X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makegroupcommand.cpp;h=68b1e84d0e7e6eb811971128d14490832ad390ae;hb=1a968f34ae2d2680eaf189a197d1a21b8dfd6c03;hp=6f640eb0732274bf6970c346dc9d6b9de553b1b4;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp index 6f640eb..68b1e84 100644 --- a/makegroupcommand.cpp +++ b/makegroupcommand.cpp @@ -14,10 +14,11 @@ //********************************************************************************************************************** vector MakeGroupCommand::setParameters(){ try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + 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); } @@ -38,7 +39,7 @@ string MakeGroupCommand::getHelpString(){ 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\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n"; return helpString; } catch(exception& e) { @@ -47,6 +48,21 @@ string MakeGroupCommand::getHelpString(){ } } //********************************************************************************************************************** +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); + } +} +//********************************************************************************************************************** MakeGroupCommand::MakeGroupCommand(){ try { abort = true; calledHelp = true; @@ -69,6 +85,7 @@ 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 { vector myArray = setParameters(); @@ -102,51 +119,71 @@ MakeGroupCommand::MakeGroupCommand(string option) { //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; } @@ -186,7 +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); @@ -195,7 +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; } } @@ -205,7 +242,7 @@ 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