*/
#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){
+GetOTURepCommand::GetOTURepCommand(string option) {
try{
globaldata = GlobalData::getInstance();
abort = 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"};
+ string Array[] = {"fasta","list","label","name", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string, string>::iterator it;
//check to make sure all parameters are valid for command
- for (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)) {
- mothurOut("Before you use the get.oturep command, you first need to read in a distance matrix."); mothurOutEndLine();
- abort = true;
+ //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 = 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 = 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 = 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 = 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 = 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 = 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; }
+ }
}
+
+
+ //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") { mothurOut("fasta is a required parameter for the get.oturep command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the get.oturep command."); m->mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not found") { mothurOut("list is a required parameter for the get.oturep command."); mothurOutEndLine(); abort = true; }
+ if (listfile == "not found") { m->mothurOut("list is a required parameter for the get.oturep command."); m->mothurOutEndLine(); abort = true; }
else if (listfile == "not open") { abort = true; }
+
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not found") { phylipfile = ""; }
+ else if (phylipfile == "not open") { abort = true; }
+ else { distFile = phylipfile; format = "phylip"; }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not found") { columnfile = ""; }
+ else if (columnfile == "not open") { abort = true; }
+ else { distFile = columnfile; format = "column"; }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+
+ if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a get.oturep command you must enter a phylip or a column."); 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 == "") { cout << "You need to provide a namefile if you are going to use the column format." << endl; 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; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); 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;
- }
-
- 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; }
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else {
- //read in group map info.
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+
+ sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found"){ 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 = "";
}
-
- 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 { mothurOut("error, no listvector."); mothurOutEndLine(); }
-
- // 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>(globaldata->gListVector->size());
- for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) {
- seqVec[currentCell->row][currentCell->column] = currentCell->dist;
+ if ((sorted == "group") && (groupfile == "")) {
+ m->mothurOut("You must provide a groupfile to sort by group. I will not sort."); m->mothurOutEndLine();
+ sorted = "";
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ if (groupfile == "") {
+ m->mothurOut("You must provide a groupfile to use groups."); m->mothurOutEndLine();
+ abort = true;
+ }else {
+ splitAtDash(groups, Groups);
}
-
- fasta = new FastaMap();
}
+ globaldata->Groups = Groups;
+
+ string temp = validParameter.validFile(parameters, "large", false); if (temp == "not found") { temp = "F"; }
+ large = isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, precision);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10.0"; }
+ convert(temp, cutoff);
+ cutoff += (5 / (precision * 10.0));
}
}
catch(exception& e) {
- errorOut(e, "GetOTURepCommand", "GetOTURepCommand");
+ m->errorOut(e, "GetOTURepCommand", "GetOTURepCommand");
exit(1);
}
}
void GetOTURepCommand::help(){
try {
- mothurOut("The get.oturep command can only be executed after a successful read.dist command.\n");
- mothurOut("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");
- mothurOut("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");
- mothurOut("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");
- mothurOut("Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, line=1-3-5, name=amazon.names).\n");
- mothurOut("The default value for line and label are all lines in your inputfile.\n");
- mothurOut("The get.oturep command outputs a .fastarep file for each distance you specify, selecting one OTU representative for each bin.\n");
