+++ /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"
-#include "inputdata.h"
-
-//**********************************************************************************************************************
-vector<string> GetGroupsCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
- CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
- CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- 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, "GetGroupsCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetGroupsCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy, design or shared file.\n";
- helpString += "It outputs a file containing the sequences in the those specified groups, or a sharedfile containing only those groups.\n";
- helpString += "The get.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group parameter is required, unless you have a current group file, or are using a shared file.\n";
- helpString += "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";
- helpString += "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";
- helpString += "The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
- helpString += "Example get.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
- helpString += "or get.groups(groups=pasture, fasta=amazon.fasta, group=amazon.groups).\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetGroupsCommand::GetGroupsCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["taxonomy"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["shared"] = tempOutNames;
- outputTypes["design"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetGroupsCommand::GetGroupsCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //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["taxonomy"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- outputTypes["shared"] = tempOutNames;
- outputTypes["design"] = 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; }
- }
-
- it = parameters.find("shared");
- //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["shared"] = inputDir + it->second; }
- }
-
- it = parameters.find("design");
- //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["design"] = 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 = ""; }
- else { m->setAccnosFile(accnosfile); }
-
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { fastafile = ""; abort = true; }
- else if (fastafile == "not found") { fastafile = ""; }
- else { m->setFastaFile(fastafile); }
-
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { namefile = ""; abort = true; }
- else if (namefile == "not found") { namefile = ""; }
- else { m->setNameFile(namefile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { groupfile = ""; abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { m->setListFile(listfile); }
-
- taxfile = validParameter.validFile(parameters, "taxonomy", true);
- if (taxfile == "not open") { taxfile = ""; abort = true; }
- else if (taxfile == "not found") { taxfile = ""; }
- else { m->setTaxonomyFile(taxfile); }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- m->splitAtDash(groups, Groups);
- m->setGroups(Groups);
- }
-
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; }
- else { m->setSharedFile(sharedfile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { groupfile = ""; abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
- designfile = validParameter.validFile(parameters, "design", true);
- if (designfile == "not open") { designfile = ""; abort = true; }
- else if (designfile == "not found") { designfile = ""; }
- else { m->setDesignFile(designfile); }
-
- if ((sharedfile == "") && (groupfile == "") && (designfile == "")) {
- //is there are current file available for any of these?
- if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
- //give priority to group, then shared
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else {
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
- }
- }
- }else {
- //give priority to shared, then group
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else {
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else {
- designfile = m->getDesignFile();
- if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("You have no current groupfile or sharedfile or designfile and one is required."); m->mothurOutEndLine(); abort = true;
- }
- }
- }
- }
- }
-
- 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 == "") && (designfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design or list."); m->mothurOutEndLine(); abort = true; }
- if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
-
- if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
- vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
- parser.getNameFile(files);
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetGroupsCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- //get groups you want to remove
- if (accnosfile != "") { readAccnos(); }
-
- if (groupfile != "") {
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- //make sure groups are valid
- //takes care of user setting groupNames that are invalid or setting groups=all
- SharedUtil* util = new SharedUtil();
- vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, gNamesOfGroups);
- groupMap->setNamesOfGroups(gNamesOfGroups);
- delete util;
-
- //fill names with names of sequences that are from the groups we want to remove
- fillNames();
-
- delete groupMap;
- }
-
- if (m->control_pressed) { 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 (sharedfile != "") { readShared(); }
- if (designfile != "") { readDesign(); }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
-
- 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();
-
- //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); }
- }
-
- itTypes = outputTypes.find("name");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
- }
-
- itTypes = outputTypes.find("group");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
- }
-
- itTypes = outputTypes.find("list");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
- }
-
