}
}
- printBlock(chimeraResults[0], out);
+ printBlock(chimeraResults[0], chimeraFlag, out);
out << endl;
}else { out << querySeq->getName() << "\tno" << endl; }
}
}
- outputString = getBlock(chimeraResults[0]);
+ outputString = getBlock(chimeraResults[0], chimeraFlag);
outputString += "\n";
//cout << outputString << endl;
//write to output file
}
}
//***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
try {
//out << ":)\n";
out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
- out << "yes\t" << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
+ out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
//out << "Similarity of parents: " << data.ab << endl;
//out << "Similarity of query to parentA: " << data.qa << endl;
}
}
//***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
try {
string outputString = "";
outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t";
outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t";
- outputString += "yes\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
+ outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
return outputString;
}
int window, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, increment;
float divR;
- void printBlock(data_struct, ostream&);
- string getBlock(data_struct);
+ void printBlock(data_struct, string, ostream&);
+ string getBlock(data_struct, string);
};
if (fastafile != "") {
if (taxFile == "") { m->mothurOut("You need to provide a taxonomy file if you are using a fasta file to generate the split."); m->mothurOutEndLine(); abort = true; }
+ if (namefile == "") { m->mothurOut("You need to provide a names file if you are using a fasta file to generate the split."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
m->mothurOut("For the distance file method, you need only provide your distance file and mothur will split the file into distinct groups. \n");
m->mothurOut("For the classification method, you need to provide your distance file and taxonomy file, and set the splitmethod to classify. \n");
m->mothurOut("You will also need to set the taxlevel you want to split by. mothur will split the sequence into distinct taxonomy groups, and split the distance file based on those groups. \n");
- m->mothurOut("For the classification method using a fasta file, you need to provide your fasta file and taxonomy file. \n");
+ m->mothurOut("For the classification method using a fasta file, you need to provide your fasta file, names file and taxonomy file. \n");
m->mothurOut("You will also need to set the taxlevel you want to split by. mothur will split the sequence into distinct taxonomy groups, and create distance files for each grouping. \n");
m->mothurOut("The phylip and column parameter allow you to enter your distance file. \n");
m->mothurOut("The fasta parameter allows you to enter your aligned fasta file. \n");
//split matrix into non-overlapping groups
SplitMatrix* split;
- if (splitmethod == "distance") { split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod, large); }
- else if (splitmethod == "classify") { split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod, large); }
- else if (splitmethod == "fasta") { split = new SplitMatrix(fastafile, taxFile, taxLevelCutoff, splitmethod); }
+ if (splitmethod == "distance") { split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod, large); }
+ else if (splitmethod == "classify") { split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod, large); }
+ else if (splitmethod == "fasta") { split = new SplitMatrix(fastafile, namefile, taxFile, taxLevelCutoff, splitmethod, processors); }
else { m->mothurOut("Not a valid splitting method. Valid splitting algorithms are distance, classify or fasta."); m->mothurOutEndLine(); return 0; }
split->split();
listFileNames.clear(); return listFileNames;
}
- //remove(thisDistFile.c_str());
- //remove(thisNamefile.c_str());
+ remove(thisDistFile.c_str());
+ remove(thisNamefile.c_str());
}
./logsd.o\\r
./geom.o\\r
./setlogfilecommand.o\\r
- -o mothur\r
+ -o ../Release/mothur\r
\r
clean : \r
rm \\r
#include "splitmatrix.h"
#include "phylotree.h"
-#include "sequencedb.h"
-#include "onegapdist.h"
-#include "dist.h"
+#include "distancecommand.h"
/***********************************************************************/
}
/***********************************************************************/
-SplitMatrix::SplitMatrix(string ffile, string tax, float c, string t){
+SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, string t, int p){
m = MothurOut::getInstance();
fastafile = ffile;
+ namefile = name;
taxFile = tax;
cutoff = c;
method = t;
+ processors = p;
}
/***********************************************************************/
createDistanceFilesFromTax(seqGroup, numGroups);
}
-
return 0;
}
/***********************************************************************/
int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numGroups){
try {
+ map<string, int> copyGroups = seqGroup;
map<string, int>::iterator it;
- map<string, int>::iterator it2;
- map<string, int> seqIndexInFasta;
+ set<string> names;
+
+ for (int i = 0; i < numGroups; i++) { //remove old temp files, just in case
+ remove((fastafile + "." + toString(i) + ".temp").c_str());
+ }
+
+ ifstream in;
+ openInputFile(fastafile, in);
+
+ //parse fastafile
+ ofstream outFile;
+ while (!in.eof()) {
+ Sequence query(in); gobble(in);
+ if (query.getName() != "") {
+
+ it = seqGroup.find(query.getName());
- //read fastafile
- SequenceDB alignDB;
-
- ifstream filehandle;
- openInputFile(fastafile, filehandle);
- int numSeqs = 0;
- while (!filehandle.eof()) {
- //input sequence info into sequencedb
- Sequence newSequence(filehandle);
+ //save names in case no namefile is given
+ if (namefile == "") { names.insert(query.getName()); }
- if (newSequence.getName() != "") {
- alignDB.push_back(newSequence);
- seqIndexInFasta[newSequence.getName()] = numSeqs;
- numSeqs++;
+ if (it != seqGroup.end()) { //not singleton
+ openOutputFileAppend((fastafile + "." + toString(it->second) + ".temp"), outFile);
+ query.printSequence(outFile);
+ outFile.close();
+
+ copyGroups.erase(it);
+ }
}
+ }
+ in.close();
+
+ //warn about sequence in groups that are not in fasta file
+ for(it = copyGroups.begin(); it != copyGroups.end(); it++) {
+ m->mothurOut("ERROR: " + it->first + " is missing from your fastafile. This could happen if your taxonomy file is not unique and your fastafile is, or it could indicate and error."); m->mothurOutEndLine();
+ exit(1);
+ }
+
+ copyGroups.clear();
+
+ //process each distance file
+ for (int i = 0; i < numGroups; i++) {
+
+ string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors);
- //takes care of white space
- gobble(filehandle);
+ Command* command = new DistanceCommand(options);
+ command->execute();
+ delete command;
+
+ remove((fastafile + "." + toString(i) + ".temp").c_str());
+
+ //remove old names files just in case
+ remove((namefile + "." + toString(i) + ".temp").c_str());
}
- filehandle.close();
- Dist* distCalculator = new oneGapDist();
+ singleton = namefile + ".extra.temp";
+ ofstream remainingNames;
+ openOutputFile(singleton, remainingNames);
+ bool wroteExtra = false;
+
+ ifstream bigNameFile;
+ openInputFile(namefile, bigNameFile);
-//still not done....
