X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makegroupcommand.cpp;h=12be82690fc7068e4d713353ee84d79aa6330ba7;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=455826a3a8ab61ec1cf7a5af44e91ba791907583;hpb=80c3fe03a8fd1635d3ad7918ff00beb973449f50;p=mothur.git diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp index 455826a..12be826 100644 --- a/makegroupcommand.cpp +++ b/makegroupcommand.cpp @@ -10,6 +10,54 @@ #include "makegroupcommand.h" #include "sequence.hpp" +//********************************************************************************************************************** +vector MakeGroupCommand::getValidParameters(){ + try { + string Array[] = {"fasta", "output","groups","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "MakeGroupCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +MakeGroupCommand::MakeGroupCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["group"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector MakeGroupCommand::getRequiredParameters(){ + try { + string Array[] = {"fasta","groups"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "MakeGroupCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector MakeGroupCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "MakeGroupCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** MakeGroupCommand::MakeGroupCommand(string option) { @@ -23,7 +71,7 @@ MakeGroupCommand::MakeGroupCommand(string option) { else { //valid paramters for this command - string AlignArray[] = {"fasta","groups","outputdir","inputdir"}; + string AlignArray[] = {"fasta","groups","output","outputdir","inputdir"}; vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); OptionParser parser(option); @@ -36,39 +84,51 @@ MakeGroupCommand::MakeGroupCommand(string option) { for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - - //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 = ""; } - + //initialize outputTypes + vector tempOutNames; + outputTypes["group"] = 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 = ""; } - - filename = outputDir; fastaFileName = validParameter.validFile(parameters, "fasta", false); if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(fastaFileName, fastaFileNames); + m->splitAtDash(fastaFileName, 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 = hasPath(fastaFileNames[i]); + 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 = openInputFile(fastaFileNames[i], in, "noerror"); + 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() + getSimpleName(fastaFileNames[i]); + string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]); m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); - ableToOpen = openInputFile(tryPath, in, "noerror"); + 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; } } @@ -79,22 +139,31 @@ MakeGroupCommand::MakeGroupCommand(string option) { //erase from file list fastaFileNames.erase(fastaFileNames.begin()+i); i--; - }else{ filename += getRootName(getSimpleName(fastaFileNames[i])); } + }else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); } } - filename += "groups"; + //prevent giantic file name + if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; } + else { filename += "groups"; } //make sure there is at least one valid file left if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } } + //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 = ""; } + + output = validParameter.validFile(parameters, "output", false); + if (output == "not found") { output = ""; } + else{ filename = output; } + groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true; } - else { splitAtDash(groups, groupsNames); } + else { m->splitAtDash(groups, groupsNames); } if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups. This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true; } } - + cout << "here" << endl; } catch(exception& e) { m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand"); @@ -111,9 +180,10 @@ MakeGroupCommand::~MakeGroupCommand(){ } void MakeGroupCommand::help(){ try { m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n"); - m->mothurOut("The make.group command parameters are fasta and groups, both are required.\n"); + m->mothurOut("The make.group command parameters are fasta, groups and output. Fasta and group are required.\n"); + m->mothurOut("The output parameter allows you to specify the name of groupfile created. \n"); m->mothurOut("The make.group command should be in the following format: \n"); - m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups. \n"); + m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups). \n"); m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n"); } @@ -128,23 +198,27 @@ void MakeGroupCommand::help(){ int MakeGroupCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { return 0; } + + if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); } + + filename = outputDir + filename; ofstream out; - openOutputFile(filename, out); + m->openOutputFile(filename, out); for (int i = 0; i < fastaFileNames.size(); i++) { - if (m->control_pressed) { out.close(); remove(filename.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; } ifstream in; - openInputFile(fastaFileNames[i], in); + m->openInputFile(fastaFileNames[i], in); while (!in.eof()) { - Sequence seq(in, "no align"); gobble(in); + Sequence seq(in, "no align"); m->gobble(in); - if (m->control_pressed) { in.close(); out.close(); remove(filename.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); remove(filename.c_str()); return 0; } if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; } } @@ -154,7 +228,7 @@ int MakeGroupCommand::execute(){ out.close(); m->mothurOutEndLine(); - m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); + m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); m->mothurOutEndLine(); return 0;