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A76714DE126DE45A003F359A /* deuniqueseqscommand.cpp */,
A7DA2050113FECD400BF472F /* filterseqscommand.h */,
A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
+ A75103D6128AE34100ABB831 /* getgroupscommand.h */,
+ A75103D7128AE34100ABB831 /* getgroupscommand.cpp */,
A7DA205B113FECD400BF472F /* getgroupcommand.h */,
A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
A7DA205D113FECD400BF472F /* getlabelcommand.h */,
A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
A7DA20F1113FECD400BF472F /* readtreecommand.h */,
A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+ A751032A128AC93F00ABB831 /* removegroupscommand.h */,
+ A751032B128AC93F00ABB831 /* removegroupscommand.cpp */,
A787A28E124CE1470076EB84 /* removelineagecommand.h */,
A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
#include "pairwiseseqscommand.h"
#include "clusterdoturcommand.h"
#include "subsamplecommand.h"
+#include "removegroupscommand.h"
+#include "getgroupscommand.h"
/*******************************************************/
commands["deunique.seqs"] = "deunique.seqs";
commands["cluster.classic"] = "cluster.classic";
commands["sub.sample"] = "sub.sample";
+ commands["remove.groups"] = "remove.groups";
+ commands["get.groups"] = "get.groups";
commands["pairwise.seqs"] = "MPIEnabled";
commands["pipeline.pds"] = "MPIEnabled";
commands["classify.seqs"] = "MPIEnabled";
else if(commandName == "cluster.fragments") { command = new ClusterFragmentsCommand(optionString); }
else if(commandName == "get.lineage") { command = new GetLineageCommand(optionString); }
else if(commandName == "remove.lineage") { command = new RemoveLineageCommand(optionString); }
+ else if(commandName == "get.groups") { command = new GetGroupsCommand(optionString); }
+ else if(commandName == "remove.groups") { command = new RemoveGroupsCommand(optionString); }
else if(commandName == "fastq.info") { command = new ParseFastaQCommand(optionString); }
else if(commandName == "pipeline.pds") { command = new PipelineCommand(optionString); }
else if(commandName == "deunique.seqs") { command = new DeUniqueSeqsCommand(optionString); }
else if(commandName == "split.groups") { pipecommand = new SplitGroupCommand(optionString); }
else if(commandName == "cluster.fragments") { pipecommand = new ClusterFragmentsCommand(optionString); }
else if(commandName == "get.lineage") { pipecommand = new GetLineageCommand(optionString); }
+ else if(commandName == "get.groups") { pipecommand = new GetGroupsCommand(optionString); }
else if(commandName == "remove.lineage") { pipecommand = new RemoveLineageCommand(optionString); }
+ else if(commandName == "remove.groups") { pipecommand = new RemoveGroupsCommand(optionString); }
else if(commandName == "fastq.info") { pipecommand = new ParseFastaQCommand(optionString); }
else if(commandName == "deunique.seqs") { pipecommand = new DeUniqueSeqsCommand(optionString); }
else if(commandName == "pairwise.seqs") { pipecommand = new PairwiseSeqsCommand(optionString); }
else if(commandName == "cluster.fragments") { shellcommand = new ClusterFragmentsCommand(); }
else if(commandName == "get.lineage") { shellcommand = new GetLineageCommand(); }
else if(commandName == "remove.lineage") { shellcommand = new RemoveLineageCommand(); }
+ else if(commandName == "get.groups") { shellcommand = new GetGroupsCommand(); }
+ else if(commandName == "remove.groups") { shellcommand = new RemoveGroupsCommand(); }
else if(commandName == "fastq.info") { shellcommand = new ParseFastaQCommand(); }
else if(commandName == "deunique.seqs") { shellcommand = new DeUniqueSeqsCommand(); }
else if(commandName == "pairwise.seqs") { shellcommand = new PairwiseSeqsCommand(); }
--- /dev/null
+/*
+ * getgroupscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/10/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "getgroupscommand.h"
+#include "sequence.hpp"
+#include "listvector.hpp"
+#include "sharedutilities.h"
+
+//**********************************************************************************************************************
+vector<string> GetGroupsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","name", "group", "accnos", "groups","list","taxonomy","outputdir","inputdir" };
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetGroupsCommand::GetGroupsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetGroupsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetGroupsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetGroupsCommand::GetGroupsCommand(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","name", "group", "accnos", "groups", "list","taxonomy","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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["list"] = 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("accnos");
+ //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["accnos"] = 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; }
+ }
+
+ it = parameters.find("taxonomy");
+ //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["taxonomy"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { abort = true; }
