#include "getoturepcommand.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){
try{
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
-
- else {
+ 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"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//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;
+ mothurOut("Before you use the get.oturep command, you first need to read in a distance matrix."); mothurOutEndLine();
abort = true;
}
//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") { mothurOut("fasta is a required parameter for the get.oturep command."); mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
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") { mothurOut("list is a required parameter for the get.oturep command."); 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; }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not found") { columnfile = ""; }
+ else if (columnfile == "not open") { abort = true; }
+
+ if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a get.oturep command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
+ else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a get.oturep command you must enter ONLY ONE of the following: phylip or column."); 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 = ""; }
else {
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 == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
namesfile = validParameter.validFile(parameters, "name", 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();
}
-
- if (abort == false) {
- if(globaldata->gSparseMatrix != NULL) { matrix = globaldata->gSparseMatrix; }
-
+ sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found"){ sorted = ""; }
+ if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {
+ mothurOut(sorted + " is not a valid option for the sorted parameter. The only options are: name, bin, size and group. I will not sort."); mothurOutEndLine();
+ sorted = "";
+ }
+
+ if ((sorted == "group") && (groupfile == "")) {
+ mothurOut("You must provide a groupfile to sort by group. I will not sort."); mothurOutEndLine();
+ sorted = "";
+ }
+
+ if (abort == false) {
+
//globaldata->gListVector bin 0 = first name read in distance matrix, globaldata->gListVector bin 1 = second name read in distance matrix
- if(globaldata->gListVector != NULL) {
-
+ if (globaldata->gListVector != NULL) {
vector<string> names;
string binnames;
//map names to rows in sparsematrix
for (int j = 0; j < names.size(); j++) {
nameToIndex[names[j]] = i;
}
-
}
- }else { cout << "error, no listvector." << endl; }
-
-// openInputFile(fastafile, in);
+ } else { mothurOut("error, no listvector."); mothurOutEndLine(); }
+
fasta = new FastaMap();
}
-
}
-
}
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";
- 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";
+ errorOut(e, "GetOTURepCommand", "GetOTURepCommand");
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";
+ 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, sorted and label. The fasta and list parameters are required.\n");
+ 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");
+ mothurOut("The get.oturep command should be in the following format: get.oturep(fasta=yourFastaFile, list=yourListFile, name=yourNamesFile, group=yourGroupFile, label=yourLabels).\n");
+ mothurOut("Example get.oturep(fasta=amazon.fasta, list=amazon.fn.list, group=amazon.groups, name=amazon.names).\n");
+ mothurOut("The default value for label is all labels in your inputfile.\n");
+ 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");
+ 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");
}
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";
+ errorOut(e, "GetOTURepCommand", "help");
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);
- }
}
//**********************************************************************************************************************
try {
if (abort == true) { return 0; }
-
- int count = 1;
int error;
//read fastafile
fasta->readFastaFile(fastafile);
- in.close();
-
- //set format to list so input can get listvector
- globaldata->setFormat("list");
+ //in.close();
+ //read distance file and generate indexed distance file that can be used by findrep function
+//....new reading class....//
//if user gave a namesfile then use it
- if (namesfile != "") {
- readNamesFile();
- }
+ if (namesfile != "") { readNamesFile(); }
+ //set format to list so input can get listvector
+ globaldata->setFormat("list");
+
//read list file
- read = new ReadOTUFile(listfile);
+ read = new ReadOTUFile(listfile);
read->read(&*globaldata);
input = globaldata->ginput;
list = globaldata->gListVector;
- ListVector* lastList = list;
+ 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))) {
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
- cout << list->getLabel() << '\t' << count << endl;
+ if (allLines == 1 || labels.count(list->getLabel()) == 1){
+ mothurOut(list->getLabel() + "\t" + toString(list->size())); mothurOutEndLine();
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);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- cout << lastList->getLabel() << '\t' << count << endl;
- error = process(lastList);
+ 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())); mothurOutEndLine();
+ error = process(list);
if (error == 1) { return 0; } //there is an error in hte input files, abort command
