X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=801029c06383e7811e5cfb14ea0c5cd629b66b67;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=252a92573d036c47f4d45235113adef1fc44727a;hpb=8742edef7a51b82834289e570d336f5a81ba1f2b;p=mothur.git diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp index 252a925..801029c 100644 --- a/removegroupscommand.cpp +++ b/removegroupscommand.cpp @@ -16,12 +16,13 @@ //********************************************************************************************************************** vector RemoveGroupsCommand::setParameters(){ try { - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta); - CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pshared); - CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pgroup); - CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist); - CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy); + 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", "", "", "none", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "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); @@ -40,9 +41,9 @@ vector RemoveGroupsCommand::setParameters(){ string RemoveGroupsCommand::getHelpString(){ try { string helpString = ""; - helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy or sharedfile.\n"; + helpString += "The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy, design or sharedfile.\n"; helpString += "It outputs a file containing the sequences NOT in the those specified groups, or with a sharedfile eliminates the groups you selected.\n"; - helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared and groups. The group parameter is required, unless you have a current group file or are using a sharedfile.\n"; + helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy, shared, design and groups. The group parameter is required, unless you have a current group file or are using a sharedfile.\n"; helpString += "You must also provide an accnos containing the list of groups to remove or set the groups parameter to the groups you wish to remove.\n"; helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like removed. You can separate group names with dashes.\n"; helpString += "The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n"; @@ -69,6 +70,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(){ outputTypes["group"] = tempOutNames; outputTypes["list"] = tempOutNames; outputTypes["shared"] = tempOutNames; + outputTypes["design"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand"); @@ -106,6 +108,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { outputTypes["group"] = tempOutNames; outputTypes["list"] = tempOutNames; outputTypes["shared"] = tempOutNames; + outputTypes["design"] = tempOutNames; //if the user changes the output directory command factory will send this info to us in the output parameter @@ -171,6 +174,14 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["shared"] = inputDir + it->second; } } + + it = parameters.find("design"); + //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["design"] = inputDir + it->second; } + } } @@ -190,6 +201,11 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { else if (namefile == "not found") { namefile = ""; } else { m->setNameFile(namefile); } + groupfile = validParameter.validFile(parameters, "group", true); + if (groupfile == "not open") { groupfile = ""; abort = true; } + else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } + listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { listfile = ""; abort = true; } else if (listfile == "not found") { listfile = ""; } @@ -199,12 +215,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { if (taxfile == "not open") { taxfile = ""; abort = true; } else if (taxfile == "not found") { taxfile = ""; } else { m->setTaxonomyFile(taxfile); } + + designfile = validParameter.validFile(parameters, "design", true); + if (designfile == "not open") { designfile = ""; abort = true; } + else if (designfile == "not found") { designfile = ""; } + else { m->setDesignFile(designfile); } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { m->splitAtDash(groups, Groups); - m->Groups = Groups; + m->setGroups(Groups); } sharedfile = validParameter.validFile(parameters, "shared", true); @@ -217,7 +238,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { else if (groupfile == "not found") { groupfile = ""; } else { m->setGroupFile(groupfile); } - if ((sharedfile == "") && (groupfile == "")) { + if ((sharedfile == "") && (groupfile == "") && (designfile == "")) { //is there are current file available for any of these? if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) { //give priority to group, then shared @@ -238,7 +259,11 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { groupfile = m->getGroupFile(); if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); } else { - m->mothurOut("You have no current groupfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true; + designfile = m->getDesignFile(); + if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current groupfile or sharedfile or designfile and one is required."); m->mothurOutEndLine(); abort = true; + } } } } @@ -246,8 +271,14 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file containing group names or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; } - if ((fastafile == "") && (namefile == "") && (groupfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; } + if ((fastafile == "") && (namefile == "") && (groupfile == "") && (sharedfile == "") && (designfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design or list."); m->mothurOutEndLine(); abort = true; } if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; } + + if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } + } } @@ -273,7 +304,8 @@ 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(); - util->setGroups(Groups, groupMap->namesOfGroups); + vector