+ else if (accnosfile == "not found") { accnosfile = ""; }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); abort = true; }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+ taxfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxfile == "not open") { abort = true; }
+ else if (taxfile == "not found") { taxfile = ""; }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+
+ if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
+
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group or list."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void GetGroupsCommand::help(){
+ try {
+ m->mothurOut("The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n");
+ m->mothurOut("It outputs a file containing the sequences in the those specified groups.\n");
+ m->mothurOut("The get.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required.\n");
+ m->mothurOut("You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n");
+ m->mothurOut("The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
+ m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
+ m->mothurOut("or get.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+int GetGroupsCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ //get groups you want to remove
+ if (accnosfile != "") { readAccnos(); }
+
+ //make sure groups are valid
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Groups, groupMap->namesOfGroups);
+ delete util;
+
+ //fill names with names of sequences that are from the groups we want to remove
+ fillNames();
+
+ if (m->control_pressed) { delete groupMap; return 0; }
+
+ //read through the correct file and output lines you want to keep
+ if (namefile != "") { readName(); }
+ if (fastafile != "") { readFasta(); }
+ if (groupfile != "") { readGroup(); }
+ if (listfile != "") { readList(); }
+ if (taxfile != "") { readTax(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOut("Selected " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
+ for (int i = 0; i < Groups.size(); i++) { m->mothurOut(Groups[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ if (outputNames.size() != 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, "GetGroupsCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetGroupsCommand::readFasta(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+ string name;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+
+ currSeq.printSequence(out);
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "readFasta");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetGroupsCommand::readList(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ //read in list vector
+ ListVector list(in);
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+
+ string newNames = "";
+ while (binnames.find_first_of(',') != -1) {
+ string name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+
+ //if that name is in the .accnos file, add it
+ if (names.count(name) != 0) { newNames += name + ","; }
+ }
+
+ //get last name
+ if (names.count(binnames) != 0) { newNames += binnames + ","; }
+
+ //if there are names in this bin add to new list
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "readList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetGroupsCommand::readName(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string name, firstCol, secondCol;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> firstCol; m->gobble(in);
+ in >> secondCol;
+
+ vector<string> parsedNames;
+ m->splitAtComma(secondCol, parsedNames);
+
+ vector<string> validSecond; validSecond.clear();
+ for (int i = 0; i < parsedNames.size(); i++) {
+ if (names.count(parsedNames[i]) != 0) {
+ validSecond.push_back(parsedNames[i]);
+ }
+ }
+
+ //if the name in the first column is in the set then print it and any other names in second column also in set
+ if (names.count(firstCol) != 0) {
+
+ wroteSomething = true;
+
+ out << firstCol << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+
+ //make first name in set you come to first column and then add the remaining names to second column
+ }else {
+
+ //you want part of this row
+ if (validSecond.size() != 0) {
+
+ wroteSomething = true;
+
+ out << validSecond[0] << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+ }
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "readName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetGroupsCommand::readGroup(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(groupfile, in);
+ string name, group;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+ in >> group; //read from second column
+
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+ out << name << '\t' << group << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "readGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetGroupsCommand::readTax(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+ in >> tax; //read from second column
+
+ //if this name is in the accnos file
+ if (names.count(name) != 0) {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "readTax");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void GetGroupsCommand::readAccnos(){
+ try {
+ Groups.clear();
+
+ ifstream in;
+ m->openInputFile(accnosfile, in);
+ string name;
+
+ while(!in.eof()){
+ in >> name;
+
+ Groups.push_back(name);
+
+ m->gobble(in);
+ }
