X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=620de95c333cdee1360157f7aa7068f3ce1f1f62;hb=a150db3c2bfd7b76420048a1e94ebe397f2c6045;hp=c0f91969eda2277e4c8b02c3a78db2a7390716fe;hpb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518;p=mothur.git diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp index c0f9196..620de95 100644 --- a/seqsummarycommand.cpp +++ b/seqsummarycommand.cpp @@ -11,49 +11,51 @@ #include "sequence.hpp" //********************************************************************************************************************** -vector SeqSummaryCommand::getValidParameters(){ +vector SeqSummaryCommand::setParameters(){ try { - string Array[] = {"fasta","name","processors","outputdir","inputdir"}; - vector 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 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 tempOutNames; - outputTypes["summary"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand"); + m->errorOut(e, "SeqSummaryCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector SeqSummaryCommand::getRequiredParameters(){ +string SeqSummaryCommand::getHelpString(){ try { - string Array[] = {"fasta"}; - vector 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 SeqSummaryCommand::getRequiredFiles(){ +SeqSummaryCommand::SeqSummaryCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["summary"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "SeqSummaryCommand", "getRequiredFiles"); + m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand"); exit(1); } } @@ -65,11 +67,10 @@ SeqSummaryCommand::SeqSummaryCommand(string option) { //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 myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -111,7 +112,11 @@ SeqSummaryCommand::SeqSummaryCommand(string option) { //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; } + } namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { namefile = ""; abort = true; } @@ -123,8 +128,9 @@ SeqSummaryCommand::SeqSummaryCommand(string option) { 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); } @@ -134,27 +140,6 @@ SeqSummaryCommand::SeqSummaryCommand(string option) { 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(){ @@ -162,6 +147,9 @@ 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; @@ -328,13 +316,14 @@ int SeqSummaryCommand::execute(){ sort(seqLength.begin(), seqLength.end()); sort(ambigBases.begin(), ambigBases.end()); sort(longHomoPolymer.begin(), longHomoPolymer.end()); - - int ptile0_25 = int(numSeqs * 0.025); - int ptile25 = int(numSeqs * 0.250); - int ptile50 = int(numSeqs * 0.500); - int ptile75 = int(numSeqs * 0.750); - int ptile97_5 = int(numSeqs * 0.975); - int ptile100 = numSeqs - 1; + int size = startPosition.size(); + + int ptile0_25 = int(size * 0.025); + int ptile25 = int(size * 0.250); + int ptile50 = int(size * 0.500); + int ptile75 = int(size * 0.750); + int ptile97_5 = int(size * 0.975); + int ptile100 = size - 1; //to compensate for blank sequences that would result in startPosition and endPostion equalling -1 if (startPosition[0] == -1) { startPosition[0] = 0; }