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
}
- if (count != 1) { delete lastList; }
- lastList = list;
+ 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++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
- cout << ". I will use " << lastList->getLabel() << "." << endl;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(list->getLabel()) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastList->getLabel() << '\t' << count << endl;
- error = process(lastList);
+ if (list != NULL) { delete list; }
+ list = input->getListVector(lastLabel);
+ mothurOut(list->getLabel() + "\t" + toString(list->size())); mothurOutEndLine();
+ error = process(list);
+ delete list;
if (error == 1) { return 0; } //there is an error in hte input files, abort command
}
- delete lastList;
- delete matrix;
- globaldata->gSparseMatrix = NULL;
delete list;
globaldata->gListVector = NULL;
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";
+ errorOut(e, "GetOTURepCommand", "execute");
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);
- }
-
}
//**********************************************************************************************************************
}
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";
+ 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";
- exit(1);
- }
}
//**********************************************************************************************************************
-string GetOTURepCommand::FindRep(int bin, string& group, ListVector* thisList) {
+string GetOTURepCommand::findRep(int bin, string& group, ListVector* thisList, int& binsize) {
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
+ string binnames = thisList->get(bin);
splitAtComma(binnames, names);
-
+ binsize = names.size();
+
//if you have a groupfile
- if(groupfile != "") {
+ if (groupfile != "") {
//find the groups that are in this bin
- for (int i = 0; i < names.size(); i++) {
+ for (size_t 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;
+ mothurOut(names[i] + " is missing from your group file. Please correct. "); mothurOutEndLine();
groupError = true;
- }else{
+ } else {
groups[groupName] = groupName;
}
}
//turn the groups into a string
- for(groupIt = groups.begin(); groupIt != groups.end(); groupIt++) { group += groupIt->first + "-"; }
-
+ 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 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++) {
+ }else{ group = ""; }
- if (it->first == names[i]) {
- binMap[it->second] = it->first;
+ // 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")) {
+ return names[0];
+ } else {
+ vector<int> seqIndex(names.size());
+ vector<float> max_dist(names.size());
- //initialize sums map
- sums[it->first] = 0.0;
- break;
- }
- }
+ //fill seqIndex and initialize sums
+ for (size_t i = 0; i < names.size(); i++) {
+ seqIndex[i] = nameToIndex[names[i]];
+ max_dist[i] = 0.0;
}
- //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;
+ // loop through all entries in seqIndex
+ SeqMap::iterator it;
+ SeqMap currMap;
+ for (size_t i=0; i < seqIndex.size(); i++) {
+ //currMap = seqVec[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);
+ }
}
}
- //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;
+ // sequence with the smallest maximum distance is the representative
+ float min = 10000;
+ int minIndex;
+ for (size_t i=0; i < max_dist.size(); i++) {
+ if (max_dist[i] < min) {
+ min = max_dist[i];
+ minIndex = i;
}
-
}
-
- return minName;
+
+ return(names[minIndex]);
}
-
}
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";
+ errorOut(e, "GetOTURepCommand", "FindRep");
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) {
try{
- string nameRep, name, sequence;
+ 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
+ string outputFileName = getRootName(listfile) + processList->getLabel() + ".rep.fasta";
+ openOutputFile(outputFileName, out);
+ vector<repStruct> reps;
- 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;
+ //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);
+
+ //print out name and sequence for that bin
+ sequence = fasta->getSequence(nameRep);
+
+ if (sequence != "not found") {
+ if (sorted == "") { //print them out
+ nameRep = nameRep + "|" + toString(i+1);
+ nameRep = nameRep + "|" + toString(binsize);
+ if (groupfile != "") {
+ nameRep = nameRep + "|" + groups;
}
+ out << ">" << nameRep << endl;
+ out << sequence << endl;
+ }else { //save them
+ repStruct newRep(nameRep, i+1, binsize, groups);
+ reps.push_back(newRep);
}
-
- out.close();
- return 0;
-
+ }else {
+ mothurOut(nameRep + " is missing from your fasta or name file. Please correct. "); mothurOutEndLine();
+ remove(outputFileName.c_str());
+ return 1;
+ }
+ }
+
+ 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 + "|" + toString(reps[i].bin);
+ outputName = outputName + "|" + toString(reps[i].size);
+ if (groupfile != "") {
+ outputName = outputName + "|" + reps[i].group;
+ }
+ out << ">" << outputName << endl;
+ out << sequence << endl;
+ }
+ }
+
+ out.close();
+ 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";
+ errorOut(e, "GetOTURepCommand", "process");
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";
- exit(1);
- }
}
//**********************************************************************************************************************
-
-
-
-
-
projects / mothur.git / blobdiff