+ in.close();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "readAccnos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetGroupsCommand::fillNames(){
+ try {
+ vector<string> seqs = groupMap->getNamesSeqs();
+
+ for (int i = 0; i < seqs.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ string group = groupMap->getGroup(seqs[i]);
+
+ if (m->inUsersGroups(group, Groups)) {
+ names.insert(seqs[i]);
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetGroupsCommand", "fillNames");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
--- /dev/null
+#ifndef GETGROUPSCOMMAND_H
+#define GETGROUPSCOMMAND_H
+
+/*
+ * getgroupscommand.h
+ * Mothur
+ *
+ * Created by westcott on 11/10/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "groupmap.h"
+
+class GetGroupsCommand : public Command {
+
+public:
+
+ GetGroupsCommand(string);
+ GetGroupsCommand();
+ ~GetGroupsCommand(){}
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
+private:
+ set<string> names;
+ string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+ bool abort;
+ vector<string> outputNames, Groups;
+ map<string, vector<string> > outputTypes;
+ GroupMap* groupMap;
+
+ int readFasta();
+ int readName();
+ int readGroup();
+ void readAccnos();
+ int readList();
+ int readTax();
+ int fillNames();
+
+};
+
+#endif
+
+
+
if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ m->mothurOut("Selected " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
+
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
--- /dev/null
+/*
+ * removegroupscommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/10/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "removegroupscommand.h"
+#include "sequence.hpp"
+#include "listvector.hpp"
+#include "sharedutilities.h"
+
+//**********************************************************************************************************************
+vector<string> RemoveGroupsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta","name", "group", "accnos", "groups","list","taxonomy","outputdir","inputdir" };
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RemoveGroupsCommand::RemoveGroupsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RemoveGroupsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RemoveGroupsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RemoveGroupsCommand::RemoveGroupsCommand(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","name", "group", "accnos", "groups", "list","taxonomy","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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["list"] = 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("accnos");
+ //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["accnos"] = 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; }
+ }
+
+ it = parameters.find("taxonomy");
+ //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["taxonomy"] = inputDir + it->second; }
+ }
+ }
+
+
+ //check for required parameters
+ accnosfile = validParameter.validFile(parameters, "accnos", true);
+ if (accnosfile == "not open") { abort = true; }
+ else if (accnosfile == "not found") { accnosfile = ""; }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); abort = true; }
+
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+
+ taxfile = validParameter.validFile(parameters, "taxonomy", true);
+ if (taxfile == "not open") { abort = true; }
+ else if (taxfile == "not found") { taxfile = ""; }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+
+ if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
+
+ if ((fastafile == "") && (namefile == "") && (groupfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group or list."); m->mothurOutEndLine(); abort = true; }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void RemoveGroupsCommand::help(){
+ try {
+ m->mothurOut("The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n");
+ m->mothurOut("It outputs a file containing the sequences NOT in the those specified groups.\n");
+ m->mothurOut("The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required.\n");
+ m->mothurOut("You must also provide an accnos containing the list of groups to remove or set the groups parameter to the groups you wish to remove.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like removed. You can separate group names with dashes.\n");
+ m->mothurOut("The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n");
+ m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n");
+ m->mothurOut("or remove.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "help");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+int RemoveGroupsCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ //get groups you want to remove
+ if (accnosfile != "") { readAccnos(); }
+
+ //make sure groups are valid
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ SharedUtil* util = new SharedUtil();
+ util->setGroups(Groups, groupMap->namesOfGroups);
+ delete util;
+
+ //fill names with names of sequences that are from the groups we want to remove
+ fillNames();
+
+ if (m->control_pressed) { delete groupMap; return 0; }
+
+ //read through the correct file and output lines you want to keep
+ if (namefile != "") { readName(); }
+ if (fastafile != "") { readFasta(); }
+ if (groupfile != "") { readGroup(); }
+ if (listfile != "") { readList(); }
