X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=05b1170bf4501ebd3131a616fdcd58a9b49e59f2;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=e5a3bb2edc7fc97dacb89393ef3a2968b64247b4;hpb=1b0bddfbf4ac5df7e2dad03c8a5350e71b052f78;p=mothur.git diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp index e5a3bb2..05b1170 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"; @@ -56,7 +57,32 @@ string RemoveGroupsCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string RemoveGroupsCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //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 == "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); + } +} //********************************************************************************************************************** RemoveGroupsCommand::RemoveGroupsCommand(){ try { @@ -69,6 +95,7 @@ RemoveGroupsCommand::RemoveGroupsCommand(){ outputTypes["group"] = tempOutNames; outputTypes["list"] = tempOutNames; outputTypes["shared"] = tempOutNames; + outputTypes["design"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand"); @@ -106,6 +133,7 @@ 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 +199,14 @@ 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; } + } } @@ -204,6 +240,11 @@ 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 = ""; } @@ -222,7 +263,7 @@ 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 @@ -243,7 +284,11 @@ 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; + } } } } @@ -251,8 +296,14 @@ 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); + } + } } @@ -269,7 +320,7 @@ int RemoveGroupsCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } //get groups you want to remove - if (accnosfile != "") { readAccnos(); } + if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); } if (groupfile != "") { groupMap = new GroupMap(groupfile); @@ -297,6 +348,7 @@ 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; } @@ -337,6 +389,11 @@ 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; @@ -353,7 +410,7 @@ int RemoveGroupsCommand::readFasta(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile); ofstream out; m->openOutputFile(outputFileName, out); @@ -433,7 +490,6 @@ int RemoveGroupsCommand::readShared(){ delete tempInput; m->setGroups(groupsToKeep); m->clearAllGroups(); - m->names.clear(); m->saveNextLabel = ""; m->printedHeaders = false; m->currentBinLabels.clear(); @@ -446,7 +502,7 @@ int RemoveGroupsCommand::readShared(){ while(lookup[0] != NULL) { - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".pick" + m->getExtension(sharedfile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("shared", sharedfile); ofstream out; m->openOutputFile(outputFileName, out); outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName); @@ -494,7 +550,7 @@ int RemoveGroupsCommand::readList(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -584,8 +640,7 @@ int RemoveGroupsCommand::readName(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(namefile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile); ofstream out; m->openOutputFile(outputFileName, out); @@ -665,8 +720,7 @@ int RemoveGroupsCommand::readGroup(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile); ofstream out; m->openOutputFile(outputFileName, out); @@ -708,17 +762,18 @@ int RemoveGroupsCommand::readGroup(){ } } //********************************************************************************************************************** -int RemoveGroupsCommand::readTax(){ +int RemoveGroupsCommand::readDesign(){ try { string thisOutputDir = outputDir; - if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile); + if (outputDir == "") { thisOutputDir += m->hasPath(designfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(designfile)) + getOutputFileNameTag("design", designfile); + ofstream out; m->openOutputFile(outputFileName, out); ifstream in; - m->openInputFile(taxfile, in); - string name, tax; + m->openInputFile(designfile, in); + string name, group; bool wroteSomething = false; int removedCount = 0; @@ -727,59 +782,80 @@ int RemoveGroupsCommand::readTax(){ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column - in >> tax; //read from second column + in >> group; //read from second column //if this name is in the accnos file - if (names.count(name) == 0) { + if (!(m->inUsersGroups(name, Groups))) { wroteSomething = true; - out << name << '\t' << tax << endl; - }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++; } } + out << name << '\t' << group << endl; + }else { removedCount++; } m->gobble(in); } in.close(); out.close(); - if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); } - outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName); + 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) + " sequences from your taxonomy file."); m->mothurOutEndLine(); + m->mothurOut("Removed " + toString(removedCount) + " groups from your design file."); m->mothurOutEndLine(); + return 0; } catch(exception& e) { - m->errorOut(e, "RemoveGroupsCommand", "readTax"); + m->errorOut(e, "RemoveGroupsCommand", "readDesign"); exit(1); } } + //********************************************************************************************************************** -void RemoveGroupsCommand::readAccnos(){ +int RemoveGroupsCommand::readTax(){ try { - Groups.clear(); + string thisOutputDir = outputDir; + if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); } + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile); + ofstream out; + m->openOutputFile(outputFileName, out); ifstream in; - m->openInputFile(accnosfile, in); - string name; + m->openInputFile(taxfile, in); + string name, tax; + + bool wroteSomething = false; + int removedCount = 0; while(!in.eof()){ - in >> name; + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } - Groups.push_back(name); + in >> name; //read from first column + in >> tax; //read from second column + + //if this name is in the accnos file + if (names.count(name) == 0) { + wroteSomething = true; + out << name << '\t' << tax << endl; + }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); } - in.close(); + in.close(); + out.close(); - m->setGroups(Groups); + if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); } + outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName); + m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine(); + + return 0; } catch(exception& e) { - m->errorOut(e, "RemoveGroupsCommand", "readAccnos"); + m->errorOut(e, "RemoveGroupsCommand", "readTax"); exit(1); } }