--- /dev/null
+//
+// removedistscommand.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 1/29/13.
+// Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#include "removedistscommand.h"
+
+//**********************************************************************************************************************
+vector<string> RemoveDistsCommand::setParameters(){
+ try {
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "PhylipColumn", "none","phylip",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "PhylipColumn", "none","column",false,false,true); parameters.push_back(pcolumn);
+ CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+ 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, "RemoveDistsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RemoveDistsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The remove.dists command removes distances from a phylip or column file related to groups or sequences listed in an accnos file.\n";
+ helpString += "The remove.dists command parameters are accnos, phylip and column.\n";
+ helpString += "The remove.dists command should be in the following format: get.dists(accnos=yourAccnos, phylip=yourPhylip).\n";
+ helpString += "Example remove.dists(accnos=final.accnos, phylip=final.an.thetayc.0.03.lt.ave.dist).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. accnos), '=' and parameters (i.e.final.accnos).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveDistsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RemoveDistsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "phylip") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "column") { pattern = "[filename],pick,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveDistsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RemoveDistsCommand::RemoveDistsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveDistsCommand", "RemoveDistsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RemoveDistsCommand::RemoveDistsCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //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();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //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 = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //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["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //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["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("accnos");
+ //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["accnos"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { abort = true; }
+ else if (accnosfile == "not found") {
+ accnosfile = m->getAccnosFile();
+ if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setAccnosFile(accnosfile); }
+
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; }
+ else { m->setPhylipFile(phylipfile); }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not open") { columnfile = ""; abort = true; }
+ else if (columnfile == "not found") { columnfile = ""; }
+ else { m->setColumnFile(columnfile); }
+
+ if ((phylipfile == "") && (columnfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to column, then phylip
+ columnfile = m->getColumnFile();
+ if (columnfile != "") { m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+ else {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a phylip or column file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveDistsCommand", "RemoveDistsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int RemoveDistsCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ //get names you want to keep
+ names = m->readAccnos(accnosfile);
+
+ if (m->control_pressed) { return 0; }
+
+ //read through the correct file and output lines you want to keep
+ if (phylipfile != "") { readPhylip(); }
+ if (columnfile != "") { readColumn(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+
+ if (outputNames.size() != 0) {
+ m->mothurOutEndLine();
+ m->mothurOut("Output File names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("phylip");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ }
+
+ itTypes = outputTypes.find("column");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
+ }
+ }
+
+ return 0;
+ }
+
+ catch(exception& e) {
+ m->errorOut(e, "RemoveDistsCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int RemoveDistsCommand::readPhylip(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(phylipfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(phylipfile));
+ variables["[extension]"] = m->getExtension(phylipfile);
+ string outputFileName = getOutputFileName("phylip", variables);
+
+ ifstream in;
+ m->openInputFile(phylipfile, in);
+
+ float distance;
+ int square, nseqs;
+ string name;
+ unsigned int row;
+ set<unsigned int> rows; //converts names in names to a index
+ row = 0;
+
+ string numTest;
+ in >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
+ //not one we want to remove
+ if (names.count(name) == 0) { rows.insert(row); }
+ row++;
+
+ //is the matrix square?
