//**********************************************************************************************************************
int GetSeqsCommand::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 selectedCount = 0;
string headers = m->getline(in); m->gobble(in);
out << headers << endl;
string test = headers; vector<string> pieces = m->splitWhiteSpace(test);
string name, rest; int thisTotal; rest = "";
while (!in.eof()) {
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
in >> name; m->gobble(in);
in >> thisTotal; m->gobble(in);
if (pieces.size() > 2) { rest = m->getline(in); m->gobble(in); }
if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
if (names.count(name) != 0) {
out << name << '\t' << thisTotal << '\t' << rest << endl;
wroteSomething = true;
selectedCount+= thisTotal;
}
}
in.close();
out.close();
//check for groups that have been eliminated
CountTable ct;
if (ct.testGroups(outputFileName)) {
ct.readTable(outputFileName, true, false);
ct.printTable(outputFileName);
}
if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
m->mothurOut("Selected " + toString(selectedCount) + " sequences from your count file."); m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSeqsCommand", "readCount");
exit(1);
}
}
//**********************************************************************************************************************
ClassifyOtuCommand::ClassifyOtuCommand(string option) {
try{
abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//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["constaxonomy"] = tempOutNames;
outputTypes["taxsummary"] = tempOutNames;
//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("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("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("reftaxonomy");
//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["reftaxonomy"] = 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("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; }
}
}
//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 = ""; }
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not found") {
//if there is a current list file, use it
listfile = m->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (listfile == "not open") { abort = true; }
else { m->setListFile(listfile); }
taxfile = validParameter.validFile(parameters, "taxonomy", true);
if (taxfile == "not found") { //if there is a current list file, use it
taxfile = m->getTaxonomyFile();
if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (taxfile == "not open") { abort = true; }
else { m->setTaxonomyFile(taxfile); }
refTaxonomy = validParameter.validFile(parameters, "reftaxonomy", true);
if (refTaxonomy == "not found") { refTaxonomy = ""; m->mothurOut("reftaxonomy is not required, but if given will keep the rankIDs in the summary file static."); m->mothurOutEndLine(); }
else if (refTaxonomy == "not open") { abort = true; }
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") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { m->setGroupFile(groupfile); }
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;
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; allLines = 1; }
else {
if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
basis = validParameter.validFile(parameters, "basis", false);
if (basis == "not found") { basis = "otu"; }
if ((basis != "otu") && (basis != "sequence")) { m->mothurOut("Invalid option for basis. basis options are otu and sequence, using otu."); m->mothurOutEndLine(); }
string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "51"; }
m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "probs", false); if (temp == "not found"){ temp = "true"; }
probs = m->isTrue(temp);
temp = validParameter.validFile(parameters, "persample", false); if (temp == "not found"){ temp = "f"; }
persample = m->isTrue(temp);
if ((groupfile == "") && (countfile == "")) { if (persample) { m->mothurOut("persample is only valid with a group file, or count file with group information. Setting persample=f.\n"); persample = false; }
}
if (countfile != "") {
CountTable cts;
if (!cts.testGroups(countfile)) {
if (persample) { m->mothurOut("persample is only valid with a group file, or count file with group information. Setting persample=f.\n"); persample = false; }
}
}
if ((cutoff < 51) || (cutoff > 100)) { m->mothurOut("cutoff must be above 50, and no greater than 100."); m->mothurOutEndLine(); abort = true; }
if (countfile == "") {
if (namefile == ""){
vector<string> files; files.push_back(taxfile);