+ string name, nameList;
+ while(!bigNameFile.eof()){
+ bigNameFile >> name >> nameList; gobble(bigNameFile);
+
+ //did this sequence get assigned a group
+ it = seqGroup.find(name);
+
+ if (it != seqGroup.end()) {
+ openOutputFileAppend((namefile + "." + toString(it->second) + ".temp"), outFile);
+ outFile << name << '\t' << nameList << endl;
+ outFile.close();
+ }else{
+ wroteExtra = true;
+ remainingNames << name << '\t' << nameList << endl;
+ }
+ }
+ bigNameFile.close();
+ remainingNames.close();
+ if (!wroteExtra) {
+ remove(singleton.c_str());
+ singleton = "none";
+ }
+
+ for(int i=0;i<numGroups;i++){
+ string tempNameFile = namefile + "." + toString(i) + ".temp";
+ string tempDistFile = getRootName(getSimpleName((fastafile + "." + toString(i) + ".temp"))) + "dist";
+
+ //if there are valid distances
+ ifstream fileHandle;
+ fileHandle.open(tempDistFile.c_str());
+ if(fileHandle) {
+ gobble(fileHandle);
+ if (!fileHandle.eof()) { //check for blank file
+ map<string, string> temp;
+ temp[tempDistFile] = tempNameFile;
+ dists.push_back(temp);
+ }
+ }
+ fileHandle.close();
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < dists.size(); i++) { remove((dists[i].begin()->first).c_str()); remove((dists[i].begin()->second).c_str()); } dists.clear(); }
return 0;
}
}
}
bigNameFile.close();
- remainingNames.close();
-
- if (!wroteExtra) {
- remove(singleton.c_str());
- singleton = "none";
- }
-
+
for(int i=0;i<numGroups;i++){
+ string tempNameFile = namefile + "." + toString(i) + ".temp";
+ string tempDistFile = distFile + "." + toString(i) + ".temp";
+
//if there are valid distances
if (validDistances[i]) {
- string tempNameFile = namefile + "." + toString(i) + ".temp";
- string tempDistFile = distFile + "." + toString(i) + ".temp";
-
map<string, string> temp;
temp[tempDistFile] = tempNameFile;
dists.push_back(temp);
+ }else{
+ ifstream in;
+ openInputFile(tempNameFile, in);
+
+ while(!in.eof()) {
+ in >> name >> nameList; gobble(in);
+ wroteExtra = true;
+ remainingNames << name << '\t' << nameList << endl;
+ }
+ in.close();
+ remove(tempNameFile.c_str());
}
}
+ remainingNames.close();
+
+ if (!wroteExtra) {
+ remove(singleton.c_str());
+ singleton = "none";
+ }
+
if (m->control_pressed) {
for (int i = 0; i < dists.size(); i++) {
remove((dists[i].begin()->first).c_str());
public:
SplitMatrix(string, string, string, float, string, bool); //column formatted distance file, namesfile, cutoff, method, large
- SplitMatrix(string, string, float, string); //fastafile, taxFile, cutoff, method
+ SplitMatrix(string, string, string, float, string, int); //fastafile, namefile, taxFile, cutoff, method, processors
~SplitMatrix();
int split();
vector< map< string, string> > dists;
float cutoff;
bool large;
+ int processors;
int splitDistance();
int splitClassify();
m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
m->mothurOut("The fasta parameter is required.\n");
- m->mothurOut("The flip parameter .... The default is 0.\n");
+ m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
m->mothurOut("The oligos parameter .... The default is "".\n");
m->mothurOut("The maxambig parameter .... The default is -1.\n");
m->mothurOut("The maxhomop parameter .... The default is 0.\n");
projects / mothur.git / commitdiff