+ char d;
+ while((d=in.get()) != EOF){
+
+ if(isalnum(d)){
+ square = 1;
+ in.putback(d);
+ for(int i=0;i<nseqs;i++){
+ in >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ //map name to row/column
+ if(square == 0){
+ for(int i=1;i<nseqs;i++){
+ in >> name;
+ if (names.count(name) == 0) { rows.insert(row); }
+ row++;
+
+ for(int j=0;j<i;j++){
+ if (m->control_pressed) { in.close(); return 0; }
+ in >> distance;
+ }
+ }
+ }
+ else{
+ for(int i=1;i<nseqs;i++){
+ in >> name;
+ if (names.count(name) == 0) { rows.insert(row); }
+ row++;
+ for(int j=0;j<nseqs;j++){
+ if (m->control_pressed) { in.close(); return 0; }
+ in >> distance;
+ }
+ }
+ }
+ in.close();
+
+ if (m->control_pressed) { return 0; }
+
+ //read through file only printing rows and columns of seqs in names
+ ifstream inPhylip;
+ m->openInputFile(phylipfile, inPhylip);
+
+ inPhylip >> numTest;
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["phylip"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ out << names.size() << endl;
+
+ unsigned int count = 0;
+ unsigned int keptCount = 0;
+ if(square == 0){
+ for(int i=0;i<nseqs;i++){
+ inPhylip >> name;
+ bool ignoreRow = false;
+
+ if (names.count(name) != 0) { ignoreRow = true; count++; }
+ else{ out << name << '\t'; keptCount++; }
+
+ for(int j=0;j<i;j++){
+ if (m->control_pressed) { inPhylip.close(); out.close(); return 0; }
+ inPhylip >> distance;
+ if (!ignoreRow) {
+ //is this a column we want
+ if(rows.count(j) != 0) { out << distance << '\t'; }
+ }
+ }
+ if (!ignoreRow) { out << endl; }
+ }
+ }
+ else{
+ for(int i=0;i<nseqs;i++){
+ inPhylip >> name;
+
+ bool ignoreRow = false;
+
+ if (names.count(name) != 0) { ignoreRow = true; count++; }
+ else{ out << name << '\t'; keptCount++; }
+
+ for(int j=0;j<nseqs;j++){
+ if (m->control_pressed) { inPhylip.close(); out.close(); return 0; }
+ inPhylip >> distance;
+ if (!ignoreRow) {
+ //is this a column we want
+ if(rows.count(j) != 0) { out << distance << '\t'; }
+ }
+ }
+ if (!ignoreRow) { out << endl; }
+ }
+ }
+ inPhylip.close();
+ out.close();
+
+ if (keptCount == 0) { m->mothurOut("Your file contains ONLY distances related to groups or sequences listed in the accnos file."); m->mothurOutEndLine(); }
+ else if (count != names.size()) {
+ m->mothurOut("[WARNING]: Your accnos file contains " + toString(names.size()) + " groups or sequences, but I only found " + toString(count) + " of them in the phylip file."); m->mothurOutEndLine();
+ //rewrite with new number
+ m->renameFile(outputFileName, outputFileName+".temp");
+ ofstream out2;
+ m->openOutputFile(outputFileName, out2);
+ out2 << keptCount << endl;
+
+ ifstream in3;
+ m->openInputFile(outputFileName+".temp", in3);
+ in3 >> nseqs; m->gobble(in3);
+ char buffer[4096];
+ while (!in3.eof()) {
+ in3.read(buffer, 4096);
+ out2.write(buffer, in3.gcount());
+ }
+ in3.close();
+ out2.close();
+ m->mothurRemove(outputFileName+".temp");
+ }
+
+ m->mothurOut("Removed " + toString(count) + " groups or sequences from your phylip file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveDistsCommand", "readPhylip");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveDistsCommand::readColumn(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(columnfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(columnfile));
+ variables["[extension]"] = m->getExtension(columnfile);
+ string outputFileName = getOutputFileName("column", variables);
+ outputTypes["column"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(columnfile, in);
+
+ set<string> removeNames;
+ string firstName, secondName;
+ float distance;
+ bool wrote = false;
+ while (!in.eof()) {
+
+ if (m->control_pressed) { out.close(); in.close(); return 0; }
+
+ in >> firstName >> secondName >> distance; m->gobble(in);
+
+ //is either names in the accnos file
+ if (names.count(firstName) != 0) {
+ removeNames.insert(firstName);
+ if (names.count(secondName) != 0) { removeNames.insert(secondName); } }
+ else if (names.count(secondName) != 0) {
+ removeNames.insert(secondName);
+ if (names.count(firstName) != 0) { removeNames.insert(firstName); } }
+ else {
+ wrote = true;
+ out << firstName << '\t' << secondName << '\t' << distance << endl;
+ }
+ }
+ in.close();
+ out.close();
+
+ if (!wrote) { m->mothurOut("Your file contains ONLY distances related to groups or sequences listed in the accnos file."); m->mothurOutEndLine(); }
+ else if (removeNames.size() != names.size()) {
+ m->mothurOut("[WARNING]: Your accnos file contains " + toString(names.size()) + " groups or sequences, but I only found " + toString(removeNames.size()) + " of them in the column file."); m->mothurOutEndLine();
+ }
+
+ m->mothurOut("Removed " + toString(removeNames.size()) + " groups or sequences from your column file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveDistsCommand", "readColumn");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff