*/
#include "getoturepcommand.h"
+#include "readphylip.h"
+#include "readcolumn.h"
+#include "formatphylip.h"
+#include "formatcolumn.h"
+#include "sharedutilities.h"
+
+
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareName(repStruct left, repStruct right){
+ return (left.name < right.name);
+}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareBin(repStruct left, repStruct right){
+ return (left.bin < right.bin);
+}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareSize(repStruct left, repStruct right){
+ return (left.size < right.size);
+}
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareGroup(repStruct left, repStruct right){
+ return (left.group < right.group);
+}
//**********************************************************************************************************************
-GetOTURepCommand::GetOTURepCommand(string option){
+vector<string> GetOTURepCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","name",false,true, true); parameters.push_back(plist);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,false, true); parameters.push_back(pfasta);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false, true); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false, true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "ColumnName","count",false,false, true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false, true); parameters.push_back(pgroup);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","",false,false, true); parameters.push_back(pcolumn);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pweighted("weighted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pweighted);
+ CommandParameter psorted("sorted", "Multiple", "none-name-bin-size-group", "none", "", "", "","",false,false); parameters.push_back(psorted);
+ CommandParameter pmethod("method", "Multiple", "distance-abundance", "distance", "", "", "","",false,false); parameters.push_back(pmethod);
+ CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+ 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, "GetOTURepCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetOTURepCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.oturep command parameters are phylip, column, list, fasta, name, group, count, large, weighted, cutoff, precision, groups, sorted, method and label. The list parameter is required, as well as phylip or column and name if you are using method=distance. If method=abundance a name or count file is required.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n";
+ helpString += "The phylip or column parameter is required for method=distance, but only one may be used. If you use a column file the name or count filename is required. \n";
+ helpString += "The method parameter allows you to select the method of selecting the representative sequence. Choices are distance and abundance. The distance method finds the sequence with the smallest maximum distance to the other sequences. If tie occurs the sequence with smallest average distance is selected. The abundance method chooses the most abundant sequence in the OTU as the representative.\n";
+ helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
+ helpString += "The get.oturep command should be in the following format: get.oturep(phylip=yourDistanceMatrix, fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n";
+ helpString += "Example get.oturep(phylip=amazon.dist, fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups).\n";
+ helpString += "The default value for label is all labels in your inputfile.\n";
+ helpString += "The sorted parameter allows you to indicate you want the output sorted. You can sort by sequence name, bin number, bin size or group. The default is no sorting, but your options are name, number, size, or group.\n";
+ helpString += "The large parameter allows you to indicate that your distance matrix is too large to fit in RAM. The default value is false.\n";
+ helpString += "The weighted parameter allows you to indicate that want to find the weighted representative. You must provide a namesfile to set weighted to true. The default value is false.\n";
+ helpString += "The representative is found by selecting the sequence that has the smallest total distance to all other sequences in the OTU. If a tie occurs the smallest average distance is used.\n";
+ helpString += "For weighted = false, mothur assumes the distance file contains only unique sequences, the list file may contain all sequences, but only the uniques are considered to become the representative. If your distance file contains all the sequences it would become weighted=true.\n";
+ helpString += "For weighted = true, mothur assumes the distance file contains only unique sequences, the list file must contain all sequences, all sequences are considered to become the representative, but unique name will be used in the output for consistency.\n";
+ helpString += "If your distance file contains all the sequence and you do not provide a name file, the weighted representative will be given, unless your listfile is unique. If you provide a namefile, then you can select weighted or unweighted.\n";
+ helpString += "The group parameter allows you provide a group file.\n";
+ helpString += "The groups parameter allows you to indicate that you want representative sequences for each group specified for each OTU, group name should be separated by dashes. ex. groups=A-B-C.\n";
+ helpString += "The get.oturep command outputs a .fastarep and .rep.names file for each distance you specify, selecting one OTU representative for each bin.\n";
+ helpString += "If you provide a groupfile, then it also appends the names of the groups present in that bin.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetOTURepCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],[tag],rep.fasta-[filename],[tag],[group],rep.fasta"; }
+ else if (type == "name") { pattern = "[filename],[tag],rep.names-[filename],[tag],[group],rep.names"; }
+ else if (type == "count") { pattern = "[filename],[tag],rep.count_table-[filename],[tag],[group],rep.count_table"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetOTURepCommand::GetOTURepCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "GetOTURepCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetOTURepCommand::GetOTURepCommand(string option) {
try{
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- lines.clear();
- labels.clear();
-
+
//allow user to run help
- if(option == "help") { help(); abort = true; }
-
- else {
- //valid paramters for this command
- string Array[] = {"fasta","list","line","label","name", "group"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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 (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //make sure the user has already run the read.otu command
- if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
- cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl;
- abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["count"] = 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("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("phylip");
+ //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["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("column");
+ //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["column"] = 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("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
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { cout << "fasta is a required parameter for the get.oturep command." << endl; abort = true; }
+ if (fastafile == "not found") { fastafile = ""; }
else if (fastafile == "not open") { abort = true; }
+ else { m->setFastaFile(fastafile); }
listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not found") { cout << "list is a required parameter for the get.oturep command." << endl; abort = true; }
