#include "deuniqueseqscommand.h"
#include "sequence.hpp"
+#include "counttable.h"
//**********************************************************************************************************************
vector<string> DeUniqueSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+ CommandParameter pname("name", "InputTypes", "", "", "namecount", "namecount", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "namecount", "namecount", "none","group",false,false,true); parameters.push_back(pcount);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
string DeUniqueSeqsCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The deunique.seqs command reads a fastafile and namefile, and creates a fastafile containing all the sequences.\n";
- helpString += "The deunique.seqs command parameters are fasta and name, both are required, unless you have valid current name and fasta files.\n";
+ helpString += "The deunique.seqs command reads a fastafile and namefile or countfile, and creates a fastafile containing all the sequences. It you provide a count file with group information a group file is also created.\n";
+ helpString += "The deunique.seqs command parameters are fasta, name and count. Fasta is required and you must provide either a name or count file.\n";
helpString += "The deunique.seqs command should be in the following format: \n";
helpString += "deunique.seqs(fasta=yourFastaFile, name=yourNameFile) \n";
helpString += "Example deunique.seqs(fasta=abrecovery.unique.fasta, name=abrecovery.names).\n";
try {
string pattern = "";
- if (type == "fasta") { pattern = "[filename],redundant.fasta"; }
+ if (type == "fasta") { pattern = "[filename],redundant.fasta"; }
+ else if (type == "group") { pattern = "[filename],redundant.groups"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
setParameters();
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "DeUniqueSeqsCommand", "DeconvoluteCommand");
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["fasta"] = 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 the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = 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; }
+ }
}
//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
}
nameFile = validParameter.validFile(parameters, "name", true);
if (nameFile == "not open") { abort = true; }
- else if (nameFile == "not found"){
- nameFile = m->getNameFile();
+ else if (nameFile == "not found"){ nameFile = ""; }
+ else { m->setNameFile(nameFile); }
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((countfile != "") && (nameFile != "")) { m->mothurOut("When executing a deunique.seqs command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
+
+
+ if ((countfile == "") && (nameFile == "")) { //look for currents
+ nameFile = m->getNameFile();
if (nameFile != "") { m->mothurOut("Using " + nameFile + " as input file for the name parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setNameFile(nameFile); }
+ else {
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("[ERROR]: You have no current name or count files one is required."); m->mothurOutEndLine(); abort = true; }
+ }
+ }
+
}
}
//prepare filenames and open files
ofstream out;
- string outFastaFile = m->getRootName(m->getSimpleName(fastaFile));
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(fastaFile); }
+ string outFastaFile = thisOutputDir + m->getRootName(m->getSimpleName(fastaFile));
int pos = outFastaFile.find("unique");
if (pos != string::npos) { outFastaFile = outputDir + outFastaFile.substr(0, pos); }
else { outFastaFile = outputDir + outFastaFile; }
outFastaFile = getOutputFileName("fasta", variables);
m->openOutputFile(outFastaFile, out);
- readNamesFile();
- if (m->control_pressed) { out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
+ map<string, string> nameMap;
+ CountTable ct;
+ ofstream outGroup;
+ string outGroupFile;
+ vector<string> groups;
+ if (nameFile != "") { m->readNames(nameFile, nameMap); }
+ else {
+ ct.readTable(countfile, true, false);
+
+ if (ct.hasGroupInfo()) {
+ thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
+ outGroupFile = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[filename]"] = outGroupFile;
+ outGroupFile = getOutputFileName("group", variables);
+ m->openOutputFile(outGroupFile, outGroup);
+ groups = ct.getNamesOfGroups();
+ }
+ }
+
+ if (m->control_pressed) { out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { outGroup.close(); m->mothurRemove(outGroupFile); } } return 0; }
ifstream in;
m->openInputFile(fastaFile, in);
while (!in.eof()) {
- if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); outputTypes.clear(); m->mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { outGroup.close(); m->mothurRemove(outGroupFile); } } return 0; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
- //look for sequence name in nameMap
- map<string, string>::iterator it = nameMap.find(seq.getName());
-
- if (it == nameMap.end()) { m->mothurOut("[ERROR]: Your namefile does not contain " + seq.getName() + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- vector<string> names;
- m->splitAtComma(it->second, names);
-
- //output sequences
- for (int i = 0; i < names.size(); i++) {
- out << ">" << names[i] << endl;
- out << seq.getAligned() << endl;
- }
-
- //remove seq from name map so we can check for seqs in namefile not in fastafile later
- nameMap.erase(it);
- }
+ if (nameFile != "") {
+ //look for sequence name in nameMap
+ map<string, string>::iterator it = nameMap.find(seq.getName());
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: Your namefile does not contain " + seq.getName() + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ vector<string> names;
+ m->splitAtComma(it->second, names);
+
+ //output sequences
+ for (int i = 0; i < names.size(); i++) {
+ out << ">" << names[i] << endl;
+ out << seq.getAligned() << endl;
+ }
+
+ //remove seq from name map so we can check for seqs in namefile not in fastafile later
+ nameMap.erase(it);
+ }
+ }else {
+ if (ct.hasGroupInfo()) {
+ vector<int> groupCounts = ct.getGroupCounts(seq.getName());
+ int count = 1;
+ for (int i = 0; i < groups.size(); i++) {
+ for (int j = 0; j < groupCounts[i]; j++) {
+ outGroup << seq.getName()+"_"+toString(count) << '\t' << groups[i] << endl; count++;
+ }
+ }
+
+ }
+
+ int numReps = ct.getNumSeqs(seq.getName()); //will report error and set m->control_pressed if not found
+ for (int i = 0; i < numReps; i++) {
+ out << ">" << seq.getName()+"_"+toString(i+1) << endl;
+ out << seq.getAligned() << endl;
+ }
+ }
}
}
in.close();
- out.close();
+ out.close();
+ if (countfile != "") { if (ct.hasGroupInfo()) { outGroup.close(); } }
- if (nameMap.size() != 0) { //then there are names in the namefile not in the fastafile
- for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
- m->mothurOut(it->first + " is not in your fasta file, but is in your name file. Please correct."); m->mothurOutEndLine();
- }
- }
-
- if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); return 0; }
+
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { m->mothurRemove(outGroupFile); } }return 0; }
+ outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
+ if (countfile != "") { if (ct.hasGroupInfo()) { outputNames.push_back(outGroupFile); outputTypes["group"].push_back(outGroupFile); } }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outFastaFile); m->mothurOutEndLine();
- outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
- 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 = "";
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "DeUniqueSeqsCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int DeUniqueSeqsCommand::readNamesFile() {
- try {
-
- ifstream inNames;
- m->openInputFile(nameFile, inNames);
-
- string name, names;
- map<string, string>::iterator it;
-
- while(inNames){
-
- if(m->control_pressed) { break; }
-
- inNames >> name; m->gobble(inNames);
- inNames >> names;
-
- it = nameMap.find(name);
-
- if (it == nameMap.end()) { nameMap[name] = names; }
- else { m->mothurOut("[ERROR]: Your namefile already contains " + name + ", aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
-
- m->gobble(inNames);
+
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
- inNames.close();
+
return 0;
-
}
catch(exception& e) {
- m->errorOut(e, "DeUniqueSeqsCommand", "readNamesFile");
+ m->errorOut(e, "DeUniqueSeqsCommand", "execute");
exit(1);
}
}
-
/**************************************************************************************/
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