nRowCells = dMatrix->seqVec[smallRow].size();
vector<int> foundCol(nColCells, 0);
- //cout << "small cell: " << smallRow << '\t' << smallCol << endl;
+ //cout << dMatrix->getNNodes() << " small cell: " << smallRow << '\t' << smallCol << endl;
int search;
bool changed;
#include "readmatrix.hpp"
#include "clusterdoturcommand.h"
+
//**********************************************************************************************************************
vector<string> ClusterCommand::setParameters(){
try {
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pcount);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
string ClusterCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The cluster command parameter options are phylip, column, name, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
+ helpString += "The cluster command parameter options are phylip, column, name, count, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
helpString += "The cluster command should be in the following format: \n";
helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
helpString += "The acceptable cluster methods are furthest, nearest, average and weighted. If no method is provided then average is assumed.\n";
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
if ((phylipfile == "") && (columnfile == "")) {
//is there are current file available for either of these?
else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
if (columnfile != "") {
- if (namefile == "") {
+ if ((namefile == "") && (countfile == "")){
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
- abort = true;
+ 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;
+ }
}
}
}
+ if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
//get user cutoff and precision or use defaults
//run unique.seqs for deconvolute results
string inputString = "phylip=" + distfile;
if (namefile != "") { inputString += ", name=" + namefile; }
+ else if (countfile != "") { inputString += ", count=" + countfile; }
inputString += ", precision=" + toString(precision);
inputString += ", method=" + method;
if (hard) { inputString += ", hard=T"; }
read->setCutoff(cutoff);
NameAssignment* nameMap = NULL;
+ CountTable* ct = NULL;
if(namefile != ""){
nameMap = new NameAssignment(namefile);
nameMap->readMap();
- }
+ read->read(nameMap);
+ }else if (countfile != "") {
+ ct = new CountTable();
+ ct->readTable(countfile);
+ read->read(ct);
+ }
- read->read(nameMap);
list = read->getListVector();
matrix = read->getDMatrix();
- rabund = new RAbundVector(list->getRAbundVector());
+
+ if(countfile != "") {
+ rabund = new RAbundVector();
+ createRabund(ct, list, rabund); //creates an rabund that includes the counts for the unique list
+ delete ct;
+ }else { rabund = new RAbundVector(list->getRAbundVector()); }
delete read;
if (m->control_pressed) { //clean up
- delete list; delete matrix; delete rabund;
- sabundFile.close();rabundFile.close();listFile.close();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- return 0;
+ delete list; delete matrix; delete rabund; if(countfile == ""){rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); }
+ listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0;
}
//create cluster
string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+ string listFileName = fileroot+ tag + ".";
+ if (countfile != "") { listFileName += "unique_"; }
+ listFileName += getOutputFileNameTag("list");
- m->openOutputFile(sabundFileName, sabundFile);
- m->openOutputFile(rabundFileName, rabundFile);
+ if (countfile == "") {
+ m->openOutputFile(sabundFileName, sabundFile);
+ m->openOutputFile(rabundFileName, rabundFile);
+ outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+ outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+
+ }
m->openOutputFile(listFileName, listFile);
-
- outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
- outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
- outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+ outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
time_t estart = time(NULL);
if (m->control_pressed) { //clean up
delete list; delete matrix; delete rabund; delete cluster;
- sabundFile.close();rabundFile.close();listFile.close();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- return 0;
+ if(countfile == "") {rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); }
+ listFile.close(); m->mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0;
}
if (print_start && m->isTrue(timing)) {
delete list;
delete rabund;
delete cluster;
-
- sabundFile.close();
- rabundFile.close();
+ if (countfile == "") {
+ sabundFile.close();
+ rabundFile.close();
+ }
listFile.close();
if (saveCutoff != cutoff) {
print_start = true;
loops = 0;
start = time(NULL);
-
- oldRAbund.setLabel(label);
- if (m->isTrue(showabund)) {
- oldRAbund.getSAbundVector().print(cout);
- }
- oldRAbund.print(rabundFile);
- oldRAbund.getSAbundVector().print(sabundFile);
-
+
+ if (countfile == "") {
+ oldRAbund.print(rabundFile);
+ oldRAbund.getSAbundVector().print(sabundFile);
+ }
+
+ oldRAbund.setLabel(label);
+ if (m->isTrue(showabund)) {
+ oldRAbund.getSAbundVector().print(cout);
+ }
+
oldList.setLabel(label);
oldList.print(listFile);
}
}
//**********************************************************************************************************************
+
+int ClusterCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund){
+ try {
+ rabund->setLabel(list->getLabel());
+ for(int i = 0; i < list->getNumBins(); i++) {
+ if (m->control_pressed) { break; }
+ vector<string> binNames;
+ string bin = list->get(i);
+ m->splitAtComma(bin, binNames);
+ int total = 0;
+ for (int j = 0; j < binNames.size(); j++) { total += ct->getNumSeqs(binNames[j]); }
+ rabund->push_back(total);
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "createRabund");
+ exit(1);
+ }
+
+}
+//**********************************************************************************************************************
#include "listvector.hpp"
#include "cluster.hpp"
#include "sparsedistancematrix.h"
+#include "counttable.h"
/* The cluster() command:
The cluster command outputs a .list , .rabund and .sabund files.