+ if (listfile == "not found") {
+ 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 list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (listfile == "not open") { abort = true; }
+ else { m->setListFile(listfile); }
+
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not found") { phylipfile = ""; }
+ else if (phylipfile == "not open") { abort = true; }
+ else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not found") { columnfile = ""; }
+ else if (columnfile == "not open") { abort = true; }
+ else { distFile = columnfile; format = "column"; m->setColumnFile(columnfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ hasGroups = false;
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not found") { countfile = ""; }
+ else if (countfile == "not open") { abort = true; countfile = ""; }
+ else {
+ m->setCountTableFile(countfile);
+ ct.readTable(countfile, true);
+ if (ct.hasGroupInfo()) { hasGroups = true; }
+ }
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "distance"; }
+ if ((method != "distance") && (method != "abundance")) {
+ m->mothurOut(method + " is not a valid option for the method parameter. The only options are: distance and abundance, aborting."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if (method == "distance") {
+ if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
+ //give priority to column, then phylip
+ columnfile = m->getColumnFile();
+ if (columnfile != "") { distFile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+ else {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { distFile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a phylip or column file before you can use the get.oturep command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a get.oturep command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
+
+ if (columnfile != "") {
+ if ((namefile == "") && (countfile == "")) {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name 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 need to provide a namefile or countfile if you are going to use the column format."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ }
+ }else if (method == "abundance") {
+ if ((namefile == "") && (countfile == "")) {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name 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 need to provide a namefile or countfile if you are going to use the abundance method."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+ if ((phylipfile != "") || (columnfile != "")) {
+ m->mothurOut("[WARNING]: A phylip or column file is not needed to use the abundance method, ignoring."); m->mothurOutEndLine();
+ phylipfile = ""; columnfile = "";
+ }
+ }
+
+ 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...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
+ if (label == "not found") { label = ""; allLines = 1; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if ((line == "") && (label == "")) {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- lines = globaldata->lines;
+
+ sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found"){ sorted = ""; }
+ if (sorted == "none") { sorted=""; }
+ if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {
+ m->mothurOut(sorted + " is not a valid option for the sorted parameter. The only options are: name, bin, size and group. I will not sort."); m->mothurOutEndLine();
+ sorted = "";
}
+
+
- namesfile = validParameter.validFile(parameters, "name", true);
- if (namesfile == "not open") { abort = true; }
- else if (namesfile == "not found") { namesfile = ""; }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else {
- //read in group map info.
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+ if ((sorted == "group") && ((groupfile == "")&& !hasGroups)) {
+ m->mothurOut("You must provide a groupfile or have a count file with group info to sort by group. I will not sort."); m->mothurOutEndLine();
+ sorted = "";
}
-
- if (abort == false) {
- if(globaldata->gSparseMatrix != NULL) { matrix = globaldata->gSparseMatrix; }
-
- //globaldata->gListVector bin 0 = first name read in distance matrix, globaldata->gListVector bin 1 = second name read in distance matrix
- if(globaldata->gListVector != NULL) {
-
- vector<string> names;
- string binnames;
- //map names to rows in sparsematrix
- for (int i = 0; i < globaldata->gListVector->size(); i++) {
- names.clear();
- binnames = globaldata->gListVector->get(i);
-
- splitAtComma(binnames, names);
-
- for (int j = 0; j < names.size(); j++) {
- nameToIndex[names[j]] = i;
- }
-
- }
- }else { cout << "error, no listvector." << endl; }
-
-// openInputFile(fastafile, in);
- fasta = new FastaMap();
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ if ((groupfile == "") && (!hasGroups)) {
+ m->mothurOut("You must provide a groupfile to use groups."); m->mothurOutEndLine();
+ abort = true;
+ }else {
+ m->splitAtDash(groups, Groups);
+ }
}
-
+ m->setGroups(Groups);
+
+ string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
+ large = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "weighted", false); if (temp == "not found") { temp = "f"; }
+ weighted = m->isTrue(temp);
+
+ if ((weighted) && (namefile == "")) { m->mothurOut("You cannot set weighted to true unless you provide a namesfile."); m->mothurOutEndLine(); abort = true; }
+
+ temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, precision);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10.0"; }
+ m->mothurConvert(temp, cutoff);
+ cutoff += (5 / (precision * 10.0));
}
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function GetOTURepCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetOTURepCommand", "GetOTURepCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetOTURepCommand class function GetOTURepCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-void GetOTURepCommand::help(){
- try {
- cout << "The get.oturep command can only be executed after a successful read.dist command." << "\n";
- cout << "The get.oturep command parameters are list, fasta, name, group, line and label. The fasta and list parameters are required, and you may not use line and label at the same time." << "\n";
- cout << "The line and label allow you to select what distance levels you would like a output files created for, and are separated by dashes." << "\n";
- cout << "The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, line=yourLines, label=yourLabels)." << "\n";
- cout << "Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, line=1-3-5, name=amazon.names)." << "\n";
- cout << "The default value for line and label are all lines in your inputfile." << "\n";
- cout << "The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin." << "\n";
- cout << "If you provide a groupfile, then it also appends the names of the groups present in that bin." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GetOTURepCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetOTURepCommand::~GetOTURepCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete fasta;
- if (groupfile != "") {
- delete groupMap; globaldata->gGroupmap = NULL;
- }
- }
}
//**********************************************************************************************************************
int GetOTURepCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- int count = 1;
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
int error;
+ list = NULL;
- //read fastafile
- fasta->readFastaFile(fastafile);
-
- in.close();
+ if (method=="distance") {
+ readDist();
+ if ((!weighted) && (namefile != "")) { readNamesFile(weighted); }
+ }else {
+ //map name -> abundance for use if findRepAbund
+ if (namefile != "") { nameToIndex = m->readNames(namefile); }
+ }
+
+ if (m->control_pressed) { if (method=="distance") { if (large) { inRow.close(); m->mothurRemove(distFile); } }return 0; }
+
+ if (groupfile != "") {
+ //read in group map info.
