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|
//
// renameseqscommand.cpp
// Mothur
//
// Created by SarahsWork on 5/28/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#include "renameseqscommand.h"
#include "sequence.hpp"
#include "groupmap.h"
//**********************************************************************************************************************
vector<string> RenameSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,true,true); parameters.push_back(pgroup);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "RenameSeqsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string RenameSeqsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The rename.seqs command reads a fastafile and groupfile with an optional namefile, and creates files with the sequence names concatenated with the group. For example if a line in the group file is 'seq1 group1', the new sequence name will be seq1_group1.\n";
helpString += "The rename.seqs command parameters are fasta, name and group. Fasta and group are required, unless a current file is available for both.\n";
helpString += "The rename.seqs command should be in the following format: \n";
helpString += "rename.seqs(fasta=yourFastaFile, group=yourGroupFile) \n";
helpString += "Example rename.seqs(fasta=abrecovery.unique.fasta, group=abrecovery.group).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "RenameSeqsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string RenameSeqsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "fasta") { pattern = "[filename],renamed,[extension]"; }
else if (type == "name") { pattern = "[filename],renamed,[extension]"; }
else if (type == "group") { pattern = "[filename],renamed,[extension]"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "RenameSeqsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
RenameSeqsCommand::RenameSeqsCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "RenameSeqsCommand", "RenameSeqsCommand");
exit(1);
}
}
/**************************************************************************************/
RenameSeqsCommand::RenameSeqsCommand(string option) {
try {
abort = false; calledHelp = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
it = parameters.find("group");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["group"] = inputDir + it->second; }
}
}
//check for required parameters
fastaFile = validParameter.validFile(parameters, "fasta", true);
if (fastaFile == "not open") { abort = true; }
else if (fastaFile == "not found") {
fastaFile = m->getFastaFile();
if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setFastaFile(fastaFile); }
//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 = "";
outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
}
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") {
groupfile = m->getGroupFile();
if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setGroupFile(groupfile); }
//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 = ""; }
nameFile = validParameter.validFile(parameters, "name", true);
if (nameFile == "not open") { abort = true; }
else if (nameFile == "not found"){ nameFile =""; }
else { m->setNameFile(nameFile); }
if (nameFile == "") {
vector<string> files; files.push_back(fastaFile);
parser.getNameFile(files);
}
}
}
catch(exception& e) {
m->errorOut(e, "RenameSeqsCommand", "RenameSeqsCommand");
exit(1);
}
}
/**************************************************************************************/
int RenameSeqsCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
GroupMap groupMap(groupfile);
groupMap.readMap();
//prepare filenames and open files
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastaFile); }
string outFastaFile = thisOutputDir + m->getRootName(m->getSimpleName(fastaFile));
map<string, string> variables;
variables["[filename]"] = outFastaFile;
variables["[extension]"] = m->getExtension(fastaFile);
outFastaFile = getOutputFileName("fasta", variables);
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
ofstream outFasta;
m->openOutputFile(outFastaFile, outFasta);
ifstream in;
m->openInputFile(fastaFile, in);
while (!in.eof()) {
if (m->control_pressed) { break; }
Sequence seq(in); m->gobble(in);
string group = groupMap.getGroup(seq.getName());
if (group == "not found") { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = seq.getName() + "_" + group;
seq.setName(newName);
seq.printSequence(outFasta);
}
}
in.close();
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
bool notDone = true;
if (nameFile != "") {
thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(nameFile); }
string outNameFile = thisOutputDir + m->getRootName(m->getSimpleName(nameFile));
variables["[filename]"] = outNameFile;
variables["[extension]"] = m->getExtension(nameFile);
outNameFile = getOutputFileName("group", variables);
outputNames.push_back(outNameFile); outputTypes["name"].push_back(outNameFile);
ofstream outName;
m->openOutputFile(outNameFile, outName);
map<string, vector<string> > nameMap;
m->readNames(nameFile, nameMap);
//process name file changing names
for (map<string, vector<string> >::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
for (int i = 0; i < (it->second).size()-1; i++) {
if (m->control_pressed) { break; }
string group = groupMap.getGroup((it->second)[i]);
if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[i] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = (it->second)[i] + "_" + group;
groupMap.renameSeq((it->second)[i], newName); //change in group file
(it->second)[i] = newName; //change in namefile
}
if (i == 0) { outName << (it->second)[i] << '\t' << (it->second)[i] << ','; }
else { outName << (it->second)[i] << ','; }
}
//print last one
if ((it->second).size() == 1) {
string group = groupMap.getGroup((it->second)[0]);
if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[0] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = (it->second)[0] + "_" + group;
groupMap.renameSeq((it->second)[0], newName); //change in group file
(it->second)[0] = newName; //change in namefile
outName << (it->second)[0] << '\t' << (it->second)[0] << endl;
}
}
else {
string group = groupMap.getGroup((it->second)[(it->second).size()-1]);
if (group == "not found") { m->mothurOut("[ERROR]: " + (it->second)[(it->second).size()-1] + " is not in your group file, please correct.\n"); m->control_pressed = true; }
else {
string newName = (it->second)[(it->second).size()-1] + "_" + group;
groupMap.renameSeq((it->second)[(it->second).size()-1], newName); //change in group file
(it->second)[(it->second).size()-1] = newName; //change in namefile
outName << (it->second)[(it->second).size()-1] << endl;
}
}
}
notDone = false;
outName.close();
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (notDone) {
vector<string> seqs = groupMap.getNamesSeqs();
for (int i = 0; i < seqs.size(); i++) {
if (m->control_pressed) { break; }
string group = groupMap.getGroup(seqs[i]);
string newName = seqs[i] + "_" + group;
groupMap.renameSeq(seqs[i], newName);
}
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
string outGroupFile = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
variables["[filename]"] = outGroupFile;
variables["[extension]"] = m->getExtension(groupfile);
outGroupFile = getOutputFileName("group", variables);
outputNames.push_back(outGroupFile); outputTypes["group"].push_back(outGroupFile);
ofstream outGroup;
m->openOutputFile(outGroupFile, outGroup);
groupMap.print(outGroup);
outGroup.close();
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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();
//set fasta file as new current fastafile
string current = "";
itTypes = outputTypes.find("fasta");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
itTypes = outputTypes.find("name");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RenameSeqsCommand", "execute");
exit(1);
}
}
/**************************************************************************************/
|
