X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makegroupcommand.cpp;h=68b1e84d0e7e6eb811971128d14490832ad390ae;hp=1c04fecb477d09e0e6de73b1307a3878fcc8e4b3;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18 diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp index 1c04fec..68b1e84 100644 --- a/makegroupcommand.cpp +++ b/makegroupcommand.cpp @@ -10,53 +10,72 @@ #include "makegroupcommand.h" #include "sequence.hpp" + //********************************************************************************************************************** -vector MakeGroupCommand::getValidParameters(){ +vector MakeGroupCommand::setParameters(){ try { - string Array[] = {"fasta", "output","groups","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pfasta); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pgroups); + CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput); + 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, "MakeGroupCommand", "getValidParameters"); + m->errorOut(e, "MakeGroupCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -MakeGroupCommand::MakeGroupCommand(){ +string MakeGroupCommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["group"] = tempOutNames; + string helpString = ""; + helpString += "The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n"; + helpString += "The make.group command parameters are fasta, groups and output. Fasta and group are required.\n"; + helpString += "The output parameter allows you to specify the name of groupfile created. \n"; + helpString += "The make.group command should be in the following format: \n"; + helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n"; + helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand"); + m->errorOut(e, "MakeGroupCommand", "getHelpString"); 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); - } +string MakeGroupCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "group") { pattern = "[filename],groups"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "MakeGroupCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** -vector MakeGroupCommand::getRequiredFiles(){ +MakeGroupCommand::MakeGroupCommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["group"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "MakeGroupCommand", "getRequiredFiles"); + m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand"); exit(1); } } + //********************************************************************************************************************** MakeGroupCommand::MakeGroupCommand(string option) { @@ -66,12 +85,10 @@ MakeGroupCommand::MakeGroupCommand(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 AlignArray[] = {"fasta","groups","output","outputdir","inputdir"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -93,57 +110,80 @@ MakeGroupCommand::MakeGroupCommand(string option) { if (inputDir == "not found"){ inputDir = ""; } 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 { + if (fastaFileName == "not found") { //if there is a current fasta file, use it + string filename = m->getFastaFile(); + if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " 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(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 = 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; + + 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(); + filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); + } + else { + m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + fastaFileNames.erase(fastaFileNames.begin()+i); + i--; } } - //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; + 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]; } } - } - in.close(); + + 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--; - }else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[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{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); m->setFastaFile(fastaFileNames[i]); } + } } //prevent giantic file name - if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; } - else { filename += "groups"; } + map variables; + variables["[filename]"] = filename; + if (fastaFileNames.size() > 3) { variables["[filename]"] = outputDir + "merge"; } + filename = getOutputFileName("group",variables); //make sure there is at least one valid file left if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; } @@ -162,37 +202,12 @@ MakeGroupCommand::MakeGroupCommand(string option) { 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"); exit(1); } } - -//********************************************************************************************************************** - -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, 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("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"); - } - catch(exception& e) { - m->errorOut(e, "MakeGroupCommand", "help"); - exit(1); - } -} - - //********************************************************************************************************************** int MakeGroupCommand::execute(){ @@ -208,7 +223,7 @@ int MakeGroupCommand::execute(){ for (int i = 0; i < fastaFileNames.size(); i++) { - if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; } ifstream in; m->openInputFile(fastaFileNames[i], in); @@ -217,7 +232,7 @@ int MakeGroupCommand::execute(){ Sequence seq(in, "no align"); m->gobble(in); - if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); remove(filename.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); m->mothurRemove(filename); return 0; } if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; } } @@ -227,9 +242,16 @@ int MakeGroupCommand::execute(){ out.close(); m->mothurOutEndLine(); - m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); + m->mothurOut("Output File Names: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename); m->mothurOutEndLine(); - + + //set group file as new current groupfile + string current = ""; + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + return 0; } catch(exception& e) {