#include "refchimeratest.h"
//**********************************************************************************************************************
-vector<string> SeqErrorCommand::getValidParameters(){
+vector<string> SeqErrorCommand::setParameters(){
try {
- string Array[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "outputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pquery("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pquery);
+ CommandParameter preference("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(preference);
+ CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(pqfile);
+ CommandParameter preport("report", "InputTypes", "", "", "none", "none", "QualReport",false,false); parameters.push_back(preport);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pignorechimeras("ignorechimeras", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pignorechimeras);
+ CommandParameter pthreshold("threshold", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pthreshold);
+ 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, "SeqErrorCommand", "getValidParameters");
+ m->errorOut(e, "SeqErrorCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SeqErrorCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The seq.error command reads a query alignment file and a reference alignment file and creates .....\n";
+ helpString += "Example seq.error(...).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+ helpString += "For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqErrorCommand", "getHelpString");
exit(1);
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-vector<string> SeqErrorCommand::getRequiredParameters(){
- try {
- string Array[] = {"query","reference"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqErrorCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SeqErrorCommand::getRequiredFiles(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqErrorCommand", "getRequiredFiles");
- exit(1);
- }
-}
//***************************************************************************************************************
SeqErrorCommand::SeqErrorCommand(string option) {
else {
string temp;
-
- //valid paramters for this command
- string AlignArray[] = {"query", "reference", "name", "qfile", "report", "threshold", "inputdir", "ignorechimeras", "outputdir"};
-
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
- it = parameters.find("query");
+ 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["query"] = inputDir + it->second; }
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("reference");
}
//check for required parameters
- queryFileName = validParameter.validFile(parameters, "query", true);
- if (queryFileName == "not found") { m->mothurOut("query is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
+ queryFileName = validParameter.validFile(parameters, "fasta", true);
+ if (queryFileName == "not found") {
+ queryFileName = m->getFastaFile();
+ if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (queryFileName == "not open") { abort = true; }
referenceFileName = validParameter.validFile(parameters, "reference", true);
//check for optional parameters
namesFileName = validParameter.validFile(parameters, "name", true);
if(namesFileName == "not found"){ namesFileName = ""; }
+ else if (namesFileName == "not open") { namesFileName = ""; abort = true; }
qualFileName = validParameter.validFile(parameters, "qfile", true);
if(qualFileName == "not found"){ qualFileName = ""; }
+ else if (qualFileName == "not open") { qualFileName = ""; abort = true; }
reportFileName = validParameter.validFile(parameters, "report", true);
if(reportFileName == "not found"){ reportFileName = ""; }
+ else if (reportFileName == "not open") { reportFileName = ""; abort = true; }
if((reportFileName != "" && qualFileName == "") || (reportFileName == "" && qualFileName != "")){
m->mothurOut("if you use either a qual file or a report file, you have to have both.");
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void SeqErrorCommand::help(){
- try {
- m->mothurOut("The seq.error command reads a query alignment file and a reference alignment file and creates .....\n");
- m->mothurOut("Example seq.error(...).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
- m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/seq.error .\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "SeqErrorCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-SeqErrorCommand::~SeqErrorCommand(){ /* void */ }
-
//***************************************************************************************************************
int SeqErrorCommand::execute(){
qualForwardMap.resize(maxLength);
qualReverseMap.resize(maxLength);
for(int i=0;i<maxLength;i++){
- qualForwardMap[i].assign(maxLength,0);
- qualReverseMap[i].assign(maxLength,0);
+ qualForwardMap[i].assign(41,0);
+ qualReverseMap[i].assign(41,0);
}
}
ofstream errorCountFile;
m->openOutputFile(errorCountFileName, errorCountFile);
outputNames.push_back(errorCountFileName); outputTypes["error.count"].push_back(errorCountFileName);
- m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n\n");
+ m->mothurOut("Overall error rate:\t" + toString((double)(totalBases - totalMatches) / (double)totalBases) + "\n");
m->mothurOut("Errors\tSequences\n");
errorCountFile << "Errors\tSequences\n";
for(int i=0;i<misMatchCounts.size();i++){
//***************************************************************************************************************
void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector<vector<int> > qualReverseMap){
- try{
-
- int lastRow = 0;
- int lastColumn = 0;
+ try{
+ int numRows = 0;
+ int numColumns = qualForwardMap[0].size();
for(int i=0;i<qualForwardMap.size();i++){
- for(int j=0;j<qualForwardMap[i].size();j++){
+ for(int j=0;j<numColumns;j++){
if(qualForwardMap[i][j] != 0){
- if(lastRow < i) { lastRow = i+2; }
- if(lastColumn < j) { lastColumn = j+2; }
+ if(numRows < i) { numRows = i+20; }
}
}
}
m->openOutputFile(qualityForwardFileName, qualityForwardFile);
outputNames.push_back(qualityForwardFileName); outputTypes["error.qual.forward"].push_back(qualityForwardFileName);
- for(int i=0;i<lastColumn;i++){ qualityForwardFile << '\t' << i; } qualityForwardFile << endl;
+ for(int i=0;i<numColumns;i++){ qualityForwardFile << '\t' << i; } qualityForwardFile << endl;
- for(int i=0;i<lastRow;i++){
+ for(int i=0;i<numRows;i++){
qualityForwardFile << i+1;
- for(int j=0;j<lastColumn;j++){
+ for(int j=0;j<numColumns;j++){
qualityForwardFile << '\t' << qualForwardMap[i][j];
}
m->openOutputFile(qualityReverseFileName, qualityReverseFile);
outputNames.push_back(qualityReverseFileName); outputTypes["error.qual.reverse"].push_back(qualityReverseFileName);
- for(int i=0;i<lastColumn;i++){ qualityReverseFile << '\t' << i; } qualityReverseFile << endl;
- for(int i=0;i<lastRow;i++){
+ for(int i=0;i<numColumns;i++){ qualityReverseFile << '\t' << i; } qualityReverseFile << endl;
+ for(int i=0;i<numRows;i++){
qualityReverseFile << i+1;
- for(int j=0;j<lastColumn;j++){
+ for(int j=0;j<numColumns;j++){
qualityReverseFile << '\t' << qualReverseMap[i][j];
}
qualityReverseFile << endl;
m->errorOut(e, "SeqErrorCommand", "printErrorFRFile");
exit(1);
}
+
}
-
//***************************************************************************************************************
projects / mothur.git / blobdiff