X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=b48ba28709acfb2b0f1355743c5a860cee1c8529;hb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;hp=5e77a1d296b1d740f9ecd58209f555f33c8ac73f;hpb=0c78e45408d8c099bc51579225ebfc227f7523b2;p=mothur.git diff --git a/getseqscommand.cpp b/getseqscommand.cpp index 5e77a1d..b48ba28 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -12,7 +12,59 @@ #include "listvector.hpp" //********************************************************************************************************************** - +vector GetSeqsCommand::getValidParameters(){ + try { + string Array[] = {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +GetSeqsCommand::GetSeqsCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["list"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetSeqsCommand::getRequiredParameters(){ + try { + string Array[] = {"accnos"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector GetSeqsCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "GetSeqsCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** GetSeqsCommand::GetSeqsCommand(string option) { try { abort = false; @@ -22,7 +74,7 @@ GetSeqsCommand::GetSeqsCommand(string option) { else { //valid paramters for this command - string Array[] = {"fasta","name", "group", "alignreport", "accnos", "list","taxonomy","outputdir","inputdir"}; + string Array[] = {"fasta","name", "group", "alignreport", "accnos", "dups", "list","taxonomy","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -36,6 +88,15 @@ GetSeqsCommand::GetSeqsCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + outputTypes["taxonomy"] = tempOutNames; + outputTypes["name"] = tempOutNames; + outputTypes["group"] = tempOutNames; + outputTypes["alignreport"] = tempOutNames; + outputTypes["list"] = 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 +108,7 @@ GetSeqsCommand::GetSeqsCommand(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 +116,7 @@ GetSeqsCommand::GetSeqsCommand(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 +124,7 @@ GetSeqsCommand::GetSeqsCommand(string option) { it = parameters.find("accnos"); //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["accnos"] = inputDir + it->second; } } @@ -71,7 +132,7 @@ GetSeqsCommand::GetSeqsCommand(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; } } @@ -79,7 +140,7 @@ GetSeqsCommand::GetSeqsCommand(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; } } @@ -87,7 +148,7 @@ GetSeqsCommand::GetSeqsCommand(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; } } @@ -95,7 +156,7 @@ GetSeqsCommand::GetSeqsCommand(string option) { it = parameters.find("taxonomy"); //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["taxonomy"] = inputDir + it->second; } } @@ -133,7 +194,7 @@ GetSeqsCommand::GetSeqsCommand(string option) { string usedDups = "true"; string temp = validParameter.validFile(parameters, "dups", false); if (temp == "not found") { temp = "false"; usedDups = ""; } - dups = isTrue(temp); + dups = m->isTrue(temp); if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; } @@ -185,7 +246,7 @@ int GetSeqsCommand::execute(){ if (listfile != "") { readList(); } if (taxfile != "") { readTax(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } if (outputNames.size() != 0) { m->mothurOutEndLine(); @@ -206,14 +267,15 @@ int GetSeqsCommand::execute(){ //********************************************************************************************************************** int GetSeqsCommand::readFasta(){ try { - if (outputDir == "") { outputDir += hasPath(fastafile); } - string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ifstream in; - openInputFile(fastafile, in); + m->openInputFile(fastafile, in); string name; bool wroteSomething = false; @@ -233,13 +295,13 @@ int GetSeqsCommand::readFasta(){ currSeq.printSequence(out); } } - gobble(in); + m->gobble(in); } in.close(); out.close(); if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); return 0; @@ -252,13 +314,14 @@ int GetSeqsCommand::readFasta(){ //********************************************************************************************************************** int GetSeqsCommand::readList(){ try { - if (outputDir == "") { outputDir += hasPath(listfile); } - string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" + getExtension(listfile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ifstream in; - openInputFile(listfile, in); + m->openInputFile(listfile, in); bool wroteSomething = false; @@ -304,13 +367,13 @@ int GetSeqsCommand::readList(){ newList.print(out); } - gobble(in); + m->gobble(in); } in.close(); out.close(); if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName); return 0; @@ -323,14 +386,15 @@ int GetSeqsCommand::readList(){ //********************************************************************************************************************** int GetSeqsCommand::readName(){ try { - if (outputDir == "") { outputDir += hasPath(namefile); } - string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ifstream in; - openInputFile(namefile, in); + m->openInputFile(namefile, in); string name, firstCol, secondCol; bool wroteSomething = false; @@ -396,13 +460,13 @@ int GetSeqsCommand::readName(){ } } } - gobble(in); + m->gobble(in); } in.close(); out.close(); if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName); return 0; @@ -416,14 +480,15 @@ int GetSeqsCommand::readName(){ //********************************************************************************************************************** int GetSeqsCommand::readGroup(){ try { - if (outputDir == "") { outputDir += hasPath(groupfile); } - string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ifstream in; - openInputFile(groupfile, in); + m->openInputFile(groupfile, in); string name, group; bool wroteSomething = false; @@ -443,13 +508,13 @@ int GetSeqsCommand::readGroup(){ out << name << '\t' << group << endl; } - gobble(in); + m->gobble(in); } in.close(); out.close(); if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName); return 0; @@ -462,13 +527,14 @@ int GetSeqsCommand::readGroup(){ //********************************************************************************************************************** int GetSeqsCommand::readTax(){ try { - if (outputDir == "") { outputDir += hasPath(taxfile); } - string outputFileName = outputDir + getRootName(getSimpleName(taxfile)) + "pick" + getExtension(taxfile); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile); ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ifstream in; - openInputFile(taxfile, in); + m->openInputFile(taxfile, in); string name, tax; bool wroteSomething = false; @@ -487,13 +553,13 @@ int GetSeqsCommand::readTax(){ out << name << '\t' << tax << endl; } - gobble(in); + m->gobble(in); } in.close(); out.close(); if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName); return 0; @@ -507,14 +573,15 @@ int GetSeqsCommand::readTax(){ //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name int GetSeqsCommand::readAlign(){ try { - if (outputDir == "") { outputDir += hasPath(alignfile); } - string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report"; + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report"; ofstream out; - openOutputFile(outputFileName, out); + m->openOutputFile(outputFileName, out); ifstream in; - openInputFile(alignfile, in); + m->openInputFile(alignfile, in); string name, junk; bool wroteSomething = false; @@ -554,13 +621,13 @@ int GetSeqsCommand::readAlign(){ } } - gobble(in); + m->gobble(in); } in.close(); out.close(); if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } - outputNames.push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName); return 0; @@ -576,7 +643,7 @@ int GetSeqsCommand::readAccnos(){ try { ifstream in; - openInputFile(accnosfile, in); + m->openInputFile(accnosfile, in); string name; while(!in.eof()){ @@ -584,7 +651,7 @@ int GetSeqsCommand::readAccnos(){ names.insert(name); - gobble(in); + m->gobble(in); } in.close();