CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
- CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter poutput("output", "Multiple", "lt-square-column", "lt", "", "", "","",false,false); parameters.push_back(poutput);
CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
- helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
helpString += "The default value for groups is all the groups in your groupfile.\n";
}
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
- if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+ if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
mode = validParameter.validFile(parameters, "mode", false); if(mode == "not found"){ mode = "average"; }
if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
try {
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-
- //output num seqs
- out << simMatrix.size() << endl;
-
+
if (output == "lt") {
+ out << simMatrix.size() << endl;
for (int b = 0; b < simMatrix.size(); b++) {
out << lookup[b]->getGroup() << '\t';
for (int n = 0; n < b; n++) {
}
out << endl;
}
+ }else if (output == "column") {
+ for (int b = 0; b < simMatrix.size(); b++) {
+ for (int n = 0; n < b; n++) {
+ out << lookup[b]->getGroup() << '\t' << lookup[n]->getGroup() << '\t' << simMatrix[b][n] << endl;
+ }
+ }
}else{
+ out << simMatrix.size() << endl;
for (int b = 0; b < simMatrix.size(); b++) {
out << lookup[b]->getGroup() << '\t';
for (int n = 0; n < simMatrix[b].size(); n++) {
--- /dev/null
+//
+// mergetaxsummarycommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 2/13/13.
+// Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#include "mergetaxsummarycommand.h"
+
+
+//**********************************************************************************************************************
+vector<string> MergeTaxSummaryCommand::setParameters(){
+ try {
+ CommandParameter pinput("input", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pinput);
+ CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string MergeTaxSummaryCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The merge.taxsummary command takes a list of tax.summary files separated by dashes and merges them into one file.";
+ helpString += "The merge.taxsummary command parameters are input and output.";
+ helpString += "Example merge.taxsummary(input=small.tax.summary-large.tax.summary, output=all.tax.summary).";
+ helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+MergeTaxSummaryCommand::MergeTaxSummaryCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["taxsummary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "MergeTaxSummaryCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+MergeTaxSummaryCommand::MergeTaxSummaryCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true; }
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["taxsummary"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+
+ string fileList = validParameter.validFile(parameters, "input", false);
+ if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine(); abort=true; }
+ else{ m->splitAtDash(fileList, fileNames); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found") { outputDir = ""; }
+
+
+ numInputFiles = fileNames.size();
+ ifstream testFile;
+ if(numInputFiles == 0){
+ m->mothurOut("you must enter two or more file names and you entered " + toString(fileNames.size()) + " file names"); m->mothurOutEndLine();
+ abort=true;
+ }
+ else{
+ for(int i=0;i<numInputFiles;i++){
+ if (inputDir != "") {
+ string path = m->hasPath(fileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fileNames[i] = inputDir + fileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
+ ableToOpen = m->openInputFile(fileNames[i], in, "noerror");
+ in.close();
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fileNames[i]);
+ m->mothurOut("Unable to open " + fileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fileNames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fileNames[i]);
+ m->mothurOut("Unable to open " + fileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fileNames[i] = tryPath;
+ }
+ }
+
+
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fileNames.erase(fileNames.begin()+i);
+ i--;
+ }
+ }
+ }
+
+ outputFileName = validParameter.validFile(parameters, "output", false);
+ if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine(); abort=true; }
+ else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "MergeTaxSummaryCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int MergeTaxSummaryCommand::execute(){
+ try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ outputFileName = m->getFullPathName(outputFileName);
+ m->mothurRemove(outputFileName);
+
+ vector<rawTaxNode> tree;
+ tree.push_back(rawTaxNode("Root"));
+ tree[0].rank = "0";
+ bool hasGroups = true;
+ set<string> groups;
+
+ for (int i = 0; i < fileNames.size(); i++) {
+
+ ifstream in;
+ m->openInputFile(fileNames[i], in);
+ string temp = m->getline(in);
+ vector<string> headers = m->splitWhiteSpace(temp);
+
+ vector<string> thisFilesGroups;
+ if (headers.size() == 5) { hasGroups = false; }
+ else { for (int j = 5; j < headers.size(); j++) { groups.insert(headers[j]); thisFilesGroups.push_back(headers[j]); } }
+
+ int level, daugterLevels, total;
+ string rankId, tax;
+ map<int, int> levelToCurrentNode;
+ levelToCurrentNode[0] = 0;
+ while (!in.eof()) {