- mothurOut("If you provide a groupfile, then it also appends the names of the groups present in that bin.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+ m->mothurOut("The get.oturep command parameters are phylip, column, list, fasta, name, group, large, cutoff, precision, groups, sorted and label. The fasta and list parameters are required, as well as phylip or column and name.\n");
+ m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
+ m->mothurOut("The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. \n");
+ m->mothurOut("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");
+ m->mothurOut("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");
+ m->mothurOut("Example get.oturep(phylip=amazon.dist, fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups).\n");
+ m->mothurOut("The default value for label is all labels in your inputfile.\n");
+ m->mothurOut("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");
+ m->mothurOut("The large parameter allows you to indicate that your distance matrix is too large to fit in RAM. The default value is false.\n");
+ m->mothurOut("The group parameter allows you provide a group file.\n");
+ m->mothurOut("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");
+ m->mothurOut("The get.oturep command outputs a .fastarep and .rep.names file for each distance you specify, selecting one OTU representative for each bin.\n");
+ m->mothurOut("If you provide a groupfile, then it also appends the names of the groups present in that bin.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
}
catch(exception& e) {
- errorOut(e, "GetOTURepCommand", "help");
+ m->errorOut(e, "GetOTURepCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
-GetOTURepCommand::~GetOTURepCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete fasta;
- if (groupfile != "") {
- delete groupMap; globaldata->gGroupmap = NULL;
- }
- }
-}
+GetOTURepCommand::~GetOTURepCommand(){}
//**********************************************************************************************************************
try {
if (abort == true) { return 0; }
-
- int count = 1;
int error;
- //read fastafile
- fasta->readFastaFile(fastafile);
+ 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; }
+
+ readMatrix->setCutoff(cutoff);
+
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ }else{ nameMap = NULL; }
+
+ readMatrix->read(nameMap);
+
+ if (m->control_pressed) { delete readMatrix; return 0; }
+
+ //get matrix
+ if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
+ globaldata->gListVector = readMatrix->getListVector();
+
+ SparseMatrix* matrix = readMatrix->getMatrix();
+
+ // 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>(globaldata->gListVector->size());
+ for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) {
+ if (m->control_pressed) { delete readMatrix; return 0; }
+ seqVec[currentCell->row][currentCell->column] = currentCell->dist;
+ }
+
+ delete matrix;
+ delete readMatrix;
+ delete nameMap;
+
+ 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; }
+
+ formatMatrix->setCutoff(cutoff);
+
+ if(namefile != ""){
+ nameMap = new NameAssignment(namefile);
+ nameMap->readMap();
+ }else{ nameMap = NULL; }
+
+ formatMatrix->read(nameMap);
+
+ if (m->control_pressed) { delete formatMatrix; return 0; }
+
+ //get matrix
+ if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
+ globaldata->gListVector = 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();
+
+ delete formatMatrix;
+ delete nameMap;
+
+ //openfile for getMap to use
+ openInputFile(distFile, inRow);
+
+ if (m->control_pressed) { inRow.close(); remove(distFile.c_str()); return 0; }
+ }
- in.close();
- //set format to list so input can get listvector
- globaldata->setFormat("list");
+ //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 { m->mothurOut("error, no listvector."); m->mothurOutEndLine(); }
- //if user gave a namesfile then use it
- if (namesfile != "") {
- readNamesFile();
+
+ if (m->control_pressed) {
+ if (large) { inRow.close(); remove(distFile.c_str()); }
+ 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 = new SharedUtil();
+ util->setGroups(Groups, groupMap->namesOfGroups, "getoturep");
+ delete util;
+ }
+ }
+
+ //set format to list so input can get listvector
+ globaldata->setFormat("list");
+
//read list file
read = new ReadOTUFile(listfile);
read->read(&*globaldata);
input = globaldata->ginput;
list = globaldata->gListVector;
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;
- set<int> userLines = lines;
-
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ if (m->control_pressed) {
+ if (large) { inRow.close(); remove(distFile.c_str()); }
+ delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
+ }
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
- mothurOut(list->getLabel() + "\t" + toString(list->size()) + "\t" + toString(count)); mothurOutEndLine();