+ groupMap = new GroupMap(groupfile);
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; m->mothurOut("Error reading your groupfile. Proceeding without groupfile."); m->mothurOutEndLine(); groupfile = ""; }
+
+ if (Groups.size() != 0) {
+ SharedUtil util;
+ vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, gNamesOfGroups, "getoturep");
+ groupMap->setNamesOfGroups(gNamesOfGroups);
+ }
+ }else if (hasGroups) {
+ if (Groups.size() != 0) {
+ SharedUtil util;
+ vector<string> gNamesOfGroups = ct.getNamesOfGroups();
+ util.setGroups(Groups, gNamesOfGroups, "getoturep");
+ }
+ }
+
+ //done with listvector from matrix
+ if (list != NULL) { delete list; }
+
+ InputData input(listfile, "list");
+ list = input.getListVector();
+ string lastLabel = list->getLabel();
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ if (m->control_pressed) { if (method=="distance") { if (large) { inRow.close(); m->mothurRemove(distFile); } } delete list; return 0; }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (allLines == 1 || labels.count(list->getLabel()) == 1){
+ m->mothurOut(list->getLabel() + "\t" + toString(list->size())); m->mothurOutEndLine();
+ error = process(list);
+ if (error == 1) { return 0; } //there is an error in hte input files, abort command
+
+ if (m->control_pressed) {
+ if (method=="distance") { if (large) { inRow.close(); m->mothurRemove(distFile); } }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete list; return 0;
+ }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector(lastLabel);
+ m->mothurOut(list->getLabel() + "\t" + toString(list->size())); m->mothurOutEndLine();
+ error = process(list);
+ if (error == 1) { return 0; } //there is an error in hte input files, abort command
+
+ if (m->control_pressed) {
+ if (method=="distance") { if (large) { inRow.close(); m->mothurRemove(distFile); } }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete list; return 0;
+ }
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector();
+ }
+
+ //output error messages about any remaining user labels
+ bool needToRun = false;
+ for (set<string>::iterator it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + (*it));
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input.getListVector(lastLabel);
+ m->mothurOut(list->getLabel() + "\t" + toString(list->size())); m->mothurOutEndLine();
+ error = process(list);
+ delete list;
+ if (error == 1) { return 0; } //there is an error in hte input files, abort command
+
+ if (m->control_pressed) {
+ if (method=="distance") { if (large) { inRow.close(); m->mothurRemove(distFile); } }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete list; return 0;
+ }
+ }
+
+ //close and remove formatted matrix file
+ if (method=="distance") { if (large) { inRow.close(); m->mothurRemove(distFile); } if (!weighted) { nameFileMap.clear(); } }
+
+ if (fastafile != "") {
+ //read fastafile
+ FastaMap* fasta = new FastaMap();
+ fasta->readFastaFile(fastafile);
+
+ //if user gave a namesfile then use it
+ if (namefile != "") { readNamesFile(fasta); }
+
+ //output create and output the .rep.fasta files
+ map<string, string>::iterator itNameFile;
+ for (itNameFile = outputNameFiles.begin(); itNameFile != outputNameFiles.end(); itNameFile++) {
+ processFastaNames(itNameFile->first, itNameFile->second, fasta);
+ }
+ delete fasta;
+ }else {
+ //output create and output the .rep.fasta files
+ map<string, string>::iterator itNameFile;
+ for (itNameFile = outputNameFiles.begin(); itNameFile != outputNameFiles.end(); itNameFile++) {
+ processNames(itNameFile->first, itNameFile->second);
+ }
+ }
+
+
+ if (groupfile != "") { delete groupMap; }
- //set format to list so input can get listvector
- globaldata->setFormat("list");
+ if (m->control_pressed) { return 0; }
- //if user gave a namesfile then use it
- if (namesfile != "") {
- readNamesFile();
+ //set fasta file as new current fastafile - use first one??
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
- //read list file
- read = new ReadOTUFile(listfile);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- list = globaldata->gListVector;
- string lastLabel = list->getLabel();
+ itTypes = outputTypes.find("name");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = labels;
- set<int> userLines = lines;
-
+ 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();
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetOTURepCommand::readDist() {
+ try {
+
+ if (!large) {
+ //read distance files
+ if (format == "column") { readMatrix = new ReadColumnMatrix(distFile); }
+ else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(distFile); }
+ else { m->mothurOut("File format error."); m->mothurOutEndLine(); return 0; }
- if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
- cout << list->getLabel() << '\t' << count << endl;
- error = process(list);
- if (error == 1) { return 0; } //there is an error in hte input files, abort command
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- userLines.erase(count);
- }
+ readMatrix->setCutoff(cutoff);
+
+ NameAssignment* nameMap = NULL;
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ readMatrix->read(nameMap);
+ }else if (countfile != "") {
+ readMatrix->read(&ct);
+ }else {
+ readMatrix->read(nameMap);
+ }
+
+ if (m->control_pressed) { delete readMatrix; return 0; }
+
+ list = readMatrix->getListVector();
+ SparseDistanceMatrix* matrix = readMatrix->getDMatrix();
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- delete list;
- list = input->getListVector(lastLabel);
-
- cout << list->getLabel() << '\t' << count << endl;
- error = process(list);
- if (error == 1) { return 0; } //there is an error in hte input files, abort command
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
+ // Create a data structure to quickly access the distance information.
