X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countseqscommand.cpp;h=dfa012eeff0f0f49c778c00b2098348a489f1855;hb=67ea6ccd74dbd64828d31b952808255f206364ff;hp=fa6fd4f09a2c0c1703a4f12b65943d6df1ac06a2;hpb=96dbe925073caefaed6e6db85659c144a806aeb1;p=mothur.git diff --git a/countseqscommand.cpp b/countseqscommand.cpp index fa6fd4f..dfa012e 100644 --- a/countseqscommand.cpp +++ b/countseqscommand.cpp @@ -15,12 +15,12 @@ //********************************************************************************************************************** vector CountSeqsCommand::setParameters(){ try { - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pname); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); - CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge); - 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 pname("name", "InputTypes", "", "", "none", "none", "none","count",false,true,true); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pgroup); + CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge); + 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); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -50,24 +50,19 @@ string CountSeqsCommand::getHelpString(){ } } //********************************************************************************************************************** -string CountSeqsCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string CountSeqsCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //is this a type this command creates - it = outputTypes.find(type); - if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } - else { - if (type == "counttable") { outputFileName = "count_table"; } - else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } - } - return outputFileName; - } - catch(exception& e) { - m->errorOut(e, "CountSeqsCommand", "getOutputFileNameTag"); - exit(1); - } + if (type == "count") { pattern = "[filename],count_table"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "CountSeqsCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** CountSeqsCommand::CountSeqsCommand(){ @@ -75,7 +70,7 @@ CountSeqsCommand::CountSeqsCommand(){ abort = true; calledHelp = true; setParameters(); vector tempOutNames; - outputTypes["counttable"] = tempOutNames; + outputTypes["count"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "CountSeqsCommand", "CountSeqsCommand"); @@ -107,7 +102,7 @@ CountSeqsCommand::CountSeqsCommand(string option) { //initialize outputTypes vector tempOutNames; - outputTypes["counttable"] = tempOutNames; + outputTypes["count"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter @@ -171,7 +166,9 @@ int CountSeqsCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } - string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("counttable"); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile)); + string outputFileName = getOutputFileName("count", variables); int total = 0; if (!large) { total = processSmall(outputFileName); } @@ -180,7 +177,7 @@ int CountSeqsCommand::execute(){ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; } //set rabund file as new current rabundfile - itTypes = outputTypes.find("counttable"); + itTypes = outputTypes.find("count"); if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { string current = (itTypes->second)[0]; m->setCountTableFile(current); } } @@ -188,7 +185,7 @@ int CountSeqsCommand::execute(){ m->mothurOutEndLine(); m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine(); m->mothurOutEndLine(); - m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); m->mothurOut(outputFileName); m->mothurOutEndLine(); m->mothurOutEndLine(); @@ -205,8 +202,8 @@ int CountSeqsCommand::execute(){ int CountSeqsCommand::processSmall(string outputFileName){ try { ofstream out; - m->openOutputFile(outputFileName, out); outputTypes["counttable"].push_back(outputFileName); - outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName); + m->openOutputFile(outputFileName, out); outputTypes["count"].push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName); out << "Representative_Sequence\ttotal\t"; GroupMap* groupMap; @@ -239,7 +236,11 @@ int CountSeqsCommand::processSmall(string outputFileName){ string firstCol, secondCol; in >> firstCol; m->gobble(in); in >> secondCol; m->gobble(in); - + //cout << firstCol << '\t' << secondCol << endl; + m->checkName(firstCol); + m->checkName(secondCol); + //cout << firstCol << '\t' << secondCol << endl; + vector names; m->splitAtChar(secondCol, names, ','); @@ -299,7 +300,7 @@ int CountSeqsCommand::processLarge(string outputFileName){ for (set::iterator it = namesOfGroups.begin(); it != namesOfGroups.end(); it++) { initial[(*it)] = 0; } ofstream out; m->openOutputFile(outputFileName, out); - outputNames.push_back(outputFileName); outputTypes["counttable"].push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName); out << "Representative_Sequence\ttotal\t"; if (groupfile == "") { out << endl; } @@ -438,6 +439,8 @@ map CountSeqsCommand::processNameFile(string name) { else { secondCol = pieces[i]; pairDone = true; columnOne=true; } if (pairDone) { + m->checkName(firstCol); + m->checkName(secondCol); //parse names into vector vector theseNames; m->splitAtComma(secondCol, theseNames); @@ -459,6 +462,8 @@ map CountSeqsCommand::processNameFile(string name) { else { secondCol = pieces[i]; pairDone = true; columnOne=true; } if (pairDone) { + m->checkName(firstCol); + m->checkName(secondCol); //parse names into vector vector theseNames; m->splitAtComma(secondCol, theseNames); @@ -510,6 +515,7 @@ map CountSeqsCommand::getGroupNames(string filename, set& n else { secondCol = pieces[i]; pairDone = true; columnOne=true; } if (pairDone) { + m->checkName(firstCol); it = groupIndex.find(secondCol); if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above groupIndex[secondCol] = count; @@ -532,6 +538,7 @@ map CountSeqsCommand::getGroupNames(string filename, set& n else { secondCol = pieces[i]; pairDone = true; columnOne=true; } if (pairDone) { + m->checkName(firstCol); it = groupIndex.find(secondCol); if (it == groupIndex.end()) { //add group, assigning the group and number so we can use vectors above groupIndex[secondCol] = count;