bool abort, hard, sim;
- string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile;
+ string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile;
double cutoff;
string showabund, timing;
int precision, length;
void printData(string label);
vector<string> outputNames;
+
+ int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
};
#endif
}
}
/************************************************************/
-//returns names of seqs
+//returns unique index for sequence like get in NameAssignment
+int CountTable::get(string seqName) {
+ try {
+
+ map<string, int>::iterator it = indexNameMap.find(seqName);
+ if (it == indexNameMap.end()) {
+ m->mothurOut("[ERROR]: " + seqName + " is not in your count table. Please correct.\n"); m->control_pressed = true;
+ }else { return it->second; }
+
+ return -1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountTable", "get");
+ exit(1);
+ }
+}
+/************************************************************/
+//create ListVector from uniques
+ListVector CountTable::getListVector() {
+ try {
+ ListVector list(indexNameMap.size());
+ for (map<string, int>::iterator it = indexNameMap.begin(); it != indexNameMap.end(); it++) {
+ if (m->control_pressed) { break; }
+ list.set(it->second, it->first);
+ }
+ return list;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CountTable", "getListVector");
+ exit(1);
+ }
+}
+
+/************************************************************/
+//returns the names of all unique sequences in file
vector<string> CountTable::getNamesOfSeqs() {
try {
vector<string> names;
#include "mothurout.h"
+#include "listvector.hpp"
class CountTable {
int getGroupIndex(string); //returns index in getGroupCounts vector of specific group
vector<string> getNamesOfSeqs();
int mergeCounts(string, string); //combines counts for 2 seqs, saving under the first name passed in.
+ int get(string); //returns unique sequence index for reading distance matrices like NameAssignment
+ ListVector getListVector();
+ int size() { return indexNameMap.size(); }
private:
string filename;
//sanity check
if (totalAbund != classifyOtuSizes[index]) {
- m->mothurOut("[ERROR: OTU " + m->currentBinLabels[h] + " contains " + toString(totalAbund) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
+ m->mothurOut("[WARNING]: OTU " + m->currentBinLabels[h] + " contains " + toString(totalAbund) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); //m->control_pressed = true; break;
}
//output repSeq
m->setFlowFile("");
}else if (types[i] == "biom") {
m->setBiomFile("");
- }else if (types[i] == "counttable") {
+ }else if (types[i] == "count") {
m->setCountTableFile("");
}else if (types[i] == "processors") {
m->setProcessors("1");
string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
- string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+ string listFileName = fileroot+ tag + ".";
+ if (countfile != "") { listFileName += "unique_"; }
+ listFileName += getOutputFileNameTag("list");
if (countfile == "") {
m->openOutputFile(sabundFileName, sabundFile);
types.insert("tree");
types.insert("flow");
types.insert("biom");
- types.insert("counttable");
+ types.insert("count");
types.insert("processors");
return types;
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
- if (counttablefile != "") { mothurOut("counttable=" + counttablefile); mothurOutEndLine(); }
+ if (counttablefile != "") { mothurOut("count=" + counttablefile); mothurOutEndLine(); }
if (processors != "1") { mothurOut("processors=" + processors); mothurOutEndLine(); }
}
int MothurOut::renameFile(string oldName, string newName){
try {
+
+ if (oldName == newName) { return 0; }
+
ifstream inTest;
int exist = openInputFile(newName, inTest, "");
inTest.close();
m->openInputFile(nameMapFile, fileHandle);
}
-
+//**********************************************************************************************************************
+NameAssignment::NameAssignment(){ m = MothurOut::getInstance(); }
//**********************************************************************************************************************
void NameAssignment::readMap(){
try{
string firstCol, secondCol, skip;
// int index = 0;
-
+
map<string, int>::iterator itData;
int rowIndex = 0;
class NameAssignment : public map<string,int> {
public:
NameAssignment(string);
- NameAssignment(){};
+ NameAssignment();
void readMap();
ListVector getListVector();
int get(string);
it->second = m->getTaxonomyFile();
}else if (it->first == "biom") {
it->second = m->getBiomFile();
- }else if (it->first == "counttable") {
+ }else if (it->first == "count") {
it->second = m->getCountTableFile();
}else {
m->mothurOut("[ERROR]: mothur does not save a current file for " + it->first); m->mothurOutEndLine();
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
-
+
if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
exit(1);
}
}
+/***********************************************************************/
+
+int ReadColumnMatrix::read(CountTable* countTable){
+ try {
+
+ string firstName, secondName;
+ float distance;
+ int nseqs = countTable->size();
+
+ DMatrix->resize(nseqs);
+ list = new ListVector(countTable->getListVector());
+
+ Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int lt = 1;
+ int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
+ int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix
+
+ //need to see if this is a square or a triangular matrix...