+ // It consists of a vector of distance maps, where each map contains
+ // all distances of a certain sequence. Vector and maps are accessed
+ // via the index of a sequence in the distance matrix
+ seqVec = vector<SeqMap>(list->size());
+ for (int i = 0; i < matrix->seqVec.size(); i++) {
+ for (int j = 0; j < matrix->seqVec[i].size(); j++) {
+ if (m->control_pressed) { delete readMatrix; return 0; }
+ //already added everyone else in row
+ if (i < matrix->seqVec[i][j].index) { seqVec[i][matrix->seqVec[i][j].index] = matrix->seqVec[i][j].dist; }
+ }
}
+ //add dummy map for unweighted calc
+ SeqMap dummy;
+ seqVec.push_back(dummy);
+ delete matrix;
+ delete readMatrix;
+ delete nameMap;
- lastLabel = list->getLabel();
+ if (m->control_pressed) { return 0; }
+ }else {
+ //process file and set up indexes
+ if (format == "column") { formatMatrix = new FormatColumnMatrix(distFile); }
+ else if (format == "phylip") { formatMatrix = new FormatPhylipMatrix(distFile); }
+ else { m->mothurOut("File format error."); m->mothurOutEndLine(); return 0; }
- delete list;
- list = input->getListVector();
- count++;
- }
-
- //output error messages about any remaining user labels
- bool needToRun = false;
- for (set<string>::iterator it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLabel) != 1) {
- cout << ". I will use " << lastLabel << "." << endl;
- needToRun = true;
- }else {
- cout << ". Please refer to " << lastLabel << "." << endl;
- }
+ formatMatrix->setCutoff(cutoff);
+
+ NameAssignment* nameMap = NULL;
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ formatMatrix->read(nameMap);
+ }else if (countfile != "") {
+ formatMatrix->read(&ct);
+ }else {
+ formatMatrix->read(nameMap);
+ }
+
+ if (m->control_pressed) { delete formatMatrix; return 0; }
+
+ list = formatMatrix->getListVector();
+ distFile = formatMatrix->getFormattedFileName();
+
+ //positions in file where the distances for each sequence begin
+ //rowPositions[1] = position in file where distance related to sequence 1 start.
+ rowPositions = formatMatrix->getRowPositions();
+ rowPositions.push_back(-1); //dummy row for unweighted calc
+
+ delete formatMatrix;
+ delete nameMap;
+
+ //openfile for getMap to use
+ m->openInputFile(distFile, inRow);
+
+ if (m->control_pressed) { inRow.close(); m->mothurRemove(distFile); return 0; }
}
- //run last line if you need to
- if (needToRun == true) {
- delete list;
- list = input->getListVector(lastLabel);
-
- cout << list->getLabel() << '\t' << count << endl;
- error = process(list);
- if (error == 1) { return 0; } //there is an error in hte input files, abort command
- delete list;
- }
- delete matrix;
- globaldata->gSparseMatrix = NULL;
- globaldata->gListVector = NULL;
+ //list bin 0 = first name read in distance matrix, list bin 1 = second name read in distance matrix
+ if (list != NULL) {
+ vector<string> names;
+ string binnames;
+ //map names to rows in sparsematrix
+ for (int i = 0; i < list->size(); i++) {
+ names.clear();
+ binnames = list->get(i);
+
+ m->splitAtComma(binnames, names);
+
+ for (int j = 0; j < names.size(); j++) {
+ nameToIndex[names[j]] = i;
+ }
+ }
+ } else { m->mothurOut("error, no listvector."); m->mothurOutEndLine(); }
- return 0;
- }
+ if (m->control_pressed) { if (large) { inRow.close(); m->mothurRemove(distFile); }return 0; }
+
+ return 0;
+ }
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetOTURepCommand", "readDist");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetOTURepCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
-
//**********************************************************************************************************************
-void GetOTURepCommand::readNamesFile() {
+void GetOTURepCommand::readNamesFile(FastaMap*& fasta) {
try {
+ ifstream in;
vector<string> dupNames;
- openInputFile(namesfile, inNames);
+ m->openInputFile(namefile, in);
string name, names, sequence;
- while(inNames){
- inNames >> name; //read from first column A
- inNames >> names; //read from second column A,B,C,D
+ while(!in.eof()){
+ in >> name; //read from first column A
+ in >> names; //read from second column A,B,C,D
dupNames.clear();
//parse names into vector
- splitAtComma(names, dupNames);
+ m->splitAtComma(names, dupNames);
//store names in fasta map
sequence = fasta->getSequence(name);
fasta->push_back(dupNames[i], sequence);
}
- gobble(inNames);
+ m->gobble(in);
}
- inNames.close();
+ in.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetOTURepCommand", "readNamesFile");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetOTURepCommand class function readNamesFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+//read names file to find the weighted rep for each bin
+void GetOTURepCommand::readNamesFile(bool w) {
+ try {
+ ifstream in;
+ vector<string> dupNames;
+ m->openInputFile(namefile, in);
+
+ string name, names, sequence;
+
+ while(!in.eof()){
+ in >> name; m->gobble(in); //read from first column A
+ in >> names; //read from second column A,B,C,D
+
+ dupNames.clear();
+
+ //parse names into vector
+ m->splitAtComma(names, dupNames);
+
+ for (int i = 0; i < dupNames.size(); i++) {
+ nameFileMap[dupNames[i]] = name;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "readNamesFile");
exit(1);
- }
+ }
}
//**********************************************************************************************************************
-string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
+string GetOTURepCommand::findRepAbund(vector<string> names, string group) {
try{
- vector<string> names;
- map<string, float> sums;
- map<int, string> binMap; //subset of namesToIndex - just member of this bin
- string binnames;
- float min = 10000;
- string minName;
- map<string, string> groups;
- map<string, string>::iterator groupIt;
-
- binnames = thisList->get(bin);
-
- //parse names into vector
- splitAtComma(binnames, names);
-
- //if you have a groupfile
- if(groupfile != "") {
- //find the groups that are in this bin
- for (int i = 0; i < names.size(); i++) {
- string groupName = groupMap->getGroup(names[i]);
- if (groupName == "not found") {
- cout << names[i] << " is missing from your group file. Please correct. " << endl;
- groupError = true;
+ vector<string> reps;
+ string rep = "notFound";
+
+ if ((names.size() == 1)) {
+ return names[0];
+ }else{
+ //fill seqIndex and initialize sums
+ int maxAbund = 0;
+ for (int i = 0; i < names.size(); i++) {
+
+ if (m->control_pressed) { return "control"; }
+
+ if (countfile != "") { //if countfile is not blank then we can assume the list file contains only uniques, otherwise we assume list file contains everyone.
