--- /dev/null
+/*
+ * getsharedotucommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 9/22/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getsharedotucommand.h"
+#include "sharedutilities.h"
+
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
+ CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
+ CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
+ 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, "GetSharedOTUCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetSharedOTUCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required, unless you have valid current files.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ helpString += "The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n";
+ helpString += "If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n";
+ helpString += "If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n";
+ helpString += "If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n";
+ helpString += "The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n";
+ helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
+ helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
+ helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
+ helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+ helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+ helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
+ helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSharedOTUCommand::GetSharedOTUCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSharedOTUCommand::GetSharedOTUCommand(string option) {
+ try {
+
+ abort = false; calledHelp = false;
+ unique = true;
+ allLines = 1;
+
+ //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;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = 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("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("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
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") {
+ listfile = m->getListFile();
+ if (listfile != "") { format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { format = "list"; m->setListFile(listfile); }
+
+ 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("No valid current group file. You must provide a group file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }else { m->setGroupFile(groupfile); }
+
+ if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); 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") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ output = validParameter.validFile(parameters, "output", false);
+ if (output == "not found") { output = ""; }
+ else if (output == "default") { output = ""; }
+
+ groups = validParameter.validFile(parameters, "unique", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ userGroups = "unique." + groups;
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
+
+ }
+
+ groups = validParameter.validFile(parameters, "shared", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ userGroups = groups;
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
+ unique = false;
+ }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+ else { m->setFastaFile(fastafile); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int GetSharedOTUCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ groupMap = new GroupMap(groupfile);
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; return 0; }
+
+ if (m->control_pressed) { delete groupMap; return 0; }
+
+ if (Groups.size() == 0) {
+ Groups = groupMap->getNamesOfGroups();
+
+ //make string for outputfile name
+ userGroups = "unique.";
+ for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
+ userGroups = userGroups.substr(0, userGroups.length()-1);
+ }else{
+ //sanity check for group names
+ SharedUtil util;
+ vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, namesOfGroups);
+ groupMap->setNamesOfGroups(namesOfGroups);
+ }
+
+ //put groups in map to find easier
+ for(int i = 0; i < Groups.size(); i++) {
+ groupFinder[Groups[i]] = Groups[i];
+ }
+
+ if (fastafile != "") {
+ ifstream inFasta;
+ m->openInputFile(fastafile, inFasta);
+
+ while(!inFasta.eof()) {
+ if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
+
+ Sequence seq(inFasta); m->gobble(inFasta);
+ if (seq.getName() != "") { seqs.push_back(seq); }
+ }
+ inFasta.close();
+ }
+
+ ListVector* lastlist = NULL;
+ string lastLabel = "";
+
+ //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;
+
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) {
+ if (lastlist != NULL) { delete lastlist; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete groupMap; return 0;
+ }
+
+ list = new ListVector(in);
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+ m->mothurOut(list->getLabel());
+ process(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ m->mothurOut(lastlist->getLabel());
+ process(lastlist);
+
+ processedLabels.insert(lastlist->getLabel());
+ userLabels.erase(lastlist->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ if (lastlist != NULL) { delete lastlist; }
+ lastlist = list;
+ }
+
+ in.close();
+
