X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removeotuscommand.cpp;h=16fd8dce8bab96b030a57effd81d218e122628a5;hp=30f337bf7fffc90bcdf7d9ebb8cc97611c6ebd29;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77 diff --git a/removeotuscommand.cpp b/removeotuscommand.cpp index 30f337b..16fd8dc 100644 --- a/removeotuscommand.cpp +++ b/removeotuscommand.cpp @@ -14,13 +14,13 @@ //********************************************************************************************************************** vector RemoveOtusCommand::setParameters(){ try { - CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup); - CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist); - CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pgroup); + CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist); + CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + 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); } @@ -52,7 +52,22 @@ string RemoveOtusCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string RemoveOtusCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "group") { pattern = "[filename],[tag],pick,[extension]"; } + else if (type == "list") { pattern = "[filename],[tag],pick,[extension]"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "RemoveOtusCommand", "getOutputPattern"); + exit(1); + } +} ///********************************************************************************************************************** RemoveOtusCommand::RemoveOtusCommand(){ try { @@ -134,7 +149,8 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { //check for required parameters accnosfile = validParameter.validFile(parameters, "accnos", true); if (accnosfile == "not open") { abort = true; } - else if (accnosfile == "not found") { accnosfile = ""; } + else if (accnosfile == "not found") { accnosfile = ""; } + else { m->setAccnosFile(accnosfile); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } @@ -142,7 +158,7 @@ RemoveOtusCommand::RemoveOtusCommand(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 group file 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; } @@ -150,7 +166,7 @@ RemoveOtusCommand::RemoveOtusCommand(string option) { listfile = m->getListFile(); if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setListFile(listfile); } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } @@ -181,12 +197,13 @@ int RemoveOtusCommand::execute(){ groupMap->readMap(); //get groups you want to remove - if (accnosfile != "") { readAccnos(); } + if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); } //make sure groups are valid //takes care of user setting groupNames that are invalid or setting groups=all SharedUtil* util = new SharedUtil(); - util->setGroups(