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|
/*
* 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"
#include "inputdata.h"
//**********************************************************************************************************************
vector<string> RemoveGroupsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT","fasta",false,false,true); parameters.push_back(pfasta);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup);
CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); 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, "RemoveGroupsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string RemoveGroupsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, count, list, taxonomy, design or sharedfile.\n";
helpString += "It outputs a file containing the sequences NOT in the those specified groups, or with a sharedfile eliminates the groups you selected.\n";
helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group or count parameter is required, unless you have a current group or count file or are using a sharedfile.\n";
helpString += "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";
helpString += "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";
helpString += "The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n";
helpString += "Example remove.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n";
helpString += "or remove.groups(groups=pasture, fasta=amazon.fasta, 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, "RemoveGroupsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string RemoveGroupsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
else if (type == "name") { pattern = "[filename],pick,[extension]"; }
else if (type == "group") { pattern = "[filename],pick,[extension]"; }
else if (type == "count") { pattern = "[filename],pick,[extension]"; }
else if (type == "list") { pattern = "[filename],pick,[extension]"; }
else if (type == "shared") { pattern = "[filename],[tag],pick,[extension]"; }
else if (type == "design") { pattern = "[filename],[tag],pick,[extension]"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
RemoveGroupsCommand::RemoveGroupsCommand(){
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;
outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
exit(1);
}
}
//**********************************************************************************************************************
RemoveGroupsCommand::RemoveGroupsCommand(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;
outputTypes["count"] = 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; }
}
it = parameters.find("count");
//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["count"] = inputDir + it->second; }
}
}
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
if (accnosfile == "not open") { accnosfile = ""; 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") { listfile = ""; 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); }
designfile = validParameter.validFile(parameters, "design", true);
if (designfile == "not open") { designfile = ""; abort = true; }
else if (designfile == "not found") { designfile = ""; }
else { m->setDesignFile(designfile); }
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); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
if ((namefile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
}
if ((groupfile != "") && (countfile != "")) {
m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
}
if ((sharedfile == "") && (groupfile == "") && (designfile == "") && (countfile == "")) {
//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 {
countfile = m->getCountTableFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current groupfile, countfile 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 {
countfile = m->getCountTableFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You have no current groupfile, designfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
}
}
}
}
}
}
if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file containing group names or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
if ((fastafile == "") && (namefile == "") && (countfile == "") && (groupfile == "") && (designfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design, count or list."); m->mothurOutEndLine(); abort = true; }
if (((groupfile == "") && (countfile == "")) && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group or count file."); m->mothurOutEndLine(); abort = true; }
if (countfile == "") {
if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
parser.getNameFile(files);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get groups you want to remove
if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
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
vector<string> namesGroups = groupMap->getNamesOfGroups();
vector<string> checkedGroups;
for (int i = 0; i < Groups.size(); i++) {
if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
else { m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
}
if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
else {
Groups = checkedGroups;
m->setGroups(Groups);
}
//fill names with names of sequences that are from the groups we want to remove
fillNames();
delete groupMap;
}else if (countfile != ""){
if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
}
CountTable ct;
ct.readTable(countfile, true, false);
if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
vector<string> gNamesOfGroups = ct.getNamesOfGroups();
SharedUtil util;
util.setGroups(Groups, gNamesOfGroups);
vector<string> namesOfSeqs = ct.getNamesOfSeqs();
sort(Groups.begin(), Groups.end());
for (int i = 0; i < namesOfSeqs.size(); i++) {
vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
names.insert(namesOfSeqs[i]);
}
}
}
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 (countfile != "") { readCount(); }
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); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
}
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); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
variables["[extension]"] = m->getExtension(fastafile);
string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(fastafile, in);
string name;
bool wroteSomething = false;
int removedCount = 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);
}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);
}else { removedCount++; }
}
}
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);
m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readFasta");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::readShared(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
//get group names from sharedfile so we can set Groups to the groupNames we want to keep
//that way we can take advantage of the reads in inputdata and sharedRabundVector
InputData* tempInput = new InputData(sharedfile, "sharedfile");
vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
variables["[extension]"] = m->getExtension(sharedfile);
//save m->Groups
vector<string> allGroupsNames = m->getAllGroups();
vector<string> mothurOutGroups = m->getGroups();
vector<string> groupsToKeep;
for (int i = 0; i < allGroupsNames.size(); i++) {
