X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.cpp;h=5ed31dd84b55ba26ee64a45e9298c84fb60a6be2;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=0c42b7dad8281b1d9edd49550c3df95ae773c7e8;hpb=1b0bddfbf4ac5df7e2dad03c8a5350e71b052f78;p=mothur.git diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp index 0c42b7d..5ed31dd 100644 --- a/getgroupscommand.cpp +++ b/getgroupscommand.cpp @@ -16,12 +16,13 @@ //********************************************************************************************************************** vector GetGroupsCommand::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 GetGroupsCommand::setParameters(){ string GetGroupsCommand::getHelpString(){ try { string helpString = ""; - helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy or shared file.\n"; + helpString += "The get.groups command selects sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy, design or shared file.\n"; helpString += "It outputs a file containing the sequences in the those specified groups, or a sharedfile containing only those groups.\n"; - helpString += "The get.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 shared file.\n"; + helpString += "The get.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 shared file.\n"; helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n"; helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n"; helpString += "The get.groups command should be in the following format: get.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n"; @@ -68,6 +69,7 @@ GetGroupsCommand::GetGroupsCommand(){ outputTypes["group"] = tempOutNames; outputTypes["list"] = tempOutNames; outputTypes["shared"] = tempOutNames; + outputTypes["design"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "GetGroupsCommand", "GetGroupsCommand"); @@ -105,6 +107,7 @@ GetGroupsCommand::GetGroupsCommand(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 @@ -170,6 +173,14 @@ GetGroupsCommand::GetGroupsCommand(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; } + } } @@ -180,12 +191,12 @@ GetGroupsCommand::GetGroupsCommand(string option) { else { m->setAccnosFile(accnosfile); } fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } + if (fastafile == "not open") { fastafile = ""; abort = true; } else if (fastafile == "not found") { fastafile = ""; } else { m->setFastaFile(fastafile); } namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not open") { abort = true; } + if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } else { m->setNameFile(namefile); } @@ -200,7 +211,7 @@ GetGroupsCommand::GetGroupsCommand(string option) { else { m->setListFile(listfile); } taxfile = validParameter.validFile(parameters, "taxonomy", true); - if (taxfile == "not open") { abort = true; } + if (taxfile == "not open") { taxfile = ""; abort = true; } else if (taxfile == "not found") { taxfile = ""; } else { m->setTaxonomyFile(taxfile); } @@ -219,9 +230,14 @@ GetGroupsCommand::GetGroupsCommand(string option) { groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { groupfile = ""; abort = true; } else if (groupfile == "not found") { groupfile = ""; } - else { m->setGroupFile(groupfile); } - - if ((sharedfile == "") && (groupfile == "")) { + else { m->setGroupFile(groupfile); } + + designfile = validParameter.validFile(parameters, "design", true); + if (designfile == "not open") { designfile = ""; abort = true; } + else if (designfile == "not found") { designfile = ""; } + else { m->setDesignFile(designfile); } + + 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 @@ -242,7 +258,11 @@ GetGroupsCommand::GetGroupsCommand(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; + } } } } @@ -250,9 +270,13 @@ GetGroupsCommand::GetGroupsCommand(string option) { if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file 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 == "") && (designfile == "") && (sharedfile == "") && (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); + } } } @@ -298,6 +322,7 @@ int GetGroupsCommand::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; } @@ -339,6 +364,11 @@ int GetGroupsCommand::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; @@ -684,6 +714,56 @@ int GetGroupsCommand::readGroup(){ exit(1); } } +//********************************************************************************************************************** +int GetGroupsCommand::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 selectedCount = 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; + selectedCount++; + } + + m->gobble(in); + } + in.close(); + out.close(); + + if (wroteSomething == false) { m->mothurOut("Your file does NOT contain groups from the groups you wish to get."); m->mothurOutEndLine(); } + outputTypes["design"].push_back(outputFileName); outputNames.push_back(outputFileName); + + m->mothurOut("Selected " + toString(selectedCount) + " groups from your design file."); m->mothurOutEndLine(); + + + return 0; + } + catch(exception& e) { + m->errorOut(e, "GetGroupsCommand", "readDesign"); + exit(1); + } +} + + //********************************************************************************************************************** int GetGroupsCommand::readTax(){ try {