if (metadatafile == "") { out << "OTU"; }
else { out << "Feature"; }
- for (int i = 0; i < numaxes; i++) { out << '\t' << "axis" << (i+1); }
+ for (int i = 0; i < numaxes; i++) { out << '\t' << "axis" << (i+1) << "\tp-value"; }
out << "\tlength" << endl;
if (method == "pearson") { calcPearson(axes, out); }
double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
r = numerator / denom;
+
+ if (isnan(r) || isinf(r)) { r = 0.0; }
+
rValues[k] = r;
out << '\t' << r;
+
+ //signifigance calc - http://faculty.vassar.edu/lowry/ch4apx.html
+ double temp = (1- (r*r)) / (double) (lookupFloat.size()-2);
+ temp = sqrt(temp);
+ double sig = r / temp;
+ if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+
+ out << '\t' << sig;
}
double sum = 0;
p = (SX2 + SY2 - di) / (2.0 * sqrt((SX2*SY2)));
+ if (isnan(p) || isinf(p)) { p = 0.0; }
+
out << '\t' << p;
pValues[j] = p;
+
+ //signifigance calc - http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
+ double temp = (lookupFloat.size()-2) / (double) (1- (p*p));
+ temp = sqrt(temp);
+ double sig = p*temp;
+ if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+
+ out << '\t' << sig;
+
}
double sum = 0;
}
double p = (numCoor - numDisCoor) / (float) count;
-
+ if (isnan(p) || isinf(p)) { p = 0.0; }
+
out << '\t' << p;
pValues[j] = p;
-
+
+ //calc signif - zA - http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient#Significance_tests
+ double numer = 3.0 * (numCoor - numDisCoor);
+ int n = scores[j].size();
+ double denom = n * (n-1) * (2*n + 5) / (double) 2.0;
+ denom = sqrt(denom);
+ double sig = numer / denom;
+
+ if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+
+ out << '\t' << sig;
}
double sum = 0;
CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
string GetGroupsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy or shared file.\n";
+ helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy, design or shared file.\n";
helpString += "It outputs a file containing the sequences in the those specified groups, or a sharedfile containing only those groups.\n";
- helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared and groups. The group parameter is required, unless you have a current group file, or are using a shared file.\n";
+ helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group parameter is required, unless you have a current group file, or are using a shared file.\n";
helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n";
helpString += "The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["shared"] = inputDir + it->second; }
}
+
+ it = parameters.find("design");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["design"] = inputDir + it->second; }
+ }
}
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
- if ((sharedfile == "") && (groupfile == "")) {
+ else { m->setGroupFile(groupfile); }
+
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { designfile = ""; abort = true; }
+ else if (designfile == "not found") { designfile = ""; }
+ else { m->setDesignFile(designfile); }
+
+ if ((sharedfile == "") && (groupfile == "") && (designfile == "")) {
//is there are current file available for any of these?
if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
//give priority to group, then shared
groupfile = m->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile or sharedfile or designfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
}
}
}
if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (designfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design or list."); m->mothurOutEndLine(); abort = true; }
if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (sharedfile != "") { readShared(); }
+ if (designfile != "") { readDesign(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
+
+ itTypes = outputTypes.find("design");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
+ }
}
return 0;
exit(1);
}
}
+//**********************************************************************************************************************
+int GetGroupsCommand::readDesign(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + "pick" + m->getExtension(designfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(designfile, in);
+ string name, group;
+
+ bool wroteSomething = false;
+ int selectedCount = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; //read from first column
+ in >> group; //read from second column
+
+ //if this name is in the accnos file
+ if (m->inUsersGroups(name, Groups)) {
+ wroteSomething = true;
+ out << name << '\t' << group << endl;
+ selectedCount++;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain groups from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ m->mothurOut("Selected " + toString(selectedCount) + " groups from your design file."); m->mothurOutEndLine();
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "readDesign");
+ exit(1);
+ }
+}
+
+
//**********************************************************************************************************************
int GetGroupsCommand::readTax(){
try {
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
- string getDescription() { return "gets sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
+ string getDescription() { return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
int execute();
map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
//then the other files need to change the unique name in their file to match.
//only add the names that need to be changed to keep the map search quick
- string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
+ string accnosfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
bool abort;
vector<string> outputNames, Groups;
GroupMap* groupMap;
int readTax();
int fillNames();
int readShared();
+ int readDesign();
};
CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
string RemoveGroupsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy or sharedfile.\n";
+ helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy, design or sharedfile.\n";
helpString += "It outputs a file containing the sequences NOT in the those specified groups, or with a sharedfile eliminates the groups you selected.\n";
- helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared and groups. The group parameter is required, unless you have a current group file or are using a sharedfile.\n";
+ helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group parameter is required, unless you have a current group file or are using a sharedfile.\n";
helpString += "You must also provide an accnos containing the list of groups to remove or set the groups parameter to the groups you wish to remove.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like removed. You can separate group names with dashes.\n";
helpString += "The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["shared"] = inputDir + it->second; }
}
+
+ it = parameters.find("design");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["design"] = inputDir + it->second; }
+ }
}
if (taxfile == "not open") { taxfile = ""; abort = true; }
else if (taxfile == "not found") { taxfile = ""; }
else { m->setTaxonomyFile(taxfile); }
+
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { designfile = ""; abort = true; }
+ else if (designfile == "not found") { designfile = ""; }
+ else { m->setDesignFile(designfile); }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
- if ((sharedfile == "") && (groupfile == "")) {
+ if ((sharedfile == "") && (groupfile == "") && (designfile == "")) {
//is there are current file available for any of these?
if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
//give priority to group, then shared
groupfile = m->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile or sharedfile or designfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
}
}
}
if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file containing group names or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
- if ((fastafile == "") && (namefile == "") && (groupfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (sharedfile == "") && (designfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design or list."); m->mothurOutEndLine(); abort = true; }
if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
if (sharedfile != "") { readShared(); }
+ if (designfile != "") { readDesign(); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
+
+ itTypes = outputTypes.find("design");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
+ }
}
return 0;
exit(1);
}
}
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readDesign(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + "pick" + m->getExtension(designfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(designfile, in);
+ string name, group;
+
+ bool wroteSomething = false;
+ int removedCount = 0;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; //read from first column
+ in >> group; //read from second column
+
+ //if this name is in the accnos file
+ if (!(m->inUsersGroups(name, Groups))) {
+ wroteSomething = true;
+ out << name << '\t' << group << endl;
+ }else { removedCount++; }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only groups from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine();
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readDesign");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
int RemoveGroupsCommand::readTax(){
try {
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getCitation() { return "http://www.mothur.org/wiki/Remove.groups"; }
- string getDescription() { return "removes sequences from a list, fasta, name, group or taxonomy file from a given group or set of groups"; }
+ string getDescription() { return "removes sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups, sharedfile;
+ string accnosfile, fastafile, namefile, groupfile, designfile, listfile, taxfile, outputDir, groups, sharedfile;
bool abort;
vector<string> outputNames, Groups;
GroupMap* groupMap;
int readList();
int readTax();
int fillNames();
+ int readDesign();
};
projects / mothur.git / commitdiff