+
+ while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
+
+
+ fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ int itA = countTable->get(firstName);
+ int itB = countTable->get(secondName);
+
+ if (m->control_pressed) { exit(1); }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && itA != itB){
+ if(itA > itB){
+ PDistCell value(itA, distance);
+
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA;
+ refCol = itB;
+ DMatrix->addCell(itB, value);
+ }
+ else if(refRow == itA && refCol == itB){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itB, value);
+ }
+ }
+ else if(itA < itB){
+ PDistCell value(itB, distance);
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = itA;
+ refCol = itB;
+ DMatrix->addCell(itA, value);
+ }
+ else if(refRow == itB && refCol == itA){
+ lt = 0;
+ }
+ else{
+ DMatrix->addCell(itA, value);
+ }
+ }
+ reading->update(itA * nseqs);
+ }
+ m->gobble(fileHandle);
+ }
+
+ if(lt == 0){ // oops, it was square
+
+ fileHandle.close(); //let's start over
+ DMatrix->clear(); //let's start over
+
+ m->openInputFile(distFile, fileHandle); //let's start over
+
+ while(fileHandle){
+ fileHandle >> firstName >> secondName >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ int itA = countTable->get(firstName);
+ int itB = countTable->get(secondName);
+
+
+ if (m->control_pressed) { exit(1); }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && itA > itB){
+ PDistCell value(itA, distance);
+ DMatrix->addCell(itB, value);
+ reading->update(itA * nseqs);
+ }
+
+ m->gobble(fileHandle);
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ fileHandle.close();
+
+ list->setLabel("0");
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadColumnMatrix", "read");
+ exit(1);
+ }
+}
/***********************************************************************/
ReadColumnMatrix::~ReadColumnMatrix(){}
ReadColumnMatrix(string, bool);
~ReadColumnMatrix();
int read(NameAssignment*);
+ int read(CountTable*);
private:
ifstream fileHandle;
string distFile;
#include "mothur.h"
#include "listvector.hpp"
#include "nameassignment.hpp"
+#include "counttable.h"
#include "sparsedistancematrix.h"
class SparseMatrix;
ReadMatrix(){ DMatrix = new SparseDistanceMatrix(); m = MothurOut::getInstance(); }
virtual ~ReadMatrix() {}
virtual int read(NameAssignment*){ return 1; }
+ virtual int read(CountTable*){ return 1; }
void setCutoff(float c) { cutoff = c; }
SparseDistanceMatrix* getDMatrix() { return DMatrix; }
exit(1);
}
}
+/***********************************************************************/
+
+int ReadPhylipMatrix::read(CountTable* countTable){
+ try {
+
+ float distance;
+ int square, nseqs;
+ string name;
+ vector<string> matrixNames;
+
+ string numTest;
+ fileHandle >> numTest >> name;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
+ matrixNames.push_back(name);
+
+ if(countTable == NULL){
+ list = new ListVector(nseqs);
+ list->set(0, name);
+ }
+ else{ list = new ListVector(countTable->getListVector()); }
+
+ if (m->control_pressed) { return 0; }
+
+ char d;
+ while((d=fileHandle.get()) != EOF){
+
+ if(isalnum(d)){
+ square = 1;
+ fileHandle.putback(d);
+ for(int i=0;i<nseqs;i++){
+ fileHandle >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ Progress* reading;
+ DMatrix->resize(nseqs);
+
+ if(square == 0){
+
+ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
+
+ int index = 0;
+
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+ //there's A LOT of repeated code throughout this method...