parser.getNameFile(files);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "ClassifyOtuCommand", "ClassifyOtuCommand");
exit(1);
}
}
int MergeGroupsCommand::processCountFile(DesignMap*& designMap){
try {
CountTable countTable;
if (!countTable.testGroups(countfile)) { m->mothurOut("[ERROR]: your countfile contains no group information, please correct.\n"); m->setControl_pressed(true); return 0; }
//read countTable
countTable.readTable(countfile, true, false);
//fill Groups - checks for "all" and for any typo groups
vector<string> nameGroups = countTable.getNamesOfGroups();
if (Groups.size() == 0) { Groups = nameGroups; }
vector<string> dnamesGroups = designMap->getNamesGroups();
//sanity check
bool error = false;
if (nameGroups.size() == dnamesGroups.size()) { //at least there are the same number
//is every group in counttable also in designmap
for (int i = 0; i < nameGroups.size(); i++) {
if (m->getControl_pressed()) { break; }
if (!util.inUsersGroups(nameGroups[i], dnamesGroups)) { error = true; break; }
}
}
if (error) { m->mothurOut("[ERROR]: Your countfile does not contain the same groups as your design file, please correct\n"); m->setControl_pressed(true); return 0; }
//user selected groups - remove some groups from table
if (Groups.size() != nameGroups.size()) {
for (int i = 0; i < nameGroups.size(); i++) {
if (!util.inUsersGroups(nameGroups[i], Groups)) { countTable.removeGroup(nameGroups[i]); }
}
}
//ask again in case order changed
nameGroups = countTable.getNamesOfGroups();
int numGroups = nameGroups.size();
//create new table
CountTable newTable;
vector<string> treatments = designMap->getCategory();
map<string, vector<int> > clearedMap;
for (int i = 0; i < treatments.size(); i++) {
newTable.addGroup(treatments[i]);
vector<int> temp;
clearedMap[treatments[i]] = temp;
}
treatments = newTable.getNamesOfGroups();
set<string> namesToRemove;
vector<string> namesOfSeqs = countTable.getNamesOfSeqs();
for (int i = 0; i < namesOfSeqs.size(); i++) {
if (m->getControl_pressed()) { break; }
vector<int> thisSeqsCounts = countTable.getGroupCounts(namesOfSeqs[i]);
map<string, vector<int> > thisSeqsMap = clearedMap;
for (int j = 0; j < numGroups; j++) {
thisSeqsMap[designMap->get(nameGroups[j])].push_back(thisSeqsCounts[j]);
}
//create new counts for seq for new table
vector<int> newCounts; int totalAbund = 0;
for (int j = 0; j < treatments.size(); j++){
int abund = mergeAbund(thisSeqsMap[treatments[j]]);
newCounts.push_back(abund); //order matters, add in count for each treatment in new table.
totalAbund += abund;
}
//add seq to new table
if(totalAbund == 0) {
namesToRemove.insert(namesOfSeqs[i]);
}else { newTable.push_back(namesOfSeqs[i], newCounts); }
}
if (error) { m->setControl_pressed(true); return 0; }
//remove sequences zeroed out by median method
if (namesToRemove.size() != 0) {
//print names
ofstream out;
string accnosFile = "accnosFile.temp";
util.openOutputFile(accnosFile, out);
//output to .accnos file
for (set<string>::iterator it = namesToRemove.begin(); it != namesToRemove.end(); it++) {
if (m->getControl_pressed()) { out.close(); util.mothurRemove(accnosFile); return 0; }
out << *it << endl;
}
out.close();
//run remove.seqs
string inputString = "accnos=" + accnosFile + ", fasta=" + fastafile;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: remove.seqs(" + inputString + ")"); m->mothurOutEndLine();
current->setMothurCalling(true);
Command* removeCommand = new RemoveSeqsCommand(inputString);
removeCommand->execute();
map<string, vector<string> > filenames = removeCommand->getOutputFiles();
delete removeCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
util.mothurRemove(accnosFile);
}
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += util.hasPath(countfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(countfile));
variables["[extension]"] = util.getExtension(countfile);
string outputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
newTable.printTable(outputFileName);
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeGroupsCommand", "processCountFile");
exit(1);
}
}
//**********************************************************************************************************************
SharedCommand::SharedCommand(string option) {
try {
abort = false; calledHelp = false; pickedGroups=false;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (!validParameter.isValidParameter(it->first, myArray, it->second)) { abort = true; }
}
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.valid(parameters, "inputdir");
