#include "sequence.hpp"
//**********************************************************************************************************************
-vector<string> SeqSummaryCommand::getValidParameters(){
+vector<string> SeqSummaryCommand::setParameters(){
try {
- string Array[] = {"fasta","name","processors","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ 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, "SeqSummaryCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SeqSummaryCommand::SeqSummaryCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
+ m->errorOut(e, "SeqSummaryCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SeqSummaryCommand::getRequiredParameters(){
+string SeqSummaryCommand::getHelpString(){
try {
- string Array[] = {"fasta"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The summary.seqs command reads a fastafile and summarizes the sequences.\n";
+ helpString += "The summary.seqs command parameters are fasta, name and processors, fasta is required, unless you have a valid current fasta file.\n";
+ helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n";
+ helpString += "The summary.seqs command should be in the following format: \n";
+ helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \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, "SeqSummaryCommand", "getRequiredParameters");
+ m->errorOut(e, "SeqSummaryCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> SeqSummaryCommand::getRequiredFiles(){
+SeqSummaryCommand::SeqSummaryCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "getRequiredFiles");
+ m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
exit(1);
}
}
//allow user to run help
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","name","processors","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); 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); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
//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 += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
- string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
- convert(temp, processors);
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void SeqSummaryCommand::help(){
- try {
- m->mothurOut("The summary.seqs command reads a fastafile and summarizes the sequences.\n");
- m->mothurOut("The summary.seqs command parameters are fasta, name and processors, fasta is required.\n");
- m->mothurOut("The name parameter allows you to enter a name file associated with your fasta file. \n");
- m->mothurOut("The summary.seqs command should be in the following format: \n");
- m->mothurOut("summary.seqs(fasta=yourFastaFile, processors=2) \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, "SeqSummaryCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-SeqSummaryCommand::~SeqSummaryCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int SeqSummaryCommand::execute(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ //set current fasta to fastafile
+ m->setFastaFile(fastafile);
+
string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
int numSeqs = 0;
//append files
for(int i=1;i<processors;i++){
m->appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
- remove((summaryFile + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((summaryFile + toString(processIDS[i]) + ".temp"));
}
}
if (startPosition[0] == -1) { startPosition[0] = 0; }
if (endPosition[0] == -1) { endPosition[0] = 0; }
- if (m->control_pressed) { remove(summaryFile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
- if (m->control_pressed) { remove(summaryFile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in);
in.close();
- remove(tempFilename.c_str());
+ m->mothurRemove(tempFilename);
}
return num;
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