X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=801029c06383e7811e5cfb14ea0c5cd629b66b67;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=f35da2e46588829480a5540cdcd1148fd54e31bf;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp index f35da2e..801029c 100644 --- a/removegroupscommand.cpp +++ b/removegroupscommand.cpp @@ -20,6 +20,7 @@ vector RemoveGroupsCommand::setParameters(){ 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); @@ -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; } + } } @@ -204,6 +215,11 @@ 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 +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 @@ -243,7 +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; + } } } } @@ -251,7 +271,7 @@ 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 != ""))){ @@ -303,6 +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; } @@ -343,6 +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; @@ -439,7 +465,6 @@ int RemoveGroupsCommand::readShared(){ delete tempInput; m->setGroups(groupsToKeep); m->clearAllGroups(); - m->names.clear(); m->saveNextLabel = ""; m->printedHeaders = false; m->currentBinLabels.clear(); @@ -713,6 +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 {