+ if(countTable == NULL){
+ list->set(i, name);
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+ for(int j=0;j<i;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ int iIndex = countTable->get(matrixNames[i]);
+ int jIndex = countTable->get(matrixNames[j]);
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+ if (iIndex < jIndex) {
+ PDistCell value(jIndex, distance);
+ DMatrix->addCell(iIndex, value);
+ }else {
+ PDistCell value(iIndex, distance);
+ DMatrix->addCell(jIndex, value);
+ }
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+ else{
+
+ reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int index = nseqs;
+
+ for(int i=1;i<nseqs;i++){
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+
+ if(countTable == NULL){
+ list->set(i, name);
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ PDistCell value(i, distance);
+ DMatrix->addCell(j, value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ int iIndex = countTable->get(matrixNames[i]);
+ int jIndex = countTable->get(matrixNames[j]);
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+ if (iIndex < jIndex) {
+ PDistCell value(jIndex, distance);
+ DMatrix->addCell(iIndex, value);
+ }else {
+ PDistCell value(iIndex, distance);
+ DMatrix->addCell(jIndex, value);
+
+ }
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ delete reading;
+
+ list->setLabel("0");
+ fileHandle.close();
+
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadPhylipMatrix", "read");
+ exit(1);
+ }
+}
/***********************************************************************/
ReadPhylipMatrix::~ReadPhylipMatrix(){}
/***********************************************************************/
ReadPhylipMatrix(string, bool);
~ReadPhylipMatrix();
int read(NameAssignment*);
+ int read(CountTable*);
private:
ifstream fileHandle;
string distFile;
helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, alignreport, taxonomy, optimize, criteria and processors.\n";
helpString += "The fasta parameter is required.\n";
helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n";
- helpString += "The start parameter .... The default is -1.\n";
- helpString += "The end parameter .... The default is -1.\n";
+ helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1.\n";
+ helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n";
helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
int length = MPIPos[start+i+1] - MPIPos[start+i];
char* buf4 = new char[length];
- memcpy(buf4, outputString.c_str(), length);
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
+ CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
try {
string helpString = "";
helpString += "The set.current command allows you to set the current files saved by mothur.\n";
- helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom and taxonomy.\n";
+ helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count and taxonomy.\n";
helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
helpString += "The set.current command should be in the following format: \n";
helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
if (path == "") { parameters["ordergroup"] = 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; }
+ }
+
it = parameters.find("relabund");
//user has given a template file
if(it != parameters.end()){
if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
else if (groupfile == "not found") { groupfile = ""; }
if (groupfile != "") { m->setGroupFile(groupfile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { m->mothurOut("Ignoring: " + parameters["count"]); m->mothurOutEndLine(); countfile = ""; }
+ else if (countfile == "not found") { countfile = ""; }
+ if (countfile != "") { m->setCountTableFile(countfile); }
designfile = validParameter.validFile(parameters, "design", true);
if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
m->setFlowFile("");
}else if (types[i] == "biom") {
m->setBiomFile("");
+ }else if (types[i] == "count") {
+ m->setCountTableFile("");
}else if (types[i] == "processors") {
m->setProcessors("1");
}else if (types[i] == "all") {
string clearTypes;
vector<string> types;
- string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
+ string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile;
string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile;
}
}
- random_shuffle(mins.begin(), mins.end()); //randomize the order of the iterators in the mins vector
+ //random_shuffle(mins.begin(), mins.end()); //randomize the order of the iterators in the mins vector
row = mins[0].row;
ull col = mins[0].col;
delete uniqueCommand;
m->mothurCalling = false;
- m->renameFile(filenames["name"][0], outputNameFileName);
- m->renameFile(filenames["fasta"][0], outputFileName);
+ m->renameFile(filenames["name"][0], outputNameFileName);
+ m->renameFile(filenames["fasta"][0], outputFileName);
outputTypes["name"].push_back(outputNameFileName); outputNames.push_back(outputNameFileName);
}
temp.close();
- //m->mothurRemove(outputNames[i]);
+ m->mothurRemove(outputNames[i]);
}
projects / mothur.git / commitdiff