CXXFLAGS += -O3
-MOTHUR_FILES = "\"../Release\""
+MOTHUR_FILES = "\"Enter_your_default_path_here\""
ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
else
CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
#endif
//header
- m->mothurOut("mothur v.1.12.1");
+ m->mothurOut("mothur v.1.12.2");
m->mothurOutEndLine();
- m->mothurOut("Last updated: 7/29/2010");
+ m->mothurOut("Last updated: 7/30/2010");
m->mothurOutEndLine();
m->mothurOutEndLine();
m->mothurOut("by");
if((i-leftIndex) <= (rightIndex-i)){ // the left gap is closer - > move stuff left there's
if(leftRoom >= insertLength){ // enough room to the left to move
+ //cout << "lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
- string leftCandidateString = candAln.substr(0,leftIndex-insertLength+1);
- string rightCandidateString = candAln.substr(leftIndex+1);
+ //cout << "lr candAln = " << candAln.length() << '\t' << leftIndex-insertLength+1 << '\t' << leftIndex+1 << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-insertLength+1));
+ string rightCandidateString = candAln.substr((leftIndex+1));
candAln = leftCandidateString + rightCandidateString;
}
else{ // not enough room to the left, have to steal some space to
+
+ //cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
string leftTemplateString = newTemplateAlign.substr(0,i); // the right
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
- string leftCandidateString = candAln.substr(0,leftIndex-leftRoom+1);
- string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
- string rightCandidateString = candAln.substr(rightIndex+(insertLength-leftRoom));
+ //cout << " in else lr candAln = " << candAln.length() << '\t' << leftIndex-leftRoom+1 << '\t' << rightIndex-leftIndex-1 << '\t' << rightIndex+(insertLength-leftRoom) << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+(insertLength-leftRoom)));
candAln = leftCandidateString + insertString + rightCandidateString;
}
}
else{ // the right gap is closer - > move stuff right there's
if(rightRoom >= insertLength){ // enough room to the right to move
+ //cout << "rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
+ //cout << "rr candAln = " << candAln.length() << '\t' << i << '\t' << rightIndex << '\t' << rightIndex+insertLength << endl;
string leftCandidateString = candAln.substr(0,rightIndex);
- string rightCandidateString = candAln.substr(rightIndex+insertLength);
+ string rightCandidateString = candAln.substr((rightIndex+insertLength));
candAln = leftCandidateString + rightCandidateString;
}
else{ // not enough room to the right, have to steal some
// space to the left lets move left and then right...
+ //cout << "in else rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
- string leftCandidateString = candAln.substr(0,leftIndex-(insertLength-rightRoom)+1);
- string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
- string rightCandidateString = candAln.substr(rightIndex+rightRoom);
+ //cout << "in else rr candAln = " << candAln.length() << '\t' << '\t' << (leftIndex-(insertLength-rightRoom)+1) << '\t' << (leftIndex+1,rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-(insertLength-rightRoom)+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+rightRoom));
candAln = leftCandidateString + insertString + rightCandidateString;
}
}
else{
// there could be a case where there isn't enough room in either direction to move stuff
-
+//cout << "in else else newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << (i+leftRoom+rightRoom) << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+leftRoom+rightRoom);
+ string rightTemplateString = newTemplateAlign.substr((i+leftRoom+rightRoom));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
- string leftCandidateString = candAln.substr(0,leftIndex-leftRoom+1);
- string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
- string rightCandidateString = candAln.substr(rightIndex+rightRoom);
+ //cout << "in else else newTemplateAlign = " << candAln.length() << '\t' << (leftIndex-leftRoom+1) << '\t' << (leftIndex+1) << '\t' << (rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+rightRoom));
candAln = leftCandidateString + insertString + rightCandidateString;
i -= (leftRoom + rightRoom);
map<string, int>::iterator childPointer;
vector<TaxNode> copy = tree;
-
+
//fill out tree
fillOutTree(0, copy);
-
- //get leaf nodes that may need externsion
+
+ //get leaf nodes that may need extension
for (int i = 0; i < copy.size(); i++) {
if (copy[i].children.size() == 0) {
leafNodes[i] = i;
}
}
-
+ //cout << "maxLevel = " << maxLevel << endl;
int copyNodes = copy.size();
//go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
int currentNode = itLeaf->second;
//this sequence is unclassified at some levels
- while(level <= maxLevel){
+ while(level < maxLevel){
level++;
try {
map<string,int>::iterator it;
- it = copy[index].children.find("unclassified");
- if (it == copy[index].children.end()) { //no unclassified at this level
- string taxon = "unclassified";
- copy.push_back(TaxNode(taxon));
- copy[index].children[taxon] = copy.size()-1;
- copy[copy.size()-1].parent = index;
- copy[copy.size()-1].level = copy[index].level + 1;
- }
+ if (copy[index].level < maxLevel) {
+ it = copy[index].children.find("unclassified");
+ if (it == copy[index].children.end()) { //no unclassified at this level
+ string taxon = "unclassified";
+ copy.push_back(TaxNode(taxon));
+ copy[index].children[taxon] = copy.size()-1;
