X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countgroupscommand.cpp;fp=countgroupscommand.cpp;h=af9993c8ef6f8ee794be8bf7b3825aa34d1a44e7;hb=d3aed959ca3b68890eeb7b815e24210bcfeb256c;hp=0000000000000000000000000000000000000000;hpb=fc1ed1ae1b022719176910ab71993bd6535810ad;p=mothur.git diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp new file mode 100644 index 0000000..af9993c --- /dev/null +++ b/countgroupscommand.cpp @@ -0,0 +1,237 @@ +/* + * countgroupscommand.cpp + * Mothur + * + * Created by westcott on 8/9/11. + * Copyright 2011 Schloss Lab. All rights reserved. + * + */ + +#include "countgroupscommand.h" +#include "sharedutilities.h" +#include "inputdata.h" + +//********************************************************************************************************************** +vector CountGroupsCommand::setParameters(){ + try { + CommandParameter pshared("shared", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pshared); + CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "sharedGroup", "none",false,false); parameters.push_back(pgroup); + 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, "CountGroupsCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string CountGroupsCommand::getHelpString(){ + try { + string helpString = ""; + helpString += "The count.groups command counts sequences from a specfic group or set of groups from the following file types: group or shared file.\n"; + helpString += "The count.groups command parameters are accnos, group, shared and groups. You must provide a group or shared file.\n"; + helpString += "The accnos parameter allows you to provide a file containing the list of groups.\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 count.groups command should be in the following format: count.groups(accnos=yourAccnos, group=yourGroupFile).\n"; + helpString += "Example count.groups(accnos=amazon.accnos, group=amazon.groups).\n"; + helpString += "or count.groups(groups=pasture, group=amazon.groups).\n"; + helpString += "Note: No spaces between parameter labels (i.e. group), '=' and parameters (i.e.yourGroupFile).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "CountGroupsCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +CountGroupsCommand::CountGroupsCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + } + catch(exception& e) { + m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand"); + exit(1); + } +} +//********************************************************************************************************************** +CountGroupsCommand::CountGroupsCommand(string option) { + try { + abort = false; calledHelp = false; + + //allow user to run help + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + map::iterator it; + + //check to make sure all parameters are valid for command + for (it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("accnos"); + //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["accnos"] = inputDir + it->second; } + } + + it = parameters.find("group"); + //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["group"] = inputDir + it->second; } + } + + it = parameters.find("shared"); + //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["shared"] = inputDir + it->second; } + } + } + + + //check for required parameters + accnosfile = validParameter.validFile(parameters, "accnos", true); + if (accnosfile == "not open") { abort = true; } + else if (accnosfile == "not found") { accnosfile = ""; } + else { m->setAccnosFile(accnosfile); } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + m->Groups = Groups; + } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { m->setSharedFile(sharedfile); } + + 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 == "")) { + //give priority to shared, then group + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + 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; + } + } + } + + if ((accnosfile == "") && (Groups.size() == 0)) { Groups.push_back("all"); m->Groups = Groups; } + } + + } + catch(exception& e) { + m->errorOut(e, "CountGroupsCommand", "CountGroupsCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int CountGroupsCommand::execute(){ + try { + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + //get groups you want to remove + if (accnosfile != "") { readAccnos(); } + + if (groupfile != "") { + GroupMap groupMap(groupfile); + groupMap.readMap(); + + //make sure groups are valid + //takes care of user setting groupNames that are invalid or setting groups=all + SharedUtil util; + util.setGroups(Groups, groupMap.namesOfGroups); + + for (int i = 0; i < Groups.size(); i++) { + m->mothurOut(Groups[i] + " contains " + toString(groupMap.getNumSeqs(Groups[i])) + "."); m->mothurOutEndLine(); + } + } + + if (m->control_pressed) { return 0; } + + if (sharedfile != "") { + InputData input(sharedfile, "sharedfile"); + vector lookup = input.getSharedRAbundVectors(); + + for (int i = 0; i < lookup.size(); i++) { + m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + "."); m->mothurOutEndLine(); + delete lookup[i]; + } + } + + return 0; + } + + catch(exception& e) { + m->errorOut(e, "CountGroupsCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** +void CountGroupsCommand::readAccnos(){ + try { + Groups.clear(); + + ifstream in; + m->openInputFile(accnosfile, in); + string name; + + while(!in.eof()){ + in >> name; + + Groups.push_back(name); + + m->gobble(in); + } + in.close(); + + m->Groups = Groups; + + } + catch(exception& e) { + m->errorOut(e, "CountGroupsCommand", "readAccnos"); + exit(1); + } +} +//********************************************************************************************************************** + +