+ int numRep = 0;
+ if (group != "") { numRep = ct.getGroupCount(names[i], group); }
+ else { numRep = ct.getGroupCount(names[i]); }
+ if (numRep > maxAbund) {
+ reps.clear();
+ reps.push_back(names[i]);
+ maxAbund = numRep;
+ }else if(numRep == maxAbund) { //tie
+ reps.push_back(names[i]);
+ }
+ }else { //name file used, we assume list file contains all sequences
+ map<string, int>::iterator itNameMap = nameToIndex.find(names[i]);
+ if (itNameMap == nameToIndex.end()) {} //assume that this sequence is not a unique
+ else {
+ if (itNameMap->second > maxAbund) {
+ reps.clear();
+ reps.push_back(names[i]);
+ maxAbund = itNameMap->second;
+ }else if(itNameMap->second == maxAbund) { //tie
+ reps.push_back(names[i]);
+ }
+ }
+ }
+ }
+
+ if (reps.size() == 0) { m->mothurOut("[ERROR]: no rep found, file mismatch?? Quitting.\n"); m->control_pressed = true; }
+ else if (reps.size() == 1) { rep = reps[0]; }
+ else { //tie
+ int index = m->getRandomIndex(reps.size()-1);
+ rep = reps[index];
+ }
+ }
+
+ return rep;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "findRepAbund");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetOTURepCommand::findRep(vector<string> names, string group) {
+ try{
+ //if using abundance
+ if (method == "abundance") { return (findRepAbund(names, group)); }
+ else { //find rep based on distance
+
+ // if only 1 sequence in bin or processing the "unique" label, then
+ // the first sequence of the OTU is the representative one
+ if ((names.size() == 1)) {
+ return names[0];
+ }else{
+ vector<int> seqIndex; //(names.size());
+ map<string, string>::iterator itNameFile;
+ map<string, int>::iterator itNameIndex;
+
+ //fill seqIndex and initialize sums
+ for (size_t i = 0; i < names.size(); i++) {
+ if (weighted) {
+ seqIndex.push_back(nameToIndex[names[i]]);
+ if (countfile != "") { //if countfile is not blank then we can assume the list file contains only uniques, otherwise we assume list file contains everyone.
+ int numRep = 0;
+ if (group != "") { numRep = ct.getGroupCount(names[i], group); }
+ else { numRep = ct.getGroupCount(names[i]); }
+ for (int j = 1; j < numRep; j++) { //don't add yourself again
+ seqIndex.push_back(nameToIndex[names[i]]);
+ }
+ }
+ }else {
+ if (namefile == "") {
+ itNameIndex = nameToIndex.find(names[i]);
+
+ if (itNameIndex == nameToIndex.end()) { // you are not in the distance file and no namesfile, then assume you are not unique
+ if (large) { seqIndex.push_back((rowPositions.size()-1)); }
+ else { seqIndex.push_back((seqVec.size()-1)); }
+ }else {
+ seqIndex.push_back(itNameIndex->second);
+ }
+
+ }else {
+ itNameFile = nameFileMap.find(names[i]);
+
+ if (itNameFile == nameFileMap.end()) {
+ m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
+ }else{
+ string name1 = itNameFile->first;
+ string name2 = itNameFile->second;
+
+ if (name1 == name2) { //then you are unique so add your real dists
+ seqIndex.push_back(nameToIndex[names[i]]);
+ }else { //add dummy
+ if (large) { seqIndex.push_back((rowPositions.size()-1)); }
+ else { seqIndex.push_back((seqVec.size()-1)); }
+ }
+ }
+ }
+ }
+ }
+
+ vector<float> max_dist(seqIndex.size(), 0.0);
+ vector<float> total_dist(seqIndex.size(), 0.0);
+
+ // loop through all entries in seqIndex
+ SeqMap::iterator it;
+ SeqMap currMap;
+ for (size_t i=0; i < seqIndex.size(); i++) {
+ if (m->control_pressed) { return "control"; }
+
+ if (!large) { currMap = seqVec[seqIndex[i]]; }
+ else { currMap = getMap(seqIndex[i]); }
+
+ for (size_t j=0; j < seqIndex.size(); j++) {
+ it = currMap.find(seqIndex[j]);
+ if (it != currMap.end()) {
+ max_dist[i] = max(max_dist[i], it->second);
+ max_dist[j] = max(max_dist[j], it->second);
+ total_dist[i] += it->second;
+ total_dist[j] += it->second;
+ }else{ //if you can't find the distance make it the cutoff
+ max_dist[i] = max(max_dist[i], cutoff);
+ max_dist[j] = max(max_dist[j], cutoff);
+ total_dist[i] += cutoff;
+ total_dist[j] += cutoff;
+ }
+ }
+ }
+
+ // sequence with the smallest maximum distance is the representative
+ //if tie occurs pick sequence with smallest average distance
+ float min = 10000;
+ int minIndex;
+ for (size_t i=0; i < max_dist.size(); i++) {
+ if (m->control_pressed) { return "control"; }
+ if (max_dist[i] < min) {
+ min = max_dist[i];
+ minIndex = i;
+ }else if (max_dist[i] == min) {
