X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=c9908fbc715f33eb33f75ff2005d51c9347678ff;hb=19fcbbdba99658f5eca244803280f9ee7f9f6607;hp=2c98e814220432e2d27cf82499235a3fe3e928bb;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp index 2c98e81..c9908fb 100644 --- a/removegroupscommand.cpp +++ b/removegroupscommand.cpp @@ -13,22 +13,53 @@ #include "sharedutilities.h" //********************************************************************************************************************** -vector RemoveGroupsCommand::getValidParameters(){ +vector RemoveGroupsCommand::setParameters(){ try { - string Array[] = {"fasta","name", "group", "accnos", "groups","list","taxonomy","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta); + CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); 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 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); } return myArray; } catch(exception& e) { - m->errorOut(e, "RemoveGroupsCommand", "getValidParameters"); + m->errorOut(e, "RemoveGroupsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +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.\n"; + helpString += "It outputs a file containing the sequences NOT in the those specified groups.\n"; + helpString += "The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required, unless you have a current group file.\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"; + helpString += "Example remove.groups(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n"; + helpString += "or remove.groups(groups=pasture, fasta=amazon.fasta, amazon.groups).\n"; + helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "RemoveGroupsCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** RemoveGroupsCommand::RemoveGroupsCommand(){ try { - abort = true; - //initialize outputTypes + abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["fasta"] = tempOutNames; outputTypes["taxonomy"] = tempOutNames; @@ -42,40 +73,16 @@ RemoveGroupsCommand::RemoveGroupsCommand(){ } } //********************************************************************************************************************** -vector RemoveGroupsCommand::getRequiredParameters(){ - try { - string Array[] = {"group"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RemoveGroupsCommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector RemoveGroupsCommand::getRequiredFiles(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RemoveGroupsCommand", "getRequiredFiles"); - exit(1); - } -} -//********************************************************************************************************************** RemoveGroupsCommand::RemoveGroupsCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"fasta","name", "group", "accnos", "groups", "list","taxonomy","outputdir","inputdir" }; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -159,26 +166,36 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { accnosfile = validParameter.validFile(parameters, "accnos", true); if (accnosfile == "not open") { abort = true; } else if (accnosfile == "not found") { accnosfile = ""; } + else { m->setAccnosFile(accnosfile); } fastafile = validParameter.validFile(parameters, "fasta", true); if (fastafile == "not open") { abort = true; } else if (fastafile == "not found") { fastafile = ""; } + else { m->setFastaFile(fastafile); } namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } - else if (groupfile == "not found") { groupfile = ""; m->mothurOut("You must provide a group file."); m->mothurOutEndLine(); abort = true; } + else if (groupfile == "not found") { + //if there is a current group file, use it + 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 and the group parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setGroupFile(groupfile); } listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } else if (listfile == "not found") { listfile = ""; } + else { m->setListFile(listfile); } taxfile = validParameter.validFile(parameters, "taxonomy", true); if (taxfile == "not open") { abort = true; } else if (taxfile == "not found") { taxfile = ""; } + else { m->setTaxonomyFile(taxfile); } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } @@ -199,30 +216,10 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option) { } //********************************************************************************************************************** -void RemoveGroupsCommand::help(){ - try { - m->mothurOut("The remove.groups command removes sequences from a specfic group or set of groups from the following file types: fasta, name, group, list, taxonomy.\n"); - m->mothurOut("It outputs a file containing the sequences NOT in the those specified groups.\n"); - m->mothurOut("The remove.groups command parameters are accnos, fasta, name, group, list, taxonomy and groups. The group parameter is required.\n"); - m->mothurOut("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"); - m->mothurOut("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"); - m->mothurOut("The remove.groups command should be in the following format: remove.groups(accnos=yourAccnos, fasta=yourFasta, group=yourGroupFile).\n"); - m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta, group=amazon.groups).\n"); - m->mothurOut("or remove.seqs(groups=pasture, fasta=amazon.fasta, amazon.groups).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "RemoveGroupsCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - int RemoveGroupsCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } groupMap = new GroupMap(groupfile); groupMap->readMap(); @@ -248,10 +245,10 @@ int RemoveGroupsCommand::execute(){ if (listfile != "") { readList(); } if (taxfile != "") { readTax(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } m->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine(); - for (int i = 0; i < Groups.size(); i++) { m->mothurOut(Groups[i]); m->mothurOutEndLine(); } + for (int i = 0; i < Groups.size(); i++) { m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine(); } m->mothurOutEndLine(); if (outputNames.size() != 0) { @@ -259,6 +256,33 @@ int RemoveGroupsCommand::execute(){ m->mothurOut("Output File names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } m->mothurOutEndLine(); + + //set fasta file as new current fastafile + string current = ""; + itTypes = outputTypes.find("fasta"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); } + } + + itTypes = outputTypes.find("name"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); } + } + + itTypes = outputTypes.find("group"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); } + } + + itTypes = outputTypes.find("list"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); } + } + + itTypes = outputTypes.find("taxonomy"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); } + } } return 0; @@ -287,7 +311,7 @@ int RemoveGroupsCommand::readFasta(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } Sequence currSeq(in); name = currSeq.getName(); @@ -342,7 +366,7 @@ int RemoveGroupsCommand::readList(){ //for each bin for (int i = 0; i < list.getNumBins(); i++) { - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } //parse out names that are in accnos file string binnames = list.get(i); @@ -405,7 +429,7 @@ int RemoveGroupsCommand::readName(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> firstCol; m->gobble(in); in >> secondCol; @@ -481,7 +505,7 @@ int RemoveGroupsCommand::readGroup(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + 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 @@ -523,7 +547,7 @@ int RemoveGroupsCommand::readTax(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + 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