--- /dev/null
+/*
+ * degapseqscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 6/21/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "degapseqscommand.h"
+#include "sequence.hpp"
+
+//***************************************************************************************************************
+
+DegapSeqsCommand::DegapSeqsCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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; }
+ }
+
+ //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 = ""; }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", false);
+ if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the degap.seqs command."); m->mothurOutEndLine(); abort = true; }
+ else {
+ splitAtDash(fastafile, fastaFileNames);
+
+ //go through files and make sure they are good, if not, then disregard them
+ for (int i = 0; i < fastaFileNames.size(); i++) {
+ if (inputDir != "") {
+ string path = hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = openInputFile(fastaFileNames[i], in);
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }
+ }
+
+ //make sure there is at least one valid file left
+ if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
+ }
+
+
+ //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 += hasPath(fastafile); //if user entered a file with a path then preserve it
+ }
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void DegapSeqsCommand::help(){
+ try {
+ m->mothurOut("The degap.seqs command reads a fastafile and removes all gap characters.\n");
+ m->mothurOut("The degap.seqs command parameter is fasta.\n");
+ m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
+ m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
+ m->mothurOut("The degap.seqs command should be in the following format: \n");
+ m->mothurOut("degap.seqs(fasta=yourFastaFile) \n");
+ m->mothurOut("Example: degap.seqs(fasta=abrecovery.align) \n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "help");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
+DegapSeqsCommand::~DegapSeqsCommand(){ /* do nothing */ }
+
+//***************************************************************************************************************
+
+
+int DegapSeqsCommand::execute(){
+ try{
+
+ if (abort == true) { return 0; }
+
+ for (int s = 0; s < fastaFileNames.size(); s++) {
+
+ m->mothurOut("Degapping sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
+ ifstream inFASTA;
+ openInputFile(fastaFileNames[s], inFASTA);
+
+ ofstream outFASTA;
+ string degapFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ng.fasta";
+ openOutputFile(degapFile, outFASTA);
+
+ while(!inFASTA.eof()){
+ if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+
+ Sequence currSeq(inFASTA); gobble(inFASTA);
+ if (currSeq.getName() != "") {
+ outFASTA << ">" << currSeq.getName() << endl;
+ outFASTA << currSeq.getUnaligned() << endl;
+ }
+ }
+ inFASTA.close();
+ outFASTA.close();
+
+ outputNames.push_back(degapFile);
+
+ if (m->control_pressed) { remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); 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, "DegapSeqsCommand", "execute");
+ exit(1);
+ }
+}
+
+//***************************************************************************************************************
+
--- /dev/null
+/*
+ * getrelabundcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 6/21/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getrelabundcommand.h"
+
+//**********************************************************************************************************************
+
+GetRelAbundCommand::GetRelAbundCommand(string option) {
+ try {
+ globaldata = GlobalData::getInstance();
+ abort = false;
+ allLines = 1;
+ labels.clear();
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string AlignArray[] = {"groups","label","scale","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+
+ 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; }
+ }
+
+ //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 += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getSharedFile() == "")) {
+ m->mothurOut("You must read a list and a group, or a shared file before you can use the get.relabund command."); m->mothurOutEndLine(); abort = true;
+ }
+
+ //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") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "totalgroup"; }
+
+ if ((scale != "totalgroup") && (scale != "totalgroup") && (scale != "totalgroup") && (scale != "totalgroup")) {
+ m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+void GetRelAbundCommand::help(){
+ try {
+ m->mothurOut("The get.relabund command can only be executed after a successful read.otu command of a list and group or shared file.\n");
+ m->mothurOut("The get.relabund command parameters are groups, scale and label. No parameters are required.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
+ m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
+ m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
+ m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
+ m->mothurOut("Example get.relabund(groups=A-B-C, scale=log10).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
+ m->mothurOut("The get.relabund command outputs a .relabund file.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+GetRelAbundCommand::~GetRelAbundCommand(){
+}
+
+//**********************************************************************************************************************
+
+int GetRelAbundCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ string outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "relabund";
+ ofstream out;
+ openOutputFile(outputFileName, out);
+
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ //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;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ getRelAbundance(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ getRelAbundance(lookup, out);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookup[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); 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) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+
+ getRelAbundance(lookup, out);
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ //reset groups parameter
+ globaldata->Groups.clear();
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ out.close();
+
+ if (m->control_pressed) { remove(outputFileName.c_str()); return 0;}
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*> thisLookUp, ofstream& out){
+ try {
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
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