+ if (taxfile != "") { readTax(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
+ for (int i = 0; i < Groups.size(); i++) { m->mothurOut(Groups[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ if (outputNames.size() != 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, "RemoveGroupsCommand", "execute");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readFasta(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+ string name;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ if (name != "") {
+ //if this name is in the accnos file
+ if (names.count(name) == 0) {
+ wroteSomething = true;
+
+ currSeq.printSequence(out);
+ }
+ }
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readFasta");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readList(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ //read in list vector
+ ListVector list(in);
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+
+ string newNames = "";
+ while (binnames.find_first_of(',') != -1) {
+ string name = binnames.substr(0,binnames.find_first_of(','));
+ binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
+
+ //if that name is in the .accnos file, add it
+ if (names.count(name) == 0) { newNames += name + ","; }
+ }
+
+ //get last name
+ if (names.count(binnames) == 0) { newNames += binnames + ","; }
+
+ //if there are names in this bin add to new list
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readName(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(namefile, in);
+ string name, firstCol, secondCol;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> firstCol; m->gobble(in);
+ in >> secondCol;
+
+ vector<string> parsedNames;
+ m->splitAtComma(secondCol, parsedNames);
+
+ vector<string> validSecond; validSecond.clear();
+ for (int i = 0; i < parsedNames.size(); i++) {
+ if (names.count(parsedNames[i]) == 0) {
+ validSecond.push_back(parsedNames[i]);
+ }
+ }
+
+ //if the name in the first column is in the set then print it and any other names in second column also in set
+ if (names.count(firstCol) == 0) {
+
+ wroteSomething = true;
+
+ out << firstCol << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+
+ //make first name in set you come to first column and then add the remaining names to second column
+ }else {
+
+ //you want part of this row
+ if (validSecond.size() != 0) {
+
+ wroteSomething = true;
+
+ out << validSecond[0] << '\t';
+
+ //you know you have at least one valid second since first column is valid
+ for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
+ out << validSecond[validSecond.size()-1] << endl;
+ }
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readGroup(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(groupfile, in);
+ string name, group;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+ in >> group; //read from second column
+
+ //if this name is in the accnos file
+ if (names.count(name) == 0) {
+ wroteSomething = true;
+ out << name << '\t' << group << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readGroup");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readTax(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+ if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ in >> name; //read from first column
+ in >> tax; //read from second column
+
+ //if this name is in the accnos file
+ if (names.count(name) == 0) {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readTax");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void RemoveGroupsCommand::readAccnos(){
+ try {
+ Groups.clear();
+
+ ifstream in;
+ m->openInputFile(accnosfile, in);
+ string name;
+
+ while(!in.eof()){
+ in >> name;
+
+ Groups.push_back(name);
+
+ m->gobble(in);
+ }
+ in.close();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readAccnos");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveGroupsCommand::fillNames(){
+ try {
+ vector<string> seqs = groupMap->getNamesSeqs();
+
+ for (int i = 0; i < seqs.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ string group = groupMap->getGroup(seqs[i]);
+
+ if (m->inUsersGroups(group, Groups)) {
+ names.insert(seqs[i]);
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "fillNames");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+
+
--- /dev/null
+#ifndef REMOVEGROUPSCOMMAND_H
+#define REMOVEGROUPSCOMMAND_H
+
+/*
+ * removegroupscommand.h
+ * Mothur
+ *
+ * Created by westcott on 11/10/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "groupmap.h"
+
+class RemoveGroupsCommand : public Command {
+
+public:
+
+ RemoveGroupsCommand(string);
+ RemoveGroupsCommand();
+ ~RemoveGroupsCommand(){}
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
+private:
+ set<string> names;
+ string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+ bool abort;
+ vector<string> outputNames, Groups;
+ map<string, vector<string> > outputTypes;
+ GroupMap* groupMap;
+
+ int readFasta();
+ int readName();
+ int readGroup();
+ void readAccnos();
+ int readList();
+ int readTax();
+ int fillNames();
+
+};
+
+#endif
+
+
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ m->mothurOut("Removed " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
+
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
projects / mothur.git / commitdiff