL;
if (complexity != 3) {
printf("Sampling supported only for complexity = 3. Exiting\n");
exit(1);
}
nupack_sample_list = (char **)calloc(nupack_num_samples, sizeof(char *));
printf("Number of Samples = %i\n",nupack_num_samples);
for(index = 0 ; index < nupack_num_samples ; index++) {
nupack_sample_list[index] = (char *) calloc(tmpLength+1,sizeof(char));
}
printf("Started Calculation\n");
pf = pfuncFull(seqNum, complexity, DNARNACOUNT, DANGLETYPE, TEMP_K - ZERO_C_IN_KELVIN, 0,
SODIUM_CONC, MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
printf("Finished Calculation\n");
if ((F_sample = fopen(sampleFile,"a")) == NULL) {
printf("Error opening file %s!\n",sampleFile);
exit(1);
}
// Print the free energy to the output file
fprintf(F_sample,"%s Free energy: %.8Le kcal/mol\n",
COMMENT_STRING,-kB*TEMP_K*logl(pf));
fprintf(F_sample,"%s Number of Samples: %i\n",COMMENT_STRING,nupack_num_samples);
// Put newline for stylistic reasons
fprintf(F_sample,"\n");
for(index = 0 ; index < nupack_num_samples ; index++) {
fprintf(F_sample, "%s\n",nupack_sample_list[index]);
free(nupack_sample_list[index]);
nupack_sample_list[index] = NULL;
}
free(nupack_sample_list);
#ifdef GC_DEBUG
CHECK_LEAKS();
#endif
return 0;
}
int seqNoise::writeOutput(string fastaFileName, string namesFileName, string uMapFileName, vector<int> finalTau, vector<int> centroids, vector<int> otuData, vector<string> sequences, vector<string> uniqueNames, vector<string> redundantNames, vector<int> seqFreq, vector<double>& distances){
try {
int numOTUs = finalTau.size();
int numSeqs = uniqueNames.size();
ofstream fastaFile(fastaFileName.c_str());
ofstream namesFile(namesFileName.c_str());
ofstream uMapFile(uMapFileName.c_str());
vector<int> maxSequenceAbund(numOTUs, 0);
vector<int> maxSequenceIndex(numOTUs, 0);
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { return 0; }
if(maxSequenceAbund[otuData[i]] < seqFreq[i]){
maxSequenceAbund[otuData[i]] = seqFreq[i];
maxSequenceIndex[otuData[i]] = i;
}
}
int count = 1;
for(int i=0;i<numOTUs;i++){
if (m->control_pressed) { return 0; }
if(finalTau[i] > 0){
if(maxSequenceIndex[i] != centroids[i] && distances[maxSequenceIndex[i]*numSeqs + centroids[i]] == 0){
// cout << uniqueNames[centroids[i]] << '\t' << uniqueNames[maxSequenceIndex[i]] << '\t' << count << endl;
centroids[i] = maxSequenceIndex[i];
}
int index = centroids[i];
fastaFile << '>' << uniqueNames[index] << endl << sequences[index] << endl;
namesFile << uniqueNames[index] << '\t';
string refSeq = sequences[index];
string redundantSeqs = redundantNames[index];;
vector<freqData> frequencyData;
for(int j=0;j<numSeqs;j++){
if(otuData[j] == i && j != index){
frequencyData.push_back(freqData(j, seqFreq[j]));
}
}
sort(frequencyData.rbegin(), frequencyData.rend());
string refDegap = degapSeq(refSeq);
vector<int> rUnalign = convertSeq(refDegap);
uMapFile << "ideal_seq_" << count << '\t' << finalTau[i] << endl;
uMapFile << uniqueNames[index] << '\t' << seqFreq[index] << "\t0\t" << refDegap << endl;
for(int j=0;j<frequencyData.size();j++){
if (m->control_pressed) { return 0; }
redundantSeqs += ',' + redundantNames[frequencyData[j].index];
uMapFile << uniqueNames[frequencyData[j].index] << '\t' << seqFreq[frequencyData[j].index] << '\t';
string querySeq = sequences[frequencyData[j].index];
string queryDegap = degapSeq(querySeq);
vector<int> qUnalign = convertSeq(queryDegap);
int udiffs = countDiffs(qUnalign, rUnalign);
uMapFile << udiffs << '\t' << queryDegap << endl;
}
uMapFile << endl;
namesFile << redundantSeqs << endl;
count++;
}
}
fastaFile.close();
namesFile.close();
uMapFile.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "seqNoise", "writeOutput");
exit(1);
}
}
