else {
//valid paramters for this command
- string Array[] = {"fasta", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir"};
+ string Array[] = {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("dist.seqs");
map<string, string>::iterator it2;
//check to make sure all parameters are valid for command
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it2->second; }
}
+
+ it2 = parameters.find("oldfasta");
+ //user has given a template file
+ if(it2 != parameters.end()){
+ path = hasPath(it2->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["oldfasta"] = inputDir + it2->second; }
+ }
+
+ it2 = parameters.find("column");
+ //user has given a template file
+ if(it2 != parameters.end()){
+ path = hasPath(it2->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it2->second; }
+ }
}
//check for required parameters
inFASTA.close();
}
+ oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
+ if (oldfastafile == "not found") { oldfastafile = ""; }
+ else if (oldfastafile == "not open") { abort = true; }
+
+ column = validParameter.validFile(parameters, "column", true);
+ if (column == "not found") { column = ""; }
+ else if (column == "not open") { abort = true; }
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
+ if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
+
+ if ((column != "") && (oldfastafile != "") && (output != "column")) { m->mothurOut("You have provided column and oldfasta, indicating you want to append distances to your column file. Your output must be in column format to do so."); m->mothurOutEndLine(); abort=true; }
+
if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
ValidCalculators validCalculator;
void DistanceCommand::help(){
try {
m->mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
- m->mothurOut("The dist.seqs command parameters are fasta, calc, countends, output, cutoff and processors. \n");
+ m->mothurOut("The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, cutoff and processors. \n");
m->mothurOut("The fasta parameter is required.\n");
+ m->mothurOut("The oldfasta and column parameters allow you to append the distances calculated to the column file.\n");
m->mothurOut("The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
m->mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n");
m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
int startTime = time(NULL);
+ //save number of new sequence
+ numNewFasta = alignDB.getNumSeqs();
+
+ //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
+ if ((oldfastafile != "") && (column != "")) { if (!(sanityCheck())) { return 0; } }
+
+ if (m->control_pressed) { return 0; }
+
int numSeqs = alignDB.getNumSeqs();
cutoff += 0.005;
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "dist";
+
+ //so we don't accidentally overwrite
+ if (outputFile == column) {
+ string tempcolumn = column + ".old";
+ rename(column.c_str(), tempcolumn.c_str());
+ }
+
remove(outputFile.c_str());
}else { //assume square
outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "square.dist";
if (output != "lt") {
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[outputFile.length()];
+ //memcpy(filename, outputFile.c_str(), outputFile.length());
- char filename[outputFile.length()];
+ char filename[1024];
strcpy(filename, outputFile.c_str());
MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
-
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ //delete filename;
if (pid == 0) { //you are the root process
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
MPI_File inMPI;
-
- char filename[outputFile.length()];
+
+ //char* filename = new char[outputFile.length()];
+ //memcpy(filename, outputFile.c_str(), outputFile.length());
+
+ char filename[1024];
strcpy(filename, outputFile.c_str());
-
+
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
//wait on chidren
for(int b = 1; b < processors; b++) {
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
string outTemp = outputFile + toString(b) + ".temp";
- char buf[outTemp.length()];
- strcpy(buf, outTemp.c_str());
+
+ char* buf = new char[outTemp.length()];
+ memcpy(buf, outTemp.c_str(), outTemp.length());
MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
-
+ delete buf;
+
int count = 0;
- while (count < fileSize) { //read 1000 characters at a time
- //send freqs
+ while (count < fileSize) {
char buf2[1];
MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
}
}
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if (output == "square") { convertMatrix(outputFile); }
+ ifstream fileHandle;
+ fileHandle.open(outputFile.c_str());
+ if(fileHandle) {
+ gobble(fileHandle);
+ if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
+ }
+
+ //append the old column file to the new one
+ if ((oldfastafile != "") && (column != "")) {
+ //we had to rename the column file so we didnt overwrite above, but we want to keep old name
+ if (outputFile == column) {
+ string tempcolumn = column + ".old";
+ appendFiles(tempcolumn, outputFile);
+ remove(tempcolumn.c_str());
+ }else{
+ appendFiles(outputFile, column);
+ remove(outputFile.c_str());
+ outputFile = column;
+ }
+ }
+
+
#ifdef USE_MPI
}
#endif
if (m->control_pressed) { outFile.close(); return 0; }
+ //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
+ //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
+ if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
+
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
if (m->control_pressed) { return 0; }
+ //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
+ //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
+ if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
+
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
//send results to parent
int length = outputString.length();
- char buf[length];
- strcpy(buf, outputString.c_str());
+
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
+ delete buf;
}
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[file.length()];
+ //memcpy(filename, file.c_str(), file.length());
- char filename[file.length()];
+ char filename[1024];
strcpy(filename, file.c_str());
-
+
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
int startTime = time(NULL);
//send results to parent
int length = outputString.length();
- char buf[length];
- strcpy(buf, outputString.c_str());
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
size += outputString.length();
outputString = "";
-
-
+ delete buf;
}
//m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
exit(1);
}
}
+/**************************************************************************************************/
+//its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
+//but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
+//also check to make sure the 2 files have the same alignment length.
+bool DistanceCommand::sanityCheck() {
+ try{
+ bool good = true;
+
+ //make sure the 2 fasta files have the same alignment length
+ ifstream in;
+ openInputFile(fastafile, in);
+ int fastaAlignLength = 0;
+ if (in) {
+ Sequence tempIn(in);
+ fastaAlignLength = tempIn.getAligned().length();
+ }
+ in.close();
+
+ ifstream in2;
+ openInputFile(oldfastafile, in2);
+ int oldfastaAlignLength = 0;
+ if (in2) {
+ Sequence tempIn2(in2);
+ oldfastaAlignLength = tempIn2.getAligned().length();
+ }
+ in2.close();
+
+ if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false; }
+
+ //read fasta file and save names as well as adding them to the alignDB
+ set<string> namesOldFasta;
+
+ ifstream inFasta;
+ openInputFile(oldfastafile, inFasta);
+
+ while (!inFasta.eof()) {
+ if (m->control_pressed) { inFasta.close(); return good; }
+
+ Sequence temp(inFasta);
+
+ if (temp.getName() != "") {
+ namesOldFasta.insert(temp.getName()); //save name
+ alignDB.push_back(temp); //add to DB
+ }
+
+ gobble(inFasta);
+ }
+
+ inFasta.close();
+
+ //read through the column file checking names and removing distances above the cutoff
+ ifstream inDist;
+ openInputFile(column, inDist);
+
+ ofstream outDist;
+ string outputFile = column + ".temp";
+ openOutputFile(outputFile, outDist);
+
+ string name1, name2;
+ float dist;
+ while (!inDist.eof()) {
+ if (m->control_pressed) { inDist.close(); outDist.close(); remove(outputFile.c_str()); return good; }
+
+ inDist >> name1 >> name2 >> dist; gobble(inDist);
+
+ //both names are in fasta file and distance is below cutoff
+ if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) { good = false; break; }
+ else{
+ if (dist <= cutoff) {
+ outDist << name1 << '\t' << name2 << '\t' << dist << endl;
+ }
+ }
+ }
+
+ inDist.close();
+ outDist.close();
+
+ if (good) {
+ remove(column.c_str());
+ rename(outputFile.c_str(), column.c_str());
+ }else{
+ remove(outputFile.c_str()); //temp file is bad because file mismatch above
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "appendFiles");
+ exit(1);
+ }
+}
+
/**************************************************************************************************
void DistanceCommand::appendFiles(string temp, string filename) {
try{
projects / mothur.git / blobdiff