#include "degapseqscommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> DegapSeqsCommand::setParameters(){
+ try {
+ 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); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DegapSeqsCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The degap.seqs command reads a fastafile and removes all gap characters.\n";
+ helpString += "The degap.seqs command parameter is fasta.\n";
+ helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required unless you have a valid current fasta file. \n";
+ helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
+ helpString += "The degap.seqs command should be in the following format: \n";
+ helpString += "degap.seqs(fasta=yourFastaFile) \n";
+ helpString += "Example: degap.seqs(fasta=abrecovery.align) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+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;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DegapSeqsCommand", "DegapSeqsCommand");
+ exit(1);
+ }
+}
//***************************************************************************************************************
-
DegapSeqsCommand::DegapSeqsCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta", "outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = 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 = ""; }
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", false);
- if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the degap.seqs command."); m->mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { fastaFileNames.push_back(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->splitAtDash(fastafile, fastaFileNames);
//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();
- ableToOpen = m->openInputFile(tryPath, in, "noerror");
- 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 (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 (!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 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]); }
}
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void DegapSeqsCommand::help(){
- try {
- m->mothurOut("The degap.seqs command reads a fastafile and removes all gap characters.\n");
- m->mothurOut("The degap.seqs command parameter is fasta.\n");
- m->mothurOut("The fasta parameter allows you to enter the fasta file containing your sequences, and is required. \n");
- m->mothurOut("You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
- m->mothurOut("The degap.seqs command should be in the following format: \n");
- m->mothurOut("degap.seqs(fasta=yourFastaFile) \n");
- m->mothurOut("Example: degap.seqs(fasta=abrecovery.align) \n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "DegapSeqsCommand", "help");
- exit(1);
- }
-}
-
//***************************************************************************************************************
-
-DegapSeqsCommand::~DegapSeqsCommand(){ /* do nothing */ }
-
-//***************************************************************************************************************
-
-
int DegapSeqsCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {
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) { 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() != "") {
inFASTA.close();
outFASTA.close();
- outputNames.push_back(degapFile);
+ outputNames.push_back(degapFile); outputTypes["fasta"].push_back(degapFile);
- if (m->control_pressed) { 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
+ string current = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
}
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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