helpString += "Example sub.sample(list=abrecovery.fn.list, group=abrecovery.groups, groups=B-C, size=20).\n";
helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
helpString += "The sub.sample command outputs a .subsample file.\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
return helpString;
}
catch(exception& e) {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
if (m->control_pressed) { return 0; }
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
//make sure that if your picked groups size is not too big
int thisSize = names.size();
if (thisSize < size) { size = thisSize; }
}
}else { //make sure size is not too large
- int smallestSize = groupMap->getNumSeqs(Groups[0]);
- for (int i = 1; i < Groups.size(); i++) {
+ vector<string> newGroups;
+ for (int i = 0; i < Groups.size(); i++) {
int thisSize = groupMap->getNumSeqs(Groups[i]);
- if (thisSize < smallestSize) { smallestSize = thisSize; }
+ if (thisSize >= size) { newGroups.push_back(Groups[i]); }
+ else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
}
- if (smallestSize < size) { size = smallestSize; m->mothurOut("You have selected a size that is larger than your smallest sample, using your samllest sample size, " + toString(smallestSize) + "."); m->mothurOutEndLine(); }
+ Groups = newGroups;
}
m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
}
}
}
+
+ if (subset.size() == 0) { m->mothurOut("The size you selected is too large, skipping fasta file."); m->mothurOutEndLine(); return 0; }
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "subsample" + m->getExtension(fastafile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
//read through fasta file outputting only the names on the subsample list
ifstream in;
m->openInputFile(fastafile, in);
int SubSampleCommand::getSubSampleShared() {
try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
InputData* input = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
if (thisSize < size) { size = thisSize; }
}
+ }else {
+ m->Groups.clear();
+ vector<SharedRAbundVector*> temp;
+ for (int i = 0; i < lookup.size(); i++) {
+ if (lookup[i]->getNumSeqs() < size) {
+ m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
+ delete lookup[i];
+ }else {
+ m->Groups.push_back(lookup[i]->getGroup());
+ temp.push_back(lookup[i]);
+ }
+ }
+ lookup = temp;
+ Groups = m->Groups;
}
- m->mothurOut("Sampling " + toString(size) + " from " + toString(lookup[0]->getNumSeqs()) + "."); m->mothurOutEndLine();
+ if (lookup.size() == 0) { m->mothurOut("The size you selected is too large, skipping shared file."); m->mothurOutEndLine(); delete input; return 0; }
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "subsample" + m->getExtension(sharedfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+
+ m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processShared(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processShared(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
processShared(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
if (thisSize < size) { size = thisSize; }
}
}else { //make sure size is not too large
- int smallestSize = groupMap->getNumSeqs(Groups[0]);
- for (int i = 1; i < Groups.size(); i++) {
+ vector<string> newGroups;
+ for (int i = 0; i < Groups.size(); i++) {
int thisSize = groupMap->getNumSeqs(Groups[i]);
- if (thisSize < smallestSize) { smallestSize = thisSize; }
+ if (thisSize >= size) { newGroups.push_back(Groups[i]); }
+ else { m->mothurOut("You have selected a size that is larger than " + Groups[i] + " number of sequences, removing " + Groups[i] + "."); m->mothurOutEndLine(); }
}
- if (smallestSize < size) { size = smallestSize; m->mothurOut("You have selected a size that is larger than your smallest sample, using your samllest sample size, " + toString(smallestSize) + "."); m->mothurOutEndLine(); }
+ Groups = newGroups;
}
m->mothurOut("Sampling " + toString(size) + " from each group."); m->mothurOutEndLine();
individual += binnames[j];
}
}
- if (subset.count(individual) != 0) { newNames += individual; }
+ if (subset.count(individual) != 0) { newNames += individual + ","; }
//if there are names in this bin add to new list
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleRabund() {
try {
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
InputData* input = new InputData(rabundfile, "rabund");
RAbundVector* rabund = input->getRAbundVector();
string lastLabel = rabund->getLabel();
if (size == 0) { //user has not set size, set size = 10%
size = int((rabund->getNumSeqs()) * 0.10);
- }
+ }else if (size > rabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping rabund file."); m->mothurOutEndLine(); delete input; delete rabund; return 0; }
m->mothurOut("Sampling " + toString(size) + " from " + toString(rabund->getNumSeqs()) + "."); m->mothurOutEndLine();
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "subsample" + m->getExtension(rabundfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
//as long as you are not at the end of the file or done wih the lines you want
while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { delete input; delete rabund; out.close(); return 0; }
//**********************************************************************************************************************
int SubSampleCommand::getSubSampleSabund() {
try {
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
+
InputData* input = new InputData(sabundfile, "sabund");
SAbundVector* sabund = input->getSAbundVector();
string lastLabel = sabund->getLabel();
if (size == 0) { //user has not set size, set size = 10%
size = int((sabund->getNumSeqs()) * 0.10);
- }
+ }else if (size > sabund->getNumSeqs()) { m->mothurOut("The size you selected is too large, skipping sabund file."); m->mothurOutEndLine(); delete input; delete sabund; return 0; }
+
m->mothurOut("Sampling " + toString(size) + " from " + toString(sabund->getNumSeqs()) + "."); m->mothurOutEndLine();
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "subsample" + m->getExtension(sabundfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+
//as long as you are not at the end of the file or done wih the lines you want
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { delete input; delete sabund; out.close(); return 0; }
projects / mothur.git / blobdiff