--- /dev/null
+//
+// renameseqscommand.cpp
+// Mothur
+//
+// Created by SarahsWork on 5/28/13.
+// Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#include "renameseqscommand.h"
+#include "sequence.hpp"
+#include "groupmap.h"
+
+//**********************************************************************************************************************
+vector<string> RenameSeqsCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ 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, "RenameSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RenameSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The rename.seqs command reads a fastafile and groupfile with an optional namefile, and creates files with the sequence names concatenated with the group. For example if a line in the group file is 'seq1 group1', the new sequence name will be seq1_group1.\n";
+ helpString += "The rename.seqs command parameters are fasta, name and group. Fasta and group are required, unless a current file is available for both.\n";
+ helpString += "The rename.seqs command should be in the following format: \n";
+ helpString += "rename.seqs(fasta=yourFastaFile, group=yourGroupFile) \n";
+ helpString += "Example rename.seqs(fasta=abrecovery.unique.fasta, group=abrecovery.group).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RenameSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RenameSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],renamed,[extension]"; }
+ else if (type == "name") { pattern = "[filename],renamed,[extension]"; }
+ else if (type == "group") { pattern = "[filename],renamed,[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, "RenameSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RenameSeqsCommand::RenameSeqsCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RenameSeqsCommand", "RenameSeqsCommand");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+RenameSeqsCommand::RenameSeqsCommand(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; }
+ }
+
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = 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 = ""; }
+ else {
+ string path;
+ it = parameters.find("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //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["name"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //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["group"] = inputDir + it->second; }
+ }
+
+ }
+
+
+ //check for required parameters
+ fastaFile = validParameter.validFile(parameters, "fasta", true);
+ if (fastaFile == "not open") { abort = true; }
+ else if (fastaFile == "not found") {
+ fastaFile = m->getFastaFile();
+ if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setFastaFile(fastaFile); }
+
+ //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 = "";
+ outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
+ }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") {
+ 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 and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setGroupFile(groupfile); }
+
+ //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 = ""; }
+
+ nameFile = validParameter.validFile(parameters, "name", true);
+ if (nameFile == "not open") { abort = true; }
+ else if (nameFile == "not found"){ nameFile =""; }
+ else { m->setNameFile(nameFile); }
+
+ if (nameFile == "") {
+ vector<string> files; files.push_back(fastaFile);
+ parser.getNameFile(files);
+ }
+
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RenameSeqsCommand", "RenameSeqsCommand");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int RenameSeqsCommand::execute() {
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ GroupMap groupMap(groupfile);
+ groupMap.readMap();
+
+ //prepare filenames and open files
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastaFile); }
+ string outFastaFile = thisOutputDir + m->getRootName(m->getSimpleName(fastaFile));
+ map<string, string> variables;
+ variables["[filename]"] = outFastaFile;
+ variables["[extension]"] = m->getExtension(fastaFile);
+ outFastaFile = getOutputFileName("fasta", variables);
+ outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+
+ ofstream outFasta;
+ m->openOutputFile(outFastaFile, outFasta);
+
+ ifstream in;
+ m->openInputFile(fastaFile, in);
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+ string group = groupMap.getGroup(seq.getName());
+ if (group == "not found") { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your group file, please correct.\n"); m->control_pressed = true; }
+ else {
+ string newName = seq.getName() + "_" + group;
+ seq.setName(newName);
+ seq.printSequence(outFasta);
+ }
+
+ }
+ in.close();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ bool notDone = true;
+ if (nameFile != "") {
+ thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(nameFile); }
+ string outNameFile = thisOutputDir + m->getRootName(m->getSimpleName(nameFile));
+ variables["[filename]"] = outNameFile;
+ variables["[extension]"] = m->getExtension(nameFile);
+ outNameFile = getOutputFileName("group", variables);
+ outputNames.push_back(outNameFile); outputTypes["name"].push_back(outNameFile);
+
+ ofstream outName;
+ m->openOutputFile(outNameFile, outName);
+
+ map<string, vector<string> > nameMap;
+ m->readNames(nameFile, nameMap);
+
+ //process name file changing names
+ for (map<string, vector<string> >::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
+ for (int i = 0; i < (it->second).size()-1; i++) {
+ if (m->control_pressed) { break; }
+ string group = groupMap.getGroup((it->second)[i]);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[i] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
+ else {
+ string newName = (it->second)[i] + "_" + group;
+ groupMap.renameSeq((it->second)[i], newName); //change in group file
+ (it->second)[i] = newName; //change in namefile
+ }
+ if (i == 0) { outName << (it->second)[i] << '\t' << (it->second)[i] << ','; }
+ else { outName << (it->second)[i] << ','; }
+ }
+
+ //print last one
+ if ((it->second).size() == 1) {
+ string group = groupMap.getGroup((it->second)[0]);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[0] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
+ else {
+ string newName = (it->second)[0] + "_" + group;
+ groupMap.renameSeq((it->second)[0], newName); //change in group file
+ (it->second)[0] = newName; //change in namefile
+
+ outName << (it->second)[0] << '\t' << (it->second)[0] << endl;
+ }
+ }
+ else {
+ string group = groupMap.getGroup((it->second)[(it->second).size()-1]);
+ if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[(it->second).size()-1] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
+ else {
+ string newName = (it->second)[(it->second).size()-1] + "_" + group;
+ groupMap.renameSeq((it->second)[(it->second).size()-1], newName); //change in group file
+ (it->second)[(it->second).size()-1] = newName; //change in namefile
+
+ outName << (it->second)[(it->second).size()-1] << endl;
+ }
+ }
+ }
+ notDone = false;
+ outName.close();
+ }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ if (notDone) {
+ vector<string> seqs = groupMap.getNamesSeqs();
+ for (int i = 0; i < seqs.size(); i++) {
+ if (m->control_pressed) { break; }
+ string group = groupMap.getGroup(seqs[i]);
+ string newName = seqs[i] + "_" + group;
+ groupMap.renameSeq(seqs[i], newName);
+ }
+ }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ string outGroupFile = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[filename]"] = outGroupFile;
+ variables["[extension]"] = m->getExtension(groupfile);
+ outGroupFile = getOutputFileName("group", variables);
+ outputNames.push_back(outGroupFile); outputTypes["group"].push_back(outGroupFile);
+
+ ofstream outGroup;
+ m->openOutputFile(outGroupFile, outGroup);
+ groupMap.print(outGroup);
+ outGroup.close();
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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(); }
+ m->mothurOutEndLine();
+
+ //set fasta file as new current fastafile
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+ }
+
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RenameSeqsCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+
projects / mothur.git / blobdiff