+ //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) {
+ m->mothurOut(lastlist->getLabel());
+ process(lastlist);
+
+ processedLabels.insert(lastlist->getLabel());
+ userLabels.erase(lastlist->getLabel());
+ }
+
+
+ //reset groups parameter
+ m->clearGroups();
+
+ if (lastlist != NULL) { delete lastlist; }
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; }
+
+ //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); }
+ }
+
+ if (output == "accnos") {
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+ }
+
+ 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, "GetSharedOTUCommand", "execute");
+ exit(1);
+ }
+}
+/***********************************************************/
+int GetSharedOTUCommand::process(ListVector* shared) {
+ try {
+
+ map<string, string> fastaMap;
+
+ ofstream outNames;
+ string outputFileNames;
+
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+ if (output != "accnos") {
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
+ }else {
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
+ }
+ m->openOutputFile(outputFileNames, outNames);
+
+ bool wroteSomething = false;
+ int num = 0;
+
+ //go through each bin, find out if shared
+ for (int i = 0; i < shared->getNumBins(); i++) {
+ if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
+
+ bool uniqueOTU = true;
+
+ map<string, int> atLeastOne;
+ for (int f = 0; f < Groups.size(); f++) {
+ atLeastOne[Groups[f]] = 0;
+ }
+
+ vector<string> namesOfSeqsInThisBin;
+
+ string names = shared->get(i);
+ while ((names.find_first_of(',') != -1)) {
+ string name = names.substr(0,names.find_first_of(','));
+ names = names.substr(names.find_first_of(',')+1, names.length());
+
+ //find group
+ string seqGroup = groupMap->getGroup(name);
+ if (output != "accnos") {
+ namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
+ }else { namesOfSeqsInThisBin.push_back(name); }
+
+ if (seqGroup == "not found") { m->mothurOut(name + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
+
+ //is this seq in one of hte groups we care about
+ it = groupFinder.find(seqGroup);
+ if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
+ else { atLeastOne[seqGroup]++; }
+ }
+
+ //get last name
+ string seqGroup = groupMap->getGroup(names);
+ if (output != "accnos") {
+ namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
+ }else { namesOfSeqsInThisBin.push_back(names); }
+
+ if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
+
+ //is this seq in one of hte groups we care about
+ it = groupFinder.find(seqGroup);
+ if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
+ else { atLeastOne[seqGroup]++; }
+
+
+ //make sure you have at least one seq from each group you want
+ bool sharedByAll = true;
+ map<string, int>::iterator it2;
+ for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
+ if (it2->second == 0) { sharedByAll = false; }
+ }
+
+ //if the user wants unique bins and this is unique then print
+ //or this the user wants shared bins and this bin is shared then print
+ if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
+
+ wroteSomething = true;
+ num++;
+
+ //output list of names
+ for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
+ outNames << namesOfSeqsInThisBin[j] << endl;
+
+ if (fastafile != "") {
+ if (output != "accnos") {
+ string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
+ seqName = seqName.substr(0,seqName.find_last_of('|'));
+ fastaMap[seqName] = namesOfSeqsInThisBin[j]; //fastaMap needs to contain just the seq name for output later
+ }else {
+ fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
+ }
+ }
+ }
+ }
+ }
+
+ outNames.close();
+
+ if (!wroteSomething) {
+ m->mothurRemove(outputFileNames);
+ string outputString = "\t" + toString(num) + " - No otus shared by groups";
+
+ string groupString = "";
+ for (int h = 0; h < Groups.size(); h++) {
+ groupString += " " + Groups[h];
+ }
+
+ outputString += groupString + ".";
+ m->mothurOut(outputString); m->mothurOutEndLine();
+ }else {
+ m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
+ outputNames.push_back(outputFileNames);
+ if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
+ else { outputTypes["accnos"].push_back(outputFileNames); }
+ }
+
+ //if fasta file provided output new fasta file
+ if ((fastafile != "") && wroteSomething) {
+ if (outputDir == "") { outputDir += m->hasPath(fastafile); }
+ string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+ ofstream outFasta;
+ m->openOutputFile(outputFileFasta, outFasta);
+ outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
+
+ for (int k = 0; k < seqs.size(); k++) {
+ if (m->control_pressed) { outFasta.close(); return 0; }
+
+ //if this is a sequence we want, output it
+ it = fastaMap.find(seqs[k].getName());
+ if (it != fastaMap.end()) {
+
+ if (output != "accnos") {
+ outFasta << ">" << it->second << endl;
+ }else {
+ outFasta << ">" << it->first << endl;
+ }
+
+ outFasta << seqs[k].getAligned() << endl;
+ }
+ }
+
+ outFasta.close();
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "process");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
projects / mothur.git / blobdiff