--- /dev/null
+/*
+ * binsequencecommand.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 4/3/09.
+ * Copyright 2009 Schloss Lab UMASS Amhers. All rights reserved.
+ *
+ */
+
+#include "binsequencecommand.h"
+
+
+//**********************************************************************************************************************
+vector<string> BinSeqCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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, "BinSeqCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string BinSeqCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The bin.seqs command parameters are list, fasta, name, label and group. The fasta and list are required, unless you have a valid current list and fasta file.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and are separated by dashes.\n";
+ helpString += "The bin.seqs command should be in the following format: bin.seqs(fasta=yourFastaFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n";
+ helpString += "Example bin.seqs(fasta=amazon.fasta, group=amazon.groups, name=amazon.names).\n";
+ helpString += "The default value for label is all lines in your inputfile.\n";
+ helpString += "The bin.seqs command outputs a .fasta file for each distance you specify appending the OTU number to each name.\n";
+ helpString += "If you provide a groupfile, then it also appends the sequences group to the name.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+BinSeqCommand::BinSeqCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+BinSeqCommand::BinSeqCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+ labels.clear();
+
+ //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["fasta"] = 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("list");
+ //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["list"] = 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 found") { //if there is a current phylip file, use it
+ 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 fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not found") {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ else if (listfile == "not open") { listfile = ""; abort = true; }
+ else { m->setListFile(listfile); }
+
+ //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(listfile); //if user entered a file with a path then preserve it
+ }
+
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ namesfile = validParameter.validFile(parameters, "name", true);
+ if (namesfile == "not open") { namesfile = ""; abort = true; }
+ else if (namesfile == "not found") { namesfile = ""; }
+ else { m->setNameFile(namesfile); }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ if (namesfile == ""){
+ vector<string> files; files.push_back(fastafile);
+ parser.getNameFile(files);
+ }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "BinSeqCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+BinSeqCommand::~BinSeqCommand(){}
+//**********************************************************************************************************************
+
+int BinSeqCommand::execute(){
+ try {
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int error = 0;
+
+ fasta = new FastaMap();
+ if (groupfile != "") {
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+ }
+
+ //read fastafile
+ fasta->readFastaFile(fastafile);
+
+ //if user gave a namesfile then use it
+ if (namesfile != "") {
+ readNamesFile();
+ }
+
+ input = new InputData(listfile, "list");
+ list = input->getListVector();
+ string lastLabel = list->getLabel();
+
+ if (m->control_pressed) { delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ error = process(list);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ error = process(list);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input->getListVector();
+ }
+
+ if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel);
+
+ error = process(list);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; delete fasta; if (groupfile != "") { delete groupMap; } return 0; }
+
+ delete list;
+ }
+
+ delete input;
+ delete fasta;
+ if (groupfile != "") { delete groupMap; }
+
+ 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();
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+void BinSeqCommand::readNamesFile() {
+ try {
+ vector<string> dupNames;
+ m->openInputFile(namesfile, inNames);
+
+ string name, names, sequence;
+
+ while(inNames){
+ inNames >> name; //read from first column A
+ inNames >> names; //read from second column A,B,C,D
+
+ dupNames.clear();
+
+ //parse names into vector
+ m->splitAtComma(names, dupNames);
+
+ //store names in fasta map
+ sequence = fasta->getSequence(name);
+ for (int i = 0; i < dupNames.size(); i++) {
+ fasta->push_back(dupNames[i], sequence);
+ }
+
+ m->gobble(inNames);
+ }
+ inNames.close();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "readNamesFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//return 1 if error, 0 otherwise
+int BinSeqCommand::process(ListVector* list) {
+ try {
+ string binnames, name, sequence;
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".fasta";
+ m->openOutputFile(outputFileName, out);
+
+ //save to output list of output file names
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
+
+ m->mothurOut(list->getLabel()); m->mothurOutEndLine();
+
+ //for each bin in the list vector
+ for (int i = 0; i < list->size(); i++) {
+
+ if (m->control_pressed) { return 1; }
+
+ binnames = list->get(i);
+ while (binnames.find_first_of(',') != -1) {
+ name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+
+ //do work for that name
+ sequence = fasta->getSequence(name);
+ if (sequence != "not found") {
+ //if you don't have groups
+ if (groupfile == "") {
+ name = name + "\t" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(name);
+ if (group == "not found") {
+ m->mothurOut(name + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }else{
+ name = name + "\t" + group + "\t" + toString(i+1);
+ out << ">" << name << endl;
+ out << sequence << endl;
+ }
+ }
+ }else {
+ m->mothurOut(name + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }
+
+ }
+
+ //get last name
+ sequence = fasta->getSequence(binnames);
+ if (sequence != "not found") {
+ //if you don't have groups
+ if (groupfile == "") {
+ binnames = binnames + "\t" + toString(i+1);
+ out << ">" << binnames << endl;
+ out << sequence << endl;
+ }else {//if you do have groups
+ string group = groupMap->getGroup(binnames);
+ if (group == "not found") {
+ m->mothurOut(binnames + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }else{
+ binnames = binnames + "\t" + group + "\t" + toString(i+1);
+ out << ">" << binnames << endl;
+ out << sequence << endl;
+ }
+ }
+ }else {
+ m->mothurOut(binnames + " is missing from your fasta or name file. Please correct. "); m->mothurOutEndLine();
+ return 1;
+ }
+ }
+
+ out.close();
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BinSeqCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff