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|
//
// getdistscommand.cpp
// Mothur
//
// Created by Sarah Westcott on 1/28/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#include "getdistscommand.h"
//**********************************************************************************************************************
vector<string> GetDistsCommand::setParameters(){
try {
CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "PhylipColumn", "none","phylip",false,false,true); parameters.push_back(pphylip);
CommandParameter pcolumn("column", "InputTypes", "", "", "none", "PhylipColumn", "none","column",false,false,true); parameters.push_back(pcolumn);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["phylip"] = tempOutNames;
outputTypes["column"] = tempOutNames;
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, "GetDistsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string GetDistsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The get.dists command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.\n";
helpString += "The get.dists command parameters are accnos, phylip and column.\n";
helpString += "The get.dists command should be in the following format: get.dists(accnos=yourAccnos, phylip=yourPhylip).\n";
helpString += "Example get.dists(accnos=final.accnos, phylip=final.an.thetayc.0.03.lt.ave.dist).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "GetDistsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string GetDistsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "phylip") { pattern = "[filename],pick,[extension]"; }
else if (type == "column") { pattern = "[filename],pick,[extension]"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "GetDistsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
GetDistsCommand::GetDistsCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos");
if (accnosfile == "not open") { abort = true; }
else if (accnosfile == "not found") {
accnosfile = current->getAccnosFile();
if (accnosfile != "") { m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter.\n"); }
else {
m->mothurOut("You have no valid accnos file and accnos is required.\n");
abort = true;
}
}else { current->setAccnosFile(accnosfile); }
phylipfile = validParameter.validFile(parameters, "phylip");
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
else { current->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column");
if (columnfile == "not open") { columnfile = ""; abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
else { current->setColumnFile(columnfile); }
if ((phylipfile == "") && (columnfile == "")) {
//is there are current file available for either of these?
//give priority to column, then phylip
columnfile = current->getColumnFile();
if (columnfile != "") { m->mothurOut("Using " + columnfile + " as input file for the column parameter.\n"); }
else {
phylipfile = current->getPhylipFile();
if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter.\n"); }
else {
m->mothurOut("No valid current files. You must provide a phylip or column file.\n"); abort = true;
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "GetDistsCommand", "GetDistsCommand");
exit(1);
}
}
//**********************************************************************************************************************
int GetDistsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
//get names you want to keep
names = util.readAccnos(accnosfile);
if (m->getControl_pressed()) { return 0; }
//read through the correct file and output lines you want to keep
if (phylipfile != "") { readPhylip(); }
if (columnfile != "") { readColumn(); }
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
if (outputNames.size() != 0) {
m->mothurOutEndLine();
m->mothurOut("Output File names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
//set fasta file as new current fastafile
string currentName = "";
itTypes = outputTypes.find("phylip");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setPhylipFile(currentName); }
}
itTypes = outputTypes.find("column");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setColumnFile(currentName); }
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetDistsCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int GetDistsCommand::readPhylip(){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(phylipfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(phylipfile));
variables["[extension]"] = util.getExtension(phylipfile);
string outputFileName = getOutputFileName("phylip", variables);
ifstream in; util.openInputFile(phylipfile, in);
float distance;
int square, nseqs; square = 0;
string name;
unsigned int row;
set<unsigned int> rows; //converts names in names to a index
row = 0;
string numTest;
in >> numTest >> name;
if (!util.isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting.\n"); exit(1); }
else { convert(numTest, nseqs); }
if (names.count(name) != 0) { rows.insert(row); }
row++;
//is the matrix square?
char d;
while((d=in.get()) != EOF){
if(isalnum(d)){
square = 1;
in.putback(d);
for(int i=0;i<nseqs;i++){
in >> distance;
}
break;
}
if(d == '\n'){
square = 0;
break;
}
}
//map name to row/column
if(square == 0){
for(int i=1;i<nseqs;i++){
in >> name;
if (names.count(name) != 0) { rows.insert(row); }
row++;
for(int j=0;j<i;j++){
if (m->getControl_pressed()) { in.close(); return 0; }
in >> distance;
}
}
}
else{
for(int i=1;i<nseqs;i++){
in >> name;
if (names.count(name) != 0) { rows.insert(row); }
row++;
for(int j=0;j<nseqs;j++){
if (m->getControl_pressed()) { in.close(); return 0; }
in >> distance;
}
}
}
in.close();
if (m->getControl_pressed()) { return 0; }
//read through file only printing rows and columns of seqs in names
ifstream inPhylip;
util.openInputFile(phylipfile, inPhylip);
inPhylip >> numTest;
ofstream out;
util.openOutputFile(outputFileName, out);
outputTypes["phylip"].push_back(outputFileName); outputNames.push_back(outputFileName);
out << names.size() << endl;
unsigned int count = 0;
if(square == 0){
for(int i=0;i<nseqs;i++){
inPhylip >> name;
bool ignoreRow = false;
if (names.count(name) == 0) { ignoreRow = true; }
else{ out << name << '\t'; count++; }
for(int j=0;j<i;j++){
if (m->getControl_pressed()) { inPhylip.close(); out.close(); return 0; }
inPhylip >> distance;
if (!ignoreRow) {
//is this a column we want
if(rows.count(j) != 0) { out << distance << '\t'; }
}
}
if (!ignoreRow) { out << endl; }
}
}
else{
for(int i=0;i<nseqs;i++){
inPhylip >> name;
bool ignoreRow = false;
if (names.count(name) == 0) { ignoreRow = true; }
else{ out << name << '\t'; count++; }
for(int j=0;j<nseqs;j++){
if (m->getControl_pressed()) { inPhylip.close(); out.close(); return 0; }
inPhylip >> distance;
if (!ignoreRow) {
//is this a column we want
if(rows.count(j) != 0) { out << distance << '\t'; }
}
}
if (!ignoreRow) { out << endl; }
}
}
inPhylip.close();
out.close();
if (count == 0) { m->mothurOut("Your file does NOT contain distances related to groups or sequences listed in the accnos file.\n"); }
else if (count != names.size()) {
m->mothurOut("[WARNING]: Your accnos file contains " + toString(names.size()) + " groups or sequences, but I only found " + toString(count) + " of them in the phylip file.\n");
//rewrite with new number
util.renameFile(outputFileName, outputFileName+".temp");
ofstream out2;
util.openOutputFile(outputFileName, out2);
out2 << count << endl;
ifstream in3;
util.openInputFile(outputFileName+".temp", in3);
in3 >> nseqs; gobble(in3);
char buffer[4096];
while (!in3.eof()) {
in3.read(buffer, 4096);
out2.write(buffer, in3.gcount());
}
in3.close();
out2.close();
util.mothurRemove(outputFileName+".temp");
}
m->mothurOut("Selected " + toString(count) + " groups or sequences from your phylip file.\n");
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetDistsCommand", "readPhylip");
exit(1);
}
}
//**********************************************************************************************************************
int GetDistsCommand::readColumn(){
try {
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(columnfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(columnfile));
variables["[extension]"] = util.getExtension(columnfile);
string outputFileName = getOutputFileName("column", variables);
outputTypes["column"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
util.openOutputFile(outputFileName, out);
ifstream in; util.openInputFile(columnfile, in);
set<string> foundNames;
string firstName, secondName;
float distance;
while (!in.eof()) {
if (m->getControl_pressed()) { out.close(); in.close(); return 0; }
in >> firstName >> secondName >> distance; gobble(in);
//are both names in the accnos file
if ((names.count(firstName) != 0) && (names.count(secondName) != 0)) {
out << firstName << '\t' << secondName << '\t' << distance << endl;
foundNames.insert(firstName);
foundNames.insert(secondName);
}
}
in.close();
out.close();
if (foundNames.size() == 0) { m->mothurOut("Your file does NOT contain distances related to groups or sequences listed in the accnos file.\n"); }
else if (foundNames.size() != names.size()) {
m->mothurOut("[WARNING]: Your accnos file contains " + toString(names.size()) + " groups or sequences, but I only found " + toString(foundNames.size()) + " of them in the column file.\n");
}
m->mothurOut("Selected " + toString(foundNames.size()) + " groups or sequences from your column file.\n");
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetDistsCommand", "readColumn");
exit(1);
}
}
//**********************************************************************************************************************
|
