X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.cpp;h=406085728838262b79100a70133600639e6c47a2;hb=e840ba0e90a2b2be39e0910e4be23dde6a14cbac;hp=d23949f497e65b262e3067d74d566d4665124412;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git diff --git a/listseqscommand.cpp b/listseqscommand.cpp index d23949f..4060857 100644 --- a/listseqscommand.cpp +++ b/listseqscommand.cpp @@ -11,18 +11,65 @@ #include "sequence.hpp" #include "listvector.hpp" +//********************************************************************************************************************** +vector ListSeqsCommand::getValidParameters(){ + try { + string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ListSeqsCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +ListSeqsCommand::ListSeqsCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["accnos"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector ListSeqsCommand::getRequiredParameters(){ + try { + string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","or"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ListSeqsCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector ListSeqsCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "ListSeqsCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** ListSeqsCommand::ListSeqsCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string Array[] = {"fasta","name", "group", "alignreport","list","outputdir","inputdir"}; + string Array[] = {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -36,6 +83,10 @@ ListSeqsCommand::ListSeqsCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["accnos"] = tempOutNames; + //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 = ""; } @@ -47,7 +98,7 @@ ListSeqsCommand::ListSeqsCommand(string option) { it = parameters.find("alignreport"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["alignreport"] = inputDir + it->second; } } @@ -55,7 +106,7 @@ ListSeqsCommand::ListSeqsCommand(string option) { it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["fasta"] = inputDir + it->second; } } @@ -63,7 +114,7 @@ ListSeqsCommand::ListSeqsCommand(string option) { it = parameters.find("list"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["list"] = inputDir + it->second; } } @@ -71,7 +122,7 @@ ListSeqsCommand::ListSeqsCommand(string option) { it = parameters.find("name"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } @@ -79,10 +130,18 @@ ListSeqsCommand::ListSeqsCommand(string option) { it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["group"] = inputDir + it->second; } } + + it = parameters.find("taxonomy"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["taxonomy"] = inputDir + it->second; } + } } //check for required parameters @@ -106,11 +165,15 @@ ListSeqsCommand::ListSeqsCommand(string option) { if (listfile == "not open") { abort = true; } else if (listfile == "not found") { listfile = ""; } + taxfile = validParameter.validFile(parameters, "taxonomy", true); + if (taxfile == "not open") { abort = true; } + else if (taxfile == "not found") { taxfile = ""; } - if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "")) { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; } + if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == "")) { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; } int okay = 1; if (outputDir != "") { okay++; } + if (inputDir != "") { okay++; } if (parameters.size() > okay) { m->mothurOut("You may only enter one file."); m->mothurOutEndLine(); abort = true; } } @@ -125,8 +188,8 @@ ListSeqsCommand::ListSeqsCommand(string option) { void ListSeqsCommand::help(){ try { - m->mothurOut("The list.seqs command reads a fasta, name, group, list or alignreport file and outputs a .accnos file containing sequence names.\n"); - m->mothurOut("The list.seqs command parameters are fasta, name, group and alignreport. You must provide one of these parameters.\n"); + m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n"); + m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport. You must provide one of these parameters.\n"); m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n"); m->mothurOut("Example list.seqs(fasta=amazon.fasta).\n"); m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); @@ -142,7 +205,7 @@ void ListSeqsCommand::help(){ int ListSeqsCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } //read functions fill names vector if (fastafile != "") { inputFileName = fastafile; readFasta(); } @@ -150,33 +213,34 @@ int ListSeqsCommand::execute(){ else if (groupfile != "") { inputFileName = groupfile; readGroup(); } else if (alignfile != "") { inputFileName = alignfile; readAlign(); } else if (listfile != "") { inputFileName = listfile; readList(); } + else if (taxfile != "") { inputFileName = taxfile; readTax(); } - if (m->control_pressed) { return 0; } + if (m->control_pressed) { outputTypes.clear(); return 0; } //sort in alphabetical order sort(names.begin(), names.end()); - if (outputDir == "") { outputDir += hasPath(inputFileName); } + if (outputDir == "") { outputDir += m->hasPath(inputFileName); } - string outputFileName = outputDir + getRootName(getSimpleName(inputFileName)) + "accnos"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + "accnos"; ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); //output to .accnos file for (int i = 0; i < names.size(); i++) { - if (m->control_pressed) { out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; } out << names[i] << endl; } out.close(); - if (m->control_pressed) { remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; } m->mothurOutEndLine(); m->mothurOut("Output File Name: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); + m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName); m->mothurOutEndLine(); return 0; @@ -193,7 +257,7 @@ int ListSeqsCommand::readFasta(){ try { ifstream in; - openInputFile(fastafile, in); + m->openInputFile(fastafile, in); string name; while(!in.eof()){ @@ -205,7 +269,7 @@ int ListSeqsCommand::readFasta(){ if (name != "") { names.push_back(name); } - gobble(in); + m->gobble(in); } in.close(); @@ -221,7 +285,7 @@ int ListSeqsCommand::readFasta(){ int ListSeqsCommand::readList(){ try { ifstream in; - openInputFile(listfile, in); + m->openInputFile(listfile, in); if(!in.eof()){ //read in list vector @@ -258,7 +322,7 @@ int ListSeqsCommand::readName(){ try { ifstream in; - openInputFile(namefile, in); + m->openInputFile(namefile, in); string name, firstCol, secondCol; while(!in.eof()){ @@ -278,7 +342,7 @@ int ListSeqsCommand::readName(){ //get name after last , names.push_back(secondCol); - gobble(in); + m->gobble(in); } in.close(); return 0; @@ -295,19 +359,19 @@ int ListSeqsCommand::readGroup(){ try { ifstream in; - openInputFile(groupfile, in); + m->openInputFile(groupfile, in); string name, group; while(!in.eof()){ if (m->control_pressed) { in.close(); return 0; } - in >> name; //read from first column + in >> name; m->gobble(in); //read from first column in >> group; //read from second column names.push_back(name); - gobble(in); + m->gobble(in); } in.close(); return 0; @@ -325,7 +389,7 @@ int ListSeqsCommand::readAlign(){ try { ifstream in; - openInputFile(alignfile, in); + m->openInputFile(alignfile, in); string name, junk; //read column headers @@ -349,7 +413,7 @@ int ListSeqsCommand::readAlign(){ names.push_back(name); - gobble(in); + m->gobble(in); } in.close(); @@ -363,3 +427,33 @@ int ListSeqsCommand::readAlign(){ } } //********************************************************************************************************************** +int ListSeqsCommand::readTax(){ + try { + + ifstream in; + m->openInputFile(taxfile, in); + string name, firstCol, secondCol; + + while(!in.eof()){ + + if (m->control_pressed) { in.close(); return 0; } + + in >> firstCol; + in >> secondCol; + + names.push_back(firstCol); + + m->gobble(in); + + } + in.close(); + + return 0; + + } + catch(exception& e) { + m->errorOut(e, "ListSeqsCommand", "readTax"); + exit(1); + } +} +//**********************************************************************************************************************