//**********************************************************************************************************************
vector<string> DegapSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ 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); }
}
}
//**********************************************************************************************************************
+string DegapSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],ng.fasta"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
DegapSeqsCommand::DegapSeqsCommand(){
try {
abort = true; calledHelp = true;
//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();
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
- if (inputDir != "") {
- string path = m->hasPath(fastaFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
- }
-
- ifstream in;
- int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
- }
- }
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+ bool ignore = false;
+ if (fastaFileNames[i] == "current") {
+ fastaFileNames[i] = m->getFastaFile();
+ if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
}
}
- in.close();
+ if (!ignore) {
+ if (inputDir != "") {
+ string path = m->hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ ifstream in;
+ int ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }else { m->setFastaFile(fastaFileNames[i]); }
}
}
ofstream outFASTA;
string tempOutputDir = outputDir;
if (outputDir == "") { tempOutputDir = m->hasPath(fastaFileNames[s]); }
- string degapFile = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+ map<string, string> variables;
+ variables["[filename]"] = tempOutputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
+ string degapFile = getOutputFileName("fasta", variables);
m->openOutputFile(degapFile, outFASTA);
while(!inFASTA.eof()){
- if (m->control_pressed) { outputTypes.clear(); inFASTA.close(); outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); inFASTA.close(); outFASTA.close(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
Sequence currSeq(inFASTA); m->gobble(inFASTA);
if (currSeq.getName() != "") {
outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
- if (m->control_pressed) { outputTypes.clear(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(degapFile); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
}
//set fasta file as new current fastafile
}
m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); 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();
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