+ 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 (large) { inRow.close(); remove(distFile.c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
+ }
+
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
- userLines.erase(count);
}
if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
delete list;
list = input->getListVector(lastLabel);
- mothurOut(list->getLabel() + "\t" + toString(list->size()) + "\t" + toString(count)); mothurOutEndLine();
+ 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 (large) { inRow.close(); remove(distFile.c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete read; delete input; delete list; globaldata->gListVector = NULL; 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();
- count++;
}
//output error messages about any remaining user labels
bool needToRun = false;
for (set<string>::iterator it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(list->getLabel()) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ 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 {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- delete list;
+ if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
- mothurOut(list->getLabel() + "\t" + toString(list->size()) + "\t" + toString(count)); mothurOutEndLine();
+ 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 (large) { inRow.close(); remove(distFile.c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete read; delete input; delete list; globaldata->gListVector = NULL; return 0;
+ }
+ }
+
+ //close and remove formatted matrix file
+ if (large) {
+ inRow.close();
+ remove(distFile.c_str());
}
- delete matrix;
- globaldata->gSparseMatrix = NULL;
- delete list;
globaldata->gListVector = NULL;
-
+ delete input; globaldata->ginput = NULL;
+ delete read;
+
+ //read fastafile
+ fasta = new FastaMap();
+ fasta->readFastaFile(fastafile);
+
+ //if user gave a namesfile then use it
+ if (namefile != "") { readNamesFile(); }
+
+ //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);
+ }
+
+ delete fasta;
+ if (groupfile != "") {
+ delete groupMap; globaldata->gGroupmap = NULL;
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "GetOTURepCommand", "execute");
+ m->errorOut(e, "GetOTURepCommand", "execute");
exit(1);
}
}
void GetOTURepCommand::readNamesFile() {
try {
vector<string> dupNames;
- openInputFile(namesfile, inNames);
+ openInputFile(namefile, inNames);
string name, names, sequence;
}
catch(exception& e) {
- errorOut(e, "GetOTURepCommand", "readNamesFile");
+ m->errorOut(e, "GetOTURepCommand", "readNamesFile");
exit(1);
}
}
//**********************************************************************************************************************
-string GetOTURepCommand::findRep(int bin, string& group, ListVector* thisList, int& binsize) {
+string GetOTURepCommand::findRep(vector<string> names) {
try{
- vector<string> names;
- map<string, string> groups;
- map<string, string>::iterator groupIt;
-
- //parse names into vector
- string binnames = thisList->get(bin);
- splitAtComma(binnames, names);
- binsize = names.size();
-
- //if you have a groupfile
- if (groupfile != "") {
- //find the groups that are in this bin
- for (size_t i = 0; i < names.size(); i++) {
- string groupName = groupMap->getGroup(names[i]);
- if (groupName == "not found") {
- mothurOut(names[i] + " is missing from your group file. Please correct. "); mothurOutEndLine();
- groupError = true;
- } else {
- groups[groupName] = groupName;
- }
- }
-
- //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);
- }
-
- // if only 1 sequence in bin or processing the "unique" line, then
+ // 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) || (list->getLabel() == "unique")) {
+ if ((names.size() == 2) || (names.size() == 1) || (list->getLabel() == "unique")) {
return names[0];
- } else {
+ }else{
vector<int> seqIndex(names.size());
vector<float> max_dist(names.size());
+ vector<float> total_dist(names.size());
//fill seqIndex and initialize sums
for (size_t i = 0; i < names.size(); i++) {
seqIndex[i] = nameToIndex[names[i]];
max_dist[i] = 0.0;
+ total_dist[i] = 0.0;
}
// loop through all entries in seqIndex
SeqMap::iterator it;
SeqMap currMap;
for (size_t i=0; i < seqIndex.size(); i++) {
- currMap = seqVec[seqIndex[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) {
- errorOut(e, "GetOTURepCommand", "FindRep");
+ m->errorOut(e, "GetOTURepCommand", "FindRep");
exit(1);
}
}
//**********************************************************************************************************************
int GetOTURepCommand::process(ListVector* processList) {
try{
- string nameRep, name, sequence;
+ string name, sequence;
+ string nameRep;
//create output file
- string outputFileName = getRootName(listfile) + processList->getLabel() + ".rep.fasta";