+ copy[copy.size()-1].parent = index;
+ copy[copy.size()-1].level = copy[index].level + 1;
+ }
- if (tree[index].level <= maxLevel) {
- for(it=tree[index].children.begin();it!=tree[index].children.end();it++){ //check your children
+
+ for(it=copy[index].children.begin();it!=copy[index].children.end();it++){ //check your children
fillOutTree(it->second, copy);
}
+
}
}
char buffer4 [2];
in.read(buffer4, 2);
header.clipQualLeft = be_int2(*(unsigned short *)(&buffer4));
- header.clipQualLeft = 5;
+ header.clipQualLeft = 5;
//read clip qual right
char buffer5 [2];
else {
//valid paramters for this command
- string Array[] = {"label","calc","abund","size","outputdir","inputdir"};
+ string Array[] = {"label","calc","abund","size","outputdir","groupmode","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
convert(temp, size);
+
+ temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "F"; }
+ groupMode = isTrue(temp);
+
}
}
try {
m->mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
m->mothurOut("The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
- m->mothurOut("The summary.single command parameters are label, calc, abund. No parameters are required.\n");
+ m->mothurOut("The summary.single command parameters are label, calc, abund and groupmode. No parameters are required.\n");
m->mothurOut("The summary.single command should be in the following format: \n");
m->mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
m->mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
validCalculator->printCalc("summary", cout);
m->mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
+ m->mothurOut("If you are running summary.single with a shared file and would like your summary results collated in one file, set groupmode=t. (Default=False).\n");
m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
}
if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; }
+ int numLines = 0;
+ int numCols = 0;
+
for (int p = 0; p < inputFileNames.size(); p++) {
+ numLines = 0;
+ numCols = 0;
+
string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])) + "summary";
globaldata->inputFileName = inputFileNames[p];
outputNames.push_back(fileNameRoot);
for(int i=0;i<sumCalculators.size();i++){
if(sumCalculators[i]->getCols() == 1){
outputFileHandle << '\t' << sumCalculators[i]->getName();
+ numCols++;
}
else{
outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+ numCols += 3;
}
}
outputFileHandle << endl;
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ numLines++;
}
if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ numLines++;
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ numLines++;
delete sabund;
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
+ if ((hadShared != "") && (groupMode)) { outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames)); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
}
}
//**********************************************************************************************************************
+string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string> outputNames) {
+ try {
+
+ ofstream out;
+ string combineFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "groups.summary";
+
+ //open combined file
+ openOutputFile(combineFileName, out);
+
+ //open each groups summary file
+ string newLabel = "";
+ ifstream* temp;
+ map<string, ifstream*> filehandles;
+ for (int i=0; i<outputNames.size(); i++) {
+ temp = new ifstream;
+ filehandles[outputNames[i]] = temp;
+ openInputFile(outputNames[i], *(temp));
+
+ //read through first line - labels
+ string tempLabel;
+ if (i == 0) { //we want to save the labels to output below
+ for (int j = 0; j < numCols+1; j++) {
+ *(temp) >> tempLabel;
+
+ if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
+ }else{ newLabel += tempLabel + '\t'; }
+ }
+ }else{ for (int j = 0; j < numCols+1; j++) { *(temp) >> tempLabel; } }
+
+ gobble(*(temp));
+ }
+
+ //output label line to new file
+ out << newLabel << endl;
+
+ //for each label
+ for (int i = 0; i < numLines; i++) {
+
+ //grab summary data for each group
+ for (int i=0; i<outputNames.size(); i++) {
+ string tempLabel;
+
+ for (int j = 0; j < numCols+1; j++) {
+ *(filehandles[outputNames[i]]) >> tempLabel;
+
+ //print to combined file
+ if (j == 1) { out << groups[i] << '\t' << tempLabel << '\t'; }
+ else{ out << tempLabel << '\t'; }
+ }
+
+ out << endl;
+ gobble(*(filehandles[outputNames[i]]));
+ }
+ }
+
+ //close each groups summary file
+ for (int i=0; i<outputNames.size(); i++) { (*(filehandles[outputNames[i]])).close(); }
+ out.close();
+
+ //return combine file name
+ return combineFileName;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
SAbundVector* sabund;
int abund, size;
- bool abort, allLines;
+ bool abort, allLines, groupMode;
set<string> labels; //holds labels to be used
string label, calc, outputDir;
vector<string> Estimators;
vector<string> groups;
vector<string> parseSharedFile(string);
+ string createGroupSummaryFile(int, int, vector<string>);
};
//save sequences level
seqLevels[name] = thisLevel;
-
+
//is this the longest taxonomy?
if (thisLevel > level) {
level = thisLevel;
testTax = tax; //testTax is used to figure out if this file has confidences we need to strip out
- }
+ }
}
int pos = testTax.find_first_of('(');
//if there are '(' then there are confidences we need to take out
if (pos != -1) { containsConfidence = true; }
-
+
return level;
}
projects / mothur.git / commitdiff