X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;h=1926ae0b017abc926c2256e2c3b0396de1dbae40;hb=c6e5f84783b39a558119835963dec3c4facb0154;hp=8bf93ce68db55f9b380307feb73d83ecf3700c5d;hpb=28d6f2bddc5c0718ae7f63648be3130a35fb0f02;p=mothur.git diff --git a/getseqscommand.cpp b/getseqscommand.cpp index 8bf93ce..1926ae0 100644 --- a/getseqscommand.cpp +++ b/getseqscommand.cpp @@ -22,7 +22,7 @@ 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); @@ -47,7 +47,7 @@ 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 +55,7 @@ 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 +63,7 @@ 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 +71,7 @@ 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 +79,7 @@ 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 +87,7 @@ 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 +95,7 @@ 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 +133,7 @@ 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; } @@ -206,14 +206,15 @@ 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; @@ -233,15 +234,13 @@ 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(); - remove(outputFileName.c_str()); - }else { outputNames.push_back(outputFileName); } + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); return 0; @@ -254,13 +253,14 @@ 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; @@ -306,15 +306,13 @@ 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(); - remove(outputFileName.c_str()); - }else { outputNames.push_back(outputFileName); } + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); return 0; @@ -327,14 +325,15 @@ 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; @@ -400,15 +399,13 @@ 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(); - remove(outputFileName.c_str()); - }else { outputNames.push_back(outputFileName); } + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); return 0; @@ -422,14 +419,15 @@ 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; @@ -449,15 +447,13 @@ 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(); - remove(outputFileName.c_str()); - }else { outputNames.push_back(outputFileName); } + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); return 0; @@ -470,13 +466,14 @@ 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; @@ -495,16 +492,14 @@ 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(); - remove(outputFileName.c_str()); - }else { outputNames.push_back(outputFileName); } - + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); + return 0; } @@ -517,14 +512,15 @@ 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; @@ -564,15 +560,13 @@ 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(); - remove(outputFileName.c_str()); - }else { outputNames.push_back(outputFileName); } + if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); } + outputNames.push_back(outputFileName); return 0; @@ -588,7 +582,7 @@ int GetSeqsCommand::readAccnos(){ try { ifstream in; - openInputFile(accnosfile, in); + m->openInputFile(accnosfile, in); string name; while(!in.eof()){ @@ -596,7 +590,7 @@ int GetSeqsCommand::readAccnos(){ names.insert(name); - gobble(in); + m->gobble(in); } in.close();