- itTypes = outputTypes.find("taxonomy");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
- }
-
- itTypes = outputTypes.find("shared");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
- }
-
- itTypes = outputTypes.find("design");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); }
- }
- }
-
- 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;
- int selectedCount = 0;
-
- while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); 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);
- selectedCount++;
- }else{
- //if you are not in the accnos file check if you are a name that needs to be changed
- map<string, string>::iterator it = uniqueToRedundant.find(name);
- if (it != uniqueToRedundant.end()) {
- wroteSomething = true;
- currSeq.setName(it->second);
- currSeq.printSequence(out);
- selectedCount++;
- }
- }
- }
- 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);
-
- m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
-
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "readFasta");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int GetGroupsCommand::readShared(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
-
- InputData input(sharedfile, "sharedfile");
- vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
-
- bool wroteSomething = false;
-
- while(lookup[0] != NULL) {
-
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".pick" + m->getExtension(sharedfile);
- ofstream out;
- m->openOutputFile(outputFileName, out);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- if (m->control_pressed) { out.close(); m->mothurRemove(outputFileName); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
-
- lookup[0]->printHeaders(out);
-
- for (int i = 0; i < lookup.size(); i++) {
- out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
- lookup[i]->print(out);
- wroteSomething = true;
-
- }
-
- //get next line to process
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input.getSharedRAbundVectors();
-
- out.close();
- }
-
- if (wroteSomething == false) { m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine(); }
-
- string groupsString = "";
- for (int i = 0; i < Groups.size()-1; i++) { groupsString += Groups[i] + ", "; }
- groupsString += Groups[Groups.size()-1];
-
- m->mothurOut("Selected groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "readShared");
- 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;
- int selectedCount = 0;
-
- while(!in.eof()){
-
- selectedCount = 0;
-
- //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(); m->mothurRemove(outputFileName); 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 + ","; selectedCount++; }
- else{
- //if you are not in the accnos file check if you are a name that needs to be changed
- map<string, string>::iterator it = uniqueToRedundant.find(name);
- if (it != uniqueToRedundant.end()) {
- newNames += it->second + ",";
- selectedCount++;
- }
- }
- }
-
- //get last name
- if (names.count(binnames) != 0) { newNames += binnames + ","; selectedCount++; }
- else{
- //if you are not in the accnos file check if you are a name that needs to be changed
- map<string, string>::iterator it = uniqueToRedundant.find(binnames);
- if (it != uniqueToRedundant.end()) {
- newNames += it->second + ",";
- selectedCount++;
- }
- }
-
- //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);
-
- m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
-
- 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;
- int selectedCount = 0;
-
- while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); 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]);
- }
- }
-
- selectedCount += validSecond.size();
-
- //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;
- uniqueToRedundant[firstCol] = validSecond[0];
- }
- }
-
- 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);
-
- m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
-
- 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;
- int selectedCount = 0;
-
- while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); 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;
- selectedCount++;
- }
-
- 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);
-
- m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "readGroup");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int GetGroupsCommand::readDesign(){
- try {
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + "pick" + m->getExtension(designfile);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ifstream in;
- m->openInputFile(designfile, in);
- string name, group;
-
- bool wroteSomething = false;
- int selectedCount = 0;
-
- while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
-
- in >> name; //read from first column
- in >> group; //read from second column
-
- //if this name is in the accnos file
- if (m->inUsersGroups(name, Groups)) {
- wroteSomething = true;
- out << name << '\t' << group << endl;
- selectedCount++;
- }
-
- m->gobble(in);
- }
- in.close();
- out.close();
-
- if (wroteSomething == false) { m->mothurOut("Your file does NOT contain groups from the groups you wish to get."); m->mothurOutEndLine(); }
- outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
-
- m->mothurOut("Selected " + toString(selectedCount) + " groups from your design file."); m->mothurOutEndLine();
-
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "readDesign");
- 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(); m->mothurRemove(outputFileName); 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;
- }else{
- //if you are not in the accnos file check if you are a name that needs to be changed
- map<string, string>::iterator it = uniqueToRedundant.find(name);
- if (it != uniqueToRedundant.end()) {
- wroteSomething = true;
- out << it->second << '\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();
-
- m->setGroups(Groups);
-
- }
- 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]);
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetGroupsCommand", "fillNames");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-
projects / mothur.git / blobdiff