+ float currentAverage = total_dist[minIndex] / (float) total_dist.size();
+ float newAverage = total_dist[i] / (float) total_dist.size();
+
+ if (newAverage < currentAverage) {
+ min = max_dist[i];
+ minIndex = i;
+ }
+ }
+ }
+
+ return(names[minIndex]);
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "FindRep");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+int GetOTURepCommand::process(ListVector* processList) {
+ try{
+ string name, sequence;
+ string nameRep;
+
+ //create output file
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+
+ ofstream newNamesOutput;
+ string outputNamesFile;
+ map<string, ofstream*> filehandles;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+
+ if (Groups.size() == 0) { //you don't want to use groups
+ variables["[tag]"] = processList->getLabel();
+ if (countfile == "") {
+ outputNamesFile = getOutputFileName("name", variables);
+ outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile);
+ }else {
+ outputNamesFile = getOutputFileName("count", variables);
+ outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile);
+ }
+ outputNameFiles[outputNamesFile] = processList->getLabel();
+ m->openOutputFile(outputNamesFile, newNamesOutput);
+ newNamesOutput << "noGroup" << endl;
+ }else{ //you want to use groups
+ ofstream* temp;
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ variables["[tag]"] = processList->getLabel();
+ variables["[group]"] = Groups[i];
+ filehandles[Groups[i]] = temp;
+ outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".";
+ if (countfile == "") {
+ outputNamesFile = getOutputFileName("name", variables);
+ outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile);
+ }else {
+ outputNamesFile = getOutputFileName("count", variables);
+ outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile);
+ }
+
+ m->openOutputFile(outputNamesFile, *(temp));
+ *(temp) << Groups[i] << endl;
+ outputNameFiles[outputNamesFile] = processList->getLabel() + "." + Groups[i];
+ }
+ }
+
+ //for each bin in the list vector
+ for (int i = 0; i < processList->size(); i++) {
+ if (m->control_pressed) {
+ out.close();
+ if (Groups.size() == 0) { //you don't want to use groups
+ newNamesOutput.close();
}else{
- groups[groupName] = groupName;
+ for (int j=0; j<Groups.size(); j++) {
+ (*(filehandles[Groups[j]])).close();
+ delete filehandles[Groups[j]];
+ }
}
+ return 0;
}
- //turn the groups into a string
- for(groupIt = groups.begin(); groupIt != groups.end(); groupIt++) { group += groupIt->first + "-"; }
+ string temp = processList->get(i);
+ vector<string> namesInBin;
+ m->splitAtComma(temp, namesInBin);
- //rip off last dash
- group = group.substr(0, group.length()-1);
+ if (Groups.size() == 0) {
+ nameRep = findRep(namesInBin, "");
+ newNamesOutput << i << '\t' << nameRep << '\t';
+
+ //put rep at first position in names line
+ string outputString = nameRep + ",";
+ for (int k=0; k<namesInBin.size()-1; k++) {//output list of names in this otu
+ if (namesInBin[k] != nameRep) { outputString += namesInBin[k] + ","; }
+ }
+
+ //output last name
+ if (namesInBin[namesInBin.size()-1] != nameRep) { outputString += namesInBin[namesInBin.size()-1]; }
+
+ if (outputString[outputString.length()-1] == ',') { //rip off comma
+ outputString = outputString.substr(0, outputString.length()-1);
+ }
+ newNamesOutput << outputString << endl;
+ }else{
+ map<string, vector<string> > NamesInGroup;
+ for (int j=0; j<Groups.size(); j++) { //initialize groups
+ NamesInGroup[Groups[j]].resize(0);
+ }
+
+ for (int j=0; j<namesInBin.size(); j++) {
+ if (groupfile != "") {
+ string thisgroup = groupMap->getGroup(namesInBin[j]);
+ if (thisgroup == "not found") { m->mothurOut(namesInBin[j] + " is not in your groupfile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ //add this name to correct group
+ if (m->inUsersGroups(thisgroup, Groups)) { NamesInGroup[thisgroup].push_back(namesInBin[j]); }
+ }else {
+ vector<string> thisSeqsGroups = ct.getGroups(namesInBin[j]);
+ for (int k = 0; k < thisSeqsGroups.size(); k++) {
+ if (m->inUsersGroups(thisSeqsGroups[k], Groups)) { NamesInGroup[thisSeqsGroups[k]].push_back(namesInBin[j]); }
+ }
+ }
+ }
+
+ //get rep for each group in otu
+ for (int j=0; j<Groups.size(); j++) {
+ if (NamesInGroup[Groups[j]].size() != 0) { //are there members from this group in this otu?