if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
groupsToKeep.push_back(allGroupsNames[i]);
}
}
if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->setGroups(mothurOutGroups); delete tempInput; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
//reset read
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
delete tempInput;
m->setGroups(groupsToKeep);
m->clearAllGroups();
m->saveNextLabel = "";
m->printedSharedHeaders = false;
m->currentSharedBinLabels.clear();
m->sharedBinLabelsInFile.clear();
InputData input(sharedfile, "sharedfile");
lookup = input.getSharedRAbundVectors();
bool wroteSomething = false;
while(lookup[0] != NULL) {
variables["[tag]"] = lookup[0]->getLabel();
string outputFileName = getOutputFileName("shared", variables);
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();
}
m->setGroups(mothurOutGroups);
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("Removed groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readShared");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::readList(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
variables["[extension]"] = m->getExtension(listfile);
ifstream in;
m->openInputFile(listfile, in);
bool wroteSomething = false;
int removedCount = 0;
while(!in.eof()){
removedCount = 0;
//read in list vector
ListVector list(in);
variables["[tag]"] = list.getLabel();
string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
vector<string> binLabels = list.getLabels();
vector<string> newBinLabels;
//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 + ","; }
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 + ",";
}else { removedCount++; }
}
}
//get last name
if (names.count(binnames) == 0) { newNames += binnames + ","; }
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 + ",";
}else { removedCount++; }
}
//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);
newBinLabels.push_back(binLabels[i]);
}
}
//print new listvector
if (newList.getNumBins() != 0) {
wroteSomething = true;
newList.setLabels(newBinLabels);
newList.printHeaders(out);
newList.print(out);
}
m->gobble(in);
out.close();
}
in.close();
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
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); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
variables["[extension]"] = m->getExtension(namefile);
string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(namefile, in);
string name, firstCol, secondCol;
bool wroteSomething = false;
int removedCount = 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]);
}
}
removedCount += parsedNames.size()-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 contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine();
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); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
variables["[extension]"] = m->getExtension(groupfile);
string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(groupfile, in);
string name, group;
bool wroteSomething = false;
int removedCount = 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;
}else { removedCount++; }
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);
m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readGroup");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::readCount(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
variables["[extension]"] = m->getExtension(countfile);
string outputFileName = getOutputFileName("count", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(countfile, in);
bool wroteSomething = false;
int removedCount = 0;
string headers = m->getline(in); m->gobble(in);
vector<string> columnHeaders = m->splitWhiteSpace(headers);
vector<string> groups;
map<int, string> originalGroupIndexes;
map<string, int> GroupIndexes;
set<int> indexOfGroupsChosen;
for (int i = 2; i < columnHeaders.size(); i++) { groups.push_back(columnHeaders[i]); originalGroupIndexes[i-2] = columnHeaders[i]; }
//sort groups to keep consistent with how we store the groups in groupmap
sort(groups.begin(), groups.end());
for (int i = 0; i < groups.size(); i++) { GroupIndexes[groups[i]] = i; }
vector<string> groupsToKeep;
for (int i = 0; i < groups.size(); i++) {
if (!m->inUsersGroups(groups[i], Groups)) { groupsToKeep.push_back(groups[i]); }
}
sort(groupsToKeep.begin(), groupsToKeep.end());
out << "Representative_Sequence\ttotal\t";
for (int i = 0; i < groupsToKeep.size(); i++) { out << groupsToKeep[i] << '\t'; indexOfGroupsChosen.insert(GroupIndexes[groupsToKeep[i]]); }
out << endl;
string name; int oldTotal;
while (!in.eof()) {
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; m->gobble(in); in >> oldTotal; m->gobble(in);
if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(oldTotal) + "\n"); }
if (names.count(name) == 0) {
//if group info, then read it
vector<int> selectedCounts; int thisTotal = 0; int temp;
for (int i = 0; i < groups.size(); i++) {
int thisIndex = GroupIndexes[originalGroupIndexes[i]];
in >> temp; m->gobble(in);
if (indexOfGroupsChosen.count(thisIndex) != 0) { //we want this group
selectedCounts.push_back(temp); thisTotal += temp;
}
}
out << name << '\t' << thisTotal << '\t';
for (int i = 0; i < selectedCounts.size(); i++) { out << selectedCounts[i] << '\t'; }
out << endl;
wroteSomething = true;
removedCount+= (oldTotal - thisTotal);
}else { m->getline(in); removedCount += oldTotal; }
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["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " sequences from your count file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readCount");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::readDesign(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile));
variables["[extension]"] = m->getExtension(designfile);
string outputFileName = getOutputFileName("design", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(designfile, in);
string name, group;
bool wroteSomething = false;
int removedCount = 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;
}else { removedCount++; }
m->gobble(in);
}
in.close();
out.close();
if (wroteSomething == false) { m->mothurOut("Your file contains only groups from the groups you wish to remove."); m->mothurOutEndLine(); }
outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readDesign");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveGroupsCommand::readTax(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
variables["[extension]"] = m->getExtension(taxfile);
string outputFileName = getOutputFileName("taxonomy", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
m->openInputFile(taxfile, in);
string name, tax;
bool wroteSomething = false;
int removedCount = 0;
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;
}else { removedCount++; } }
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);
m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "readTax");
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]);
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "fillNames");
exit(1);
}
}
//**********************************************************************************************************************
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