+
+ if (m->control_pressed) { return 0; }
+
+ in >> level >> rankId >> tax >> daugterLevels >> total; m->gobble(in);
+ map<string, int> groupCounts;
+ if (thisFilesGroups.size() != 0) {
+ for (int j = 0; j < thisFilesGroups.size(); j++) {
+ int tempNum; in >> tempNum; m->gobble(in);
+ groupCounts[thisFilesGroups[j]] = tempNum;
+ }
+ }
+
+ if (level == 0) {}
+ else {
+ map<int, int>::iterator itParent = levelToCurrentNode.find(level-1);
+ int parent = 0;
+ if (itParent == levelToCurrentNode.end()) { m->mothurOut("[ERROR]: situation I didnt expect.\n"); }
+ else { parent = itParent->second; }
+
+ levelToCurrentNode[level] = addTaxToTree(tree, level, parent, tax, total, groupCounts);
+ }
+ }
+ in.close();
+ }
+
+ if (!hasGroups && (groups.size() != 0)) { groups.clear(); m->mothurOut("[WARNING]: not all files contain group breakdown, ignoring group counts.\n"); }
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ print(out, tree, groups);
+
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["taxsummary"].push_back(outputFileName);
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int MergeTaxSummaryCommand::addTaxToTree(vector<rawTaxNode>& tree, int level, int currentNode, string taxon, int total, map<string, int> groups){
+ try {
+ map<string, int>::iterator childPointer;
+
+ childPointer = tree[currentNode].children.find(taxon);
+ int nodeToIncrement = 0;
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, increment counts
+ nodeToIncrement = childPointer->second;
+ tree[nodeToIncrement].total += total;
+
+ for (map<string, int>::iterator itGroups = groups.begin(); itGroups != groups.end(); itGroups++) {
+ map<string, int>::iterator it = tree[nodeToIncrement].groupCount.find(itGroups->first);
+ if (it == tree[nodeToIncrement].groupCount.end()) { tree[nodeToIncrement].groupCount[itGroups->first] = itGroups->second; }
+ else { it->second += itGroups->second; }
+ }
+ }
+ else{ //otherwise, create it
+ tree.push_back(rawTaxNode(taxon));
+ tree[currentNode].children[taxon] = tree.size()-1;
+ tree[tree.size()-1].parent = currentNode;
+ nodeToIncrement = tree.size()-1;
+ tree[nodeToIncrement].total = total;
+ tree[nodeToIncrement].level = level;
+ for (map<string, int>::iterator itGroups = groups.begin(); itGroups != groups.end(); itGroups++) {
+ tree[nodeToIncrement].groupCount[itGroups->first] = itGroups->second;
+ }
+ }
+
+ return nodeToIncrement;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "addSeqToTree");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int MergeTaxSummaryCommand::assignRank(int index, vector<rawTaxNode>& tree){
+ try {
+ map<string,int>::iterator it;
+ int counter = 1;
+
+ for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+ if (m->control_pressed) { return 0; }
+ tree[it->second].rank = tree[index].rank + '.' + toString(counter);
+ counter++;
+
+ assignRank(it->second, tree);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "assignRank");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int MergeTaxSummaryCommand::print(ofstream& out, vector<rawTaxNode>& tree, set<string> groups){
+ try {
+
+ assignRank(0, tree);
+ vector<string> mGroups;
+ //print labels
+ out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
+ for (set<string>::iterator it = groups.begin(); it != groups.end(); it++) { out << (*it) << '\t'; }
+ out << endl;
+
+ for (set<string>::iterator it2 = groups.begin(); it2 != groups.end(); it2++) { tree[0].groupCount[*it2] = 0; }
+
+ map<string,int>::iterator it;
+ for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
+ tree[0].total += tree[it->second].total;
+ for (set<string>::iterator it2 = groups.begin(); it2 != groups.end(); it2++) {
+ map<string, int>:: iterator itGroups = tree[it->second].groupCount.find(*it2);
+ if (itGroups != tree[it->second].groupCount.end()) {
+ tree[0].groupCount[*it2] += itGroups->second;
+ }
+ }
+ }
+
+
+ //print root
+ out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << tree[0].children.size() << "\t" << tree[0].total << "\t";
+
+ for (set<string>::iterator it = groups.begin(); it != groups.end(); it++) {
+ map<string, int>:: iterator itGroups = tree[0].groupCount.find(*it);
+ int num = 0;
+ if (itGroups != tree[0].groupCount.end()) { num = itGroups->second; }
+ out << num << '\t';
+ }
+ out << endl;
+
+ //print rest
+ print(0, out, tree, groups);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "print");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int MergeTaxSummaryCommand::print(int i, ofstream& out, vector<rawTaxNode>& tree, set<string> groups){
+ try {
+ map<string,int>::iterator it;
+ for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
+
+ //print root
+ out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << tree[it->second].children.size() << "\t" << tree[it->second].total << "\t";
+
+ for (set<string>::iterator it2 = groups.begin(); it2 != groups.end(); it2++) {
+ map<string, int>:: iterator itGroups = tree[it->second].groupCount.find(*it2);
+ int num = 0;
+ if (itGroups != tree[it->second].groupCount.end()) { num = itGroups->second; }
+ out << num << '\t';
+ }
+ out << endl;
+
+ print(it->second, out, tree, groups);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MergeTaxSummaryCommand", "print");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
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