+ //get rep for each group
+ nameRep = findRep(NamesInGroup[Groups[j]], Groups[j]);
+
+ //output group rep and other members of this group
+ (*(filehandles[Groups[j]])) << i << '\t' << nameRep << '\t';
+
+ //put rep at first position in names line
+ string outputString = nameRep + ",";
+ for (int k=0; k<NamesInGroup[Groups[j]].size()-1; k++) {//output list of names in this otu from this group
+ if (NamesInGroup[Groups[j]][k] != nameRep) { outputString += NamesInGroup[Groups[j]][k] + ","; }
+ }
+
+ //output last name
+ if (NamesInGroup[Groups[j]][NamesInGroup[Groups[j]].size()-1] != nameRep) { outputString += NamesInGroup[Groups[j]][NamesInGroup[Groups[j]].size()-1]; }
+
+ if (outputString[outputString.length()-1] == ',') { //rip off comma
+ outputString = outputString.substr(0, outputString.length()-1);
+ }
+ (*(filehandles[Groups[j]])) << outputString << endl;
+ }
+ }
+ }
+ }
+
+ if (Groups.size() == 0) { //you don't want to use groups
+ newNamesOutput.close();
+ }else{
+ for (int i=0; i<Groups.size(); i++) {
+ (*(filehandles[Groups[i]])).close();
+ delete filehandles[Groups[i]];
+ }
}
- //if only 1 sequence in bin then that's the rep
- if (names.size() == 1) { return names[0]; }
- else {
- //fill binMap
- for (int i = 0; i < names.size(); i++) {
- for (map<string, int>::iterator it = nameToIndex.begin(); it != nameToIndex.end(); it++) {
+ return 0;
- if (it->first == names[i]) {
- binMap[it->second] = it->first;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetOTURepCommand::processFastaNames(string filename, string label, FastaMap*& fasta) {
+ try{
- //initialize sums map
- sums[it->first] = 0.0;
- break;
+ //create output file
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[tag]"] = label;
+ string outputFileName = getOutputFileName("fasta",variables);
+ m->openOutputFile(outputFileName, out);
+ vector<repStruct> reps;
+ outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
+
+ ofstream out2;
+ string tempNameFile = filename + ".temp";
+ m->openOutputFile(tempNameFile, out2);
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ int i = 0;
+ string tempGroup = "";
+ in >> tempGroup; m->gobble(in);
+
+ CountTable thisCt;
+ if (countfile != "") {
+ thisCt.readTable(countfile, true);
+ if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
+ }
+
+ int thistotal = 0;
+ while (!in.eof()) {
+ string rep, binnames;
+ in >> i >> rep >> binnames; m->gobble(in);
+
+ vector<string> names;
+ m->splitAtComma(binnames, names);
+ int binsize = names.size();
+
+ if (countfile == "") { out2 << rep << '\t' << binnames << endl; }
+ else {
+ if (tempGroup == "noGroup") {
+ for (int j = 0; j < names.size(); j++) {
+ if (names[j] != rep) { thisCt.mergeCounts(rep, names[j]); }
+ }
+ binsize = thisCt.getNumSeqs(rep);
+ }else {
+ int total = 0;
+ for (int j = 0; j < names.size(); j++) { total += thisCt.getGroupCount(names[j], tempGroup); }
+ out2 << rep << '\t' << total << '\t' << total << endl;
+ binsize = total;
+ }
+ }
+ thistotal += binsize;
+ //if you have a groupfile
+ string group = "";
+ map<string, string> groups;
+ map<string, string>::iterator groupIt;
+ if (groupfile != "") {
+ //find the groups that are in this bin
+ for (int i = 0; i < names.size(); i++) {
+ string groupName = groupMap->getGroup(names[i]);
+ if (groupName == "not found") {
+ m->mothurOut(names[i] + " is missing from your group file. Please correct. "); m->mothurOutEndLine();
+ groupError = true;
+ } else {
+ groups[groupName] = groupName;
}
}
- }
-
- //go through each cell in the sparsematrix
- for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
- //is this a distance between 2 members of this bin
- map<int, string>::iterator it = binMap.find(currentCell->row);
- map<int, string>::iterator it2 = binMap.find(currentCell->column);
- //sum the distance of the sequences in the bin to eachother
- if ((it != binMap.end()) && (it2 != binMap.end())) {
- //this is a cell that repesents the distance between to of this bins members
- sums[it->second] += currentCell->dist;
- sums[it2->second] += currentCell->dist;
+ //turn the groups into a string
+ for (groupIt = groups.begin(); groupIt != groups.end(); groupIt++) {
+ group += groupIt->first + "-";
}
- }
-
- //smallest sum is the representative
- for (map<string, float>::iterator it4 = sums.begin(); it4 != sums.end(); it4++) {
- if (it4->second < min) {
- min = it4->second;
- minName = it4->first;
+ //rip off last dash
+ group = group.substr(0, group.length()-1);
+ }else if (hasGroups) {
+ map<string, string> groups;
+ for (int i = 0; i < names.size(); i++) {
+ vector<string> thisSeqsGroups = ct.getGroups(names[i]);
+ for (int j = 0; j < thisSeqsGroups.size(); j++) { groups[thisSeqsGroups[j]] = thisSeqsGroups[j]; }
+ }
+ //turn the groups into a string
+ for (groupIt = groups.begin(); groupIt != groups.end(); groupIt++) {
+ group += groupIt->first + "-";
}
+ //rip off last dash
+ group = group.substr(0, group.length()-1);
+ //cout << group << endl;
+ }
+ else{ group = ""; }
+
+ //print out name and sequence for that bin
+ string sequence = fasta->getSequence(rep);
+
+ if (sequence != "not found") {
+ if (sorted == "") { //print them out
