X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removegroupscommand.cpp;h=64f9ab6822301310e975e6bbe58736e953eed4f2;hp=86ddf946a9d51c1df7e43783e0470bf5aead6301;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=5b72d1cf3fa48730e5bb70d59cced1e43e1fe424 diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp index 86ddf94..64f9ab6 100644 --- a/removegroupscommand.cpp +++ b/removegroupscommand.cpp @@ -16,17 +16,18 @@ //********************************************************************************************************************** vector RemoveGroupsCommand::setParameters(){ try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta); - CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared); - CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname); - CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount); - CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup); CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pdesign); - CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist); - CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy); - CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos); - 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", "FNGLT","fasta",false,false,true); parameters.push_back(pfasta); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup); + CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist); + CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); parameters.push_back(ptaxonomy); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos); + 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); } @@ -58,31 +59,26 @@ string RemoveGroupsCommand::getHelpString(){ } } //********************************************************************************************************************** -string RemoveGroupsCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string RemoveGroupsCommand::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 == "fasta") { outputFileName = "pick" + m->getExtension(inputName); } - else if (type == "taxonomy") { outputFileName = "pick" + m->getExtension(inputName); } - else if (type == "name") { outputFileName = "pick" + m->getExtension(inputName); } - else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); } - else if (type == "count") { outputFileName = "pick" + m->getExtension(inputName); } - else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); } - else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); } - else if (type == "design") { outputFileName = "pick" + m->getExtension(inputName); } - 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, "RemoveGroupsCommand", "getOutputFileNameTag"); - exit(1); - } + if (type == "fasta") { pattern = "[filename],pick,[extension]"; } + else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; } + else if (type == "name") { pattern = "[filename],pick,[extension]"; } + else if (type == "group") { pattern = "[filename],pick,[extension]"; } + else if (type == "count") { pattern = "[filename],pick,[extension]"; } + else if (type == "list") { pattern = "[filename],pick,[extension]"; } + else if (type == "shared") { pattern = "[filename],[tag],pick,[extension]"; } + else if (type == "design") { pattern = "[filename],pick,[extension]"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "RemoveGroupsCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** RemoveGroupsCommand::RemoveGroupsCommand(){ @@ -359,11 +355,19 @@ int RemoveGroupsCommand::execute(){ //make sure groups are valid //takes care of user setting groupNames that are invalid or setting groups=all - SharedUtil* util = new SharedUtil(); vector namesGroups = groupMap->getNamesOfGroups(); - util->setGroups(Groups, namesGroups); - delete util; - + vector checkedGroups; + for (int i = 0; i < Groups.size(); i++) { + if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); } + else { m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); } + } + + if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; } + else { + Groups = checkedGroups; + m->setGroups(Groups); + } + //fill names with names of sequences that are from the groups we want to remove fillNames(); @@ -373,7 +377,7 @@ int RemoveGroupsCommand::execute(){ m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n"); } CountTable ct; - ct.readTable(countfile); + ct.readTable(countfile, true); if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; } vector gNamesOfGroups = ct.getNamesOfGroups(); @@ -468,7 +472,10 @@ int RemoveGroupsCommand::readFasta(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)); + variables["[extension]"] = m->getExtension(fastafile); + string outputFileName = getOutputFileName("fasta", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -529,6 +536,10 @@ int RemoveGroupsCommand::readShared(){ //that way we can take advantage of the reads in inputdata and sharedRabundVector InputData* tempInput = new InputData(sharedfile, "sharedfile"); vector lookup = tempInput->getSharedRAbundVectors(); + + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)); + variables["[extension]"] = m->getExtension(sharedfile); //save m->Groups vector allGroupsNames = m->getAllGroups(); @@ -560,7 +571,8 @@ int RemoveGroupsCommand::readShared(){ while(lookup[0] != NULL) { - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile); + variables["[tag]"] = lookup[0]->getLabel(); + string outputFileName = getOutputFileName("shared", variables); ofstream out; m->openOutputFile(outputFileName, out); outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName); @@ -608,7 +620,11 @@ int RemoveGroupsCommand::readList(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[extension]"] = m->getExtension(listfile); + string outputFileName = getOutputFileName("list", variables); + ofstream out; m->openOutputFile(outputFileName, out); @@ -698,7 +714,10 @@ int RemoveGroupsCommand::readName(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile)); + variables["[extension]"] = m->getExtension(namefile); + string outputFileName = getOutputFileName("name", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -778,7 +797,10 @@ int RemoveGroupsCommand::readGroup(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)); + variables["[extension]"] = m->getExtension(groupfile); + string outputFileName = getOutputFileName("group", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -824,7 +846,10 @@ int RemoveGroupsCommand::readCount(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(countfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile)); + variables["[extension]"] = m->getExtension(countfile); + string outputFileName = getOutputFileName("count", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -905,7 +930,10 @@ int RemoveGroupsCommand::readDesign(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(designfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile)); + variables["[extension]"] = m->getExtension(designfile); + string outputFileName = getOutputFileName("design", variables); ofstream out; m->openOutputFile(outputFileName, out); @@ -953,7 +981,10 @@ int RemoveGroupsCommand::readTax(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)); + variables["[extension]"] = m->getExtension(taxfile); + string outputFileName = getOutputFileName("taxonomy", variables); ofstream out; m->openOutputFile(outputFileName, out);