#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());
projects / mothur.git / blobdiff