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
path = util.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("count");
//user has given a template file
if(it != parameters.end()){
path = util.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; }
}
it = parameters.find("biom");
//user has given a template file
if(it != parameters.end()){
path = util.hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["biom"] = inputDir + it->second; }
}
}
vector<string> tempOutNames;
outputTypes["shared"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["map"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.valid(parameters, "outputdir"); if (outputDir == "not found"){ outputDir = ""; }
//check for required parameters
listfile = validParameter.validFile(parameters, "list");
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { current->setListFile(listfile); }
biomfile = validParameter.validFile(parameters, "biom");
if (biomfile == "not open") { biomfile = ""; abort = true; }
else if (biomfile == "not found") { biomfile = ""; }
else { current->setBiomFile(biomfile); }
ordergroupfile = validParameter.validFile(parameters, "ordergroup");
if (ordergroupfile == "not open") { abort = true; }
else if (ordergroupfile == "not found") { ordergroupfile = ""; }
groupfile = validParameter.validFile(parameters, "group");
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
else { current->setGroupFile(groupfile); }
countfile = validParameter.validFile(parameters, "count");
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
else {
current->setCountFile(countfile);
CountTable temp;
if (!temp.testGroups(countfile)) {
m->mothurOut("\n[WARNING]: Your count file does not have group info, all reads will be assigned to mothurGroup.\n");
temp.readTable(countfile, false, false); //dont read groups
map<string, int> seqs = temp.getNameMap();
CountTable newCountTable;
newCountTable.addGroup("mothurGroup");
for (map<string, int>::iterator it = seqs.begin(); it != seqs.end(); it++) {
vector<int> counts; counts.push_back(it->second);
newCountTable.push_back(it->first, counts);
}
string newCountfileName = util.getRootName(countfile) + "mothurGroup" + util.getExtension(countfile);
newCountTable.printTable(newCountfileName);
current->setCountFile(newCountfileName);
countfile = newCountfileName;
outputNames.push_back(newCountfileName);
}
}
if ((biomfile == "") && (listfile == "") && (countfile == "")) { //you must provide at least one of the following
//is there are current file available for either of these?
//give priority to list, then biom, then count
listfile = current->getListFile();
if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter.\n"); }
else {
biomfile = current->getBiomFile();
if (biomfile != "") { m->mothurOut("Using " + biomfile + " as input file for the biom parameter.\n"); }
else {
countfile = current->getCountFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter.\n"); }
else {
m->mothurOut("[ERROR]: No valid current files. You must provide a list or biom or count file before you can use the make.shared command.\n"); abort = true;
}
}
}
}
else if ((biomfile != "") && (listfile != "")) { m->mothurOut("When executing a make.shared command you must enter ONLY ONE of the following: list or biom.\n"); abort = true; }
if (listfile != "") {
if ((groupfile == "") && (countfile == "")) {
groupfile = current->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter.\n"); }
else {
countfile = current->getCountFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter.\n"); }
else { m->mothurOut("[ERROR]: You need to provide a groupfile or countfile if you are going to use the list format.\n"); abort = true; }
}
}
}
string groups = validParameter.valid(parameters, "groups");
if (groups == "not found") { groups = ""; }
else {
pickedGroups=true;
util.splitAtDash(groups, Groups);
if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }
}
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string label = validParameter.valid(parameters, "label");
if (label == "not found") { label = ""; }
else {
if(label != "all") { util.splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
if ((listfile == "") && (biomfile == "") && (countfile != "")) { //building a shared file from a count file, require label
if (labels.size() == 0) {
m->mothurOut("[ERROR]: You must provide a label when converting a count file to a shared file, please correct.\n"); abort = true;
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SharedCommand", "SharedCommand");
exit(1);
}
}