+++ /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);
- }
-}
-
-//**********************************************************************************************************************