+ rep = rep + "\t" + toString(i+1);
+ rep = rep + "|" + toString(binsize);
+ if (group != "") {
+ rep = rep + "|" + group;
+ }
+ out << ">" << rep << endl;
+ out << sequence << endl;
+ }else { //save them
+ repStruct newRep(rep, i+1, binsize, group);
+ reps.push_back(newRep);
+ }
+ }else {
+ m->mothurOut(rep + " is missing from your fasta or name file, ignoring. Please correct."); m->mothurOutEndLine();
}
+ }
+
- return minName;
+ if (sorted != "") { //then sort them and print them
+ if (sorted == "name") { sort(reps.begin(), reps.end(), compareName); }
+ else if (sorted == "bin") { sort(reps.begin(), reps.end(), compareBin); }
+ else if (sorted == "size") { sort(reps.begin(), reps.end(), compareSize); }
+ else if (sorted == "group") { sort(reps.begin(), reps.end(), compareGroup); }
+
+ //print them
+ for (int i = 0; i < reps.size(); i++) {
+ string sequence = fasta->getSequence(reps[i].name);
+ string outputName = reps[i].name + "\t" + toString(reps[i].bin);
+ outputName = outputName + "|" + toString(reps[i].size);
+ if (reps[i].group != "") {
+ outputName = outputName + "|" + reps[i].group;
+ }
+ out << ">" << outputName << endl;
+ out << sequence << endl;
+ }
}
-
+
+ in.close();
+ out.close();
+ out2.close();
+
+ m->mothurRemove(filename);
+ rename(tempNameFile.c_str(), filename.c_str());
+
+ if ((countfile != "") && (tempGroup == "noGroup")) { thisCt.printTable(filename); }
+
+ return 0;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function FindRep. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetOTURepCommand", "processFastaNames");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetOTURepCommand class function FindRep. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
//**********************************************************************************************************************
-int GetOTURepCommand::process(ListVector* processList) {
+int GetOTURepCommand::processNames(string filename, string label) {
try{
- string nameRep, name, sequence;
-
- //create output file
- string outputFileName = getRootName(listfile) + processList->getLabel() + ".rep.fasta";
- openOutputFile(outputFileName, out);
-
- //for each bin in the list vector
- for (int i = 0; i < processList->size(); i++) {
- string groups;
- nameRep = FindRep(i, groups, processList);
-
- //print out name and sequence for that bin
- sequence = fasta->getSequence(nameRep);
+
+ //create output file
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+
+ ofstream out2;
+ string tempNameFile = filename + ".temp";
+ m->openOutputFile(tempNameFile, out2);
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ int i = 0;
+ string rep, binnames;
+
+ string tempGroup = "";
+ in >> tempGroup; m->gobble(in);
+
+ CountTable thisCt;
+ if (countfile != "") {
+ thisCt.readTable(countfile, true);
+ if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
+ }
+
+ while (!in.eof()) {
+ if (m->control_pressed) { break; }
+ in >> i >> rep >> binnames; m->gobble(in);
+
+ if (countfile == "") { out2 << rep << '\t' << binnames << endl; }
+ else {
+ vector<string> names;
+ m->splitAtComma(binnames, names);
+ if (tempGroup == "noGroup") {
+ for (int j = 0; j < names.size(); j++) {
+ if (names[j] != rep) { thisCt.mergeCounts(rep, names[j]); }
+ }
+ }else {
+ int total = 0;
+ for (int j = 0; j < names.size(); j++) { total += thisCt.getGroupCount(names[j], tempGroup); }
+ out2 << rep << '\t' << total << '\t' << total << endl;
+ }
+ }
- if (sequence != "not found") {
- if (groupfile == "") {
- nameRep = nameRep + "|" + toString(i+1);
- out << ">" << nameRep << endl;
- out << sequence << endl;
- }else {
- nameRep = nameRep + "|" + groups + "|" + toString(i+1);
- out << ">" << nameRep << endl;
- out << sequence << endl;
- }
- }else {
- cout << nameRep << " is missing from your fasta or name file. Please correct. " << endl;
- remove(outputFileName.c_str());
- return 1;
- }
- }
-
- out.close();
- return 0;
-
+ }
+ in.close();
+ out2.close();
+
+ m->mothurRemove(filename);
+ rename(tempNameFile.c_str(), filename.c_str());
+
+ if ((countfile != "") && (tempGroup == "noGroup")) { thisCt.printTable(filename); }
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetOTURepCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GetOTURepCommand", "processNames");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetOTURepCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+SeqMap GetOTURepCommand::getMap(int row) {
+ try {
+ SeqMap rowMap;
+
+ //make sure this row exists in the file, it may not if the seq did not have any distances below the cutoff
+ if (rowPositions[row] != -1){
+ //go to row in file
+ inRow.seekg(rowPositions[row]);
+
+ int rowNum, numDists, colNum;
+ float dist;
+
+ inRow >> rowNum >> numDists;
+
+ for(int i = 0; i < numDists; i++) {
+ inRow >> colNum >> dist;
+ rowMap[colNum] = dist;
+
+ }
+ }
+
+ return rowMap;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "getMap");
exit(1);
- }
+ }
}
-
//**********************************************************************************************************************
-
-
-
-
projects / mothur.git / blobdiff