- openOutputFile(outputFileName, out);
-
+ if (outputDir == "") { outputDir += hasPath(listfile); }
+
+ ofstream newNamesOutput;
+ string outputNamesFile;
+ map<string, ofstream*> filehandles;
+
+ if (Groups.size() == 0) { //you don't want to use groups
+ outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + ".rep.names";
+ openOutputFile(outputNamesFile, newNamesOutput);
+ outputNames.push_back(outputNamesFile);
+ outputNameFiles[outputNamesFile] = processList->getLabel();
+ }else{ //you want to use groups
+ ofstream* temp;
+ for (int i=0; i<Groups.size(); i++) {
+ temp = new ofstream;
+ filehandles[Groups[i]] = temp;
+ outputNamesFile = outputDir + getRootName(getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".rep.names";
+
+ openOutputFile(outputNamesFile, *(temp));
+ outputNames.push_back(outputNamesFile);
+ outputNameFiles[outputNamesFile] = processList->getLabel() + "." + Groups[i];
+ }
+ }
+
//for each bin in the list vector
for (int i = 0; i < processList->size(); i++) {
- string groups;
- int binsize;
- nameRep = findRep(i, groups, processList, binsize);
+ if (m->control_pressed) {
+ out.close();
+ if (Groups.size() == 0) { //you don't want to use groups
+ newNamesOutput.close();
+ }else{
+ for (int j=0; j<Groups.size(); j++) {
+ (*(filehandles[Groups[j]])).close();
+ delete filehandles[Groups[j]];
+ }
+ }
+ return 0;
+ }
+
+ string temp = processList->get(i);
+ vector<string> namesInBin;
+ splitAtComma(temp, namesInBin);
+
+ if (Groups.size() == 0) {
+ nameRep = findRep(namesInBin);
+ newNamesOutput << i << '\t' << nameRep << '\t' << processList->get(i) << 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++) {
+ 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; }
+
+ if (inUsersGroups(thisgroup, Groups)) { //add this name to correct group
+ NamesInGroup[thisgroup].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]]);
+
+ //output group rep and other members of this group
+ (*(filehandles[Groups[j]])) << i << '\t' << nameRep << '\t';
+
+ for (int k=0; k<NamesInGroup[Groups[j]].size()-1; k++) {//output list of names in this otu from this group
+ (*(filehandles[Groups[j]])) << NamesInGroup[Groups[j]][k] << ",";
+ }
+ //output last name
+ (*(filehandles[Groups[j]])) << NamesInGroup[Groups[j]][NamesInGroup[Groups[j]].size()-1] << 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]];
+ }
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetOTURepCommand", "process");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int GetOTURepCommand::processNames(string filename, string label) {
+ try{
+ //create output file
+ if (outputDir == "") { outputDir += hasPath(listfile); }
+ string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + label + ".rep.fasta";
+ openOutputFile(outputFileName, out);
+ vector<repStruct> reps;
+ outputNames.push_back(outputFileName);
+
+ ofstream out2;
+ string tempNameFile = filename + ".temp";
+ openOutputFile(tempNameFile, out2);
+
+ ifstream in;
+ openInputFile(filename, in);
+
+ int i = 0;
+ while (!in.eof()) {
+ string rep, binnames;
+ in >> i >> rep >> binnames; gobble(in);
+ out2 << rep << '\t' << binnames << endl;
+
+ vector<string> names;
+ splitAtComma(binnames, names);
+ int binsize = names.size();
+
+ //if you have a groupfile
+ string group = "";
+ if (groupfile != "") {
+ map<string, string> groups;
+ map<string, string>::iterator groupIt;
+
+ //find the groups that are in this bin
+ for (size_t 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;
+ }
+ }
+
+ //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);
+ }else{ group = ""; }
+
+
//print out name and sequence for that bin
- sequence = fasta->getSequence(nameRep);
+ string sequence = fasta->getSequence(rep);
if (sequence != "not found") {
- nameRep = nameRep + "|" + toString(i+1);
- nameRep = nameRep + "|" + toString(binsize);
+ if (sorted == "") { //print them out
+ rep = rep + "\t" + toString(i+1);
+ rep = rep + "|" + toString(binsize);
+ if (groupfile != "") {
+ 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();
+ }
+ }
+
+
+ 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 (groupfile != "") {
- nameRep = nameRep + "|" + groups;
+ outputName = outputName + "|" + reps[i].group;
}
- out << ">" << nameRep << endl;
+ out << ">" << outputName << endl;
out << sequence << endl;
- } else {
- mothurOut(nameRep + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
- remove(outputFileName.c_str());
- return 1;
}
}
-
+
out.close();
+ out2.close();
+
+ remove(filename.c_str());
+ rename(tempNameFile.c_str(), filename.c_str());
+
return 0;
}
catch(exception& e) {
- errorOut(e, "GetOTURepCommand", "process");
+ m->errorOut(e, "GetOTURepCommand", "processNames");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+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