namesGroups = groupMap->getNamesOfGroups(); + util->setGroups(Groups, namesGroups); delete util; //fill names with names of sequences that are from the groups we want to remove @@ -291,6 +323,7 @@ int RemoveGroupsCommand::execute(){ if (listfile != "") { readList(); } if (taxfile != "") { readTax(); } if (sharedfile != "") { readShared(); } + if (designfile != "") { readDesign(); } if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } @@ -331,6 +364,11 @@ int RemoveGroupsCommand::execute(){ if (itTypes != outputTypes.end()) { if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); } } + + itTypes = outputTypes.find("design"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setDesignFile(current); } + } } return 0; @@ -369,9 +407,16 @@ int RemoveGroupsCommand::readFasta(){ //if this name is in the accnos file if (names.count(name) == 0) { wroteSomething = true; - - currSeq.printSequence(out); - }else { removedCount++; } + currSeq.printSequence(out); + }else { + //if you are not in the accnos file check if you are a name that needs to be changed + map::iterator it = uniqueToRedundant.find(name); + if (it != uniqueToRedundant.end()) { + wroteSomething = true; + currSeq.setName(it->second); + currSeq.printSequence(out); + }else { removedCount++; } + } } m->gobble(in); } @@ -403,24 +448,23 @@ int RemoveGroupsCommand::readShared(){ vector lookup = tempInput->getSharedRAbundVectors(); //save m->Groups - vector allGroupsNames = m->namesOfGroups; - vector mothurOutGroups = m->Groups; + vector allGroupsNames = m->getAllGroups(); + vector mothurOutGroups = m->getGroups(); vector groupsToKeep; for (int i = 0; i < allGroupsNames.size(); i++) { - if (!m->inUsersGroups(allGroupsNames[i], m->Groups)) { + if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) { groupsToKeep.push_back(allGroupsNames[i]); } } - if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->Groups = mothurOutGroups; delete tempInput; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } + if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->setGroups(mothurOutGroups); delete tempInput; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; } //reset read for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } delete tempInput; - m->Groups = groupsToKeep; - m->namesOfGroups.clear(); - m->names.clear(); + m->setGroups(groupsToKeep); + m->clearAllGroups(); m->saveNextLabel = ""; m->printedHeaders = false; m->currentBinLabels.clear(); @@ -458,7 +502,7 @@ int RemoveGroupsCommand::readShared(){ } - m->Groups = mothurOutGroups; + m->setGroups(mothurOutGroups); if (wroteSomething == false) { m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine(); } @@ -517,12 +561,23 @@ int RemoveGroupsCommand::readList(){ //if that name is in the .accnos file, add it if (names.count(name) == 0) { newNames += name + ","; } - else { removedCount++; } + else { + //if you are not in the accnos file check if you are a name that needs to be changed + map::iterator it = uniqueToRedundant.find(name); + if (it != uniqueToRedundant.end()) { + newNames += it->second + ","; + }else { removedCount++; } + } } //get last name if (names.count(binnames) == 0) { newNames += binnames + ","; } - else { removedCount++; } + else { //if you are not in the accnos file check if you are a name that needs to be changed + map::iterator it = uniqueToRedundant.find(binnames); + if (it != uniqueToRedundant.end()) { + newNames += it->second + ","; + }else { removedCount++; } + } //if there are names in this bin add to new list if (newNames != "") { @@ -614,6 +669,7 @@ int RemoveGroupsCommand::readName(){ //you know you have at least one valid second since first column is valid for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; } out << validSecond[validSecond.size()-1] << endl; + uniqueToRedundant[firstCol] = validSecond[0]; } } @@ -682,6 +738,54 @@ int RemoveGroupsCommand::readGroup(){ exit(1); } } +//********************************************************************************************************************** +int RemoveGroupsCommand::readDesign(){ + try { + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(designfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + "pick" + m->getExtension(designfile); + + ofstream out; + m->openOutputFile(outputFileName, out); + + ifstream in; + m->openInputFile(designfile, in); + string name, group; + + bool wroteSomething = false; + int removedCount = 0; + + while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } + + in >> name; //read from first column + in >> group; //read from second column + + //if this name is in the accnos file + if (!(m->inUsersGroups(name, Groups))) { + wroteSomething = true; + out << name << '\t' << group << endl; + }else { removedCount++; } + + m->gobble(in); + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file contains only groups from the groups you wish to remove."); m->mothurOutEndLine(); } + outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName); + + m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine(); + + + return 0; + } + catch(exception& e) { + m->errorOut(e, "RemoveGroupsCommand", "readDesign"); + exit(1); + } +} + //********************************************************************************************************************** int RemoveGroupsCommand::readTax(){ try { @@ -708,7 +812,12 @@ int RemoveGroupsCommand::readTax(){ if (names.count(name) == 0) { wroteSomething = true; out << name << '\t' << tax << endl; - }else { removedCount++; } + }else { //if you are not in the accnos file check if you are a name that needs to be changed + map::iterator it = uniqueToRedundant.find(name); + if (it != uniqueToRedundant.end()) { + wroteSomething = true; + out << it->second << '\t' << tax << endl; + }else { removedCount++; } } m->gobble(in); } @@ -745,7 +854,7 @@ void RemoveGroupsCommand::readAccnos(){ } in.close(); - m->Groups = Groups; + m->setGroups(Groups); } catch(exception& e) {