#include "onegapignore.h"
//**********************************************************************************************************************
-
+vector<string> DistanceCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir","compress"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DistanceCommand::DistanceCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DistanceCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DistanceCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
DistanceCommand::DistanceCommand(string option) {
try {
abort = false;
else {
//valid paramters for this command
- string Array[] = {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir"};
+ string Array[] = {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir","compress"};
+
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
temp = validParameter.validFile(parameters, "processors", false); if(temp == "not found"){ temp = "1"; }
convert(temp, processors);
+ temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
+ convert(temp, compress);
+
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; }
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, oldfasta, column, calc, countends, output, cutoff and processors. \n");
+ m->mothurOut("The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, 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 cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
m->mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
+ m->mothurOut("The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n");
m->mothurOut("The dist.seqs command should be in the following format: \n");
m->mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
m->mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
if (output == "lt") { //does the user want lower triangle phylip formatted file
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
- remove(outputFile.c_str());
+ remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+ outputTypes["column"].push_back(outputFile);
//so we don't accidentally overwrite
if (outputFile == column) {
}else { //assume square
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
remove(outputFile.c_str());
+ outputTypes["phylip"].push_back(outputFile);
}
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
- char buf[4];
- MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
+ char buf[5];
+ MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
}
}else { //you are a child process
//do your part
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
- char buf[4];
+ char buf[5];
strcpy(buf, "done");
//tell parent you are done.
- MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+ MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
MPI_File_close(&outMPI);
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
- if (m->control_pressed) { delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; return 0; }
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
for(int b = 1; b < processors; b++) {
unsigned long int fileSize;
- if (m->control_pressed) { MPI_File_close(&outMPI); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); delete distCalculator; return 0; }
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
#endif
#endif
- if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
}
#endif
- if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
delete distCalculator;
m->mothurOut(outputFile); m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+
+
+ if (m->isTrue(compress)) {
+ m->mothurOut("Compressing..."); m->mothurOutEndLine();
+ m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
+ system(("gzip -v " + outputFile).c_str());
+ outputNames.push_back(outputFile + ".gz");
+ }else { outputNames.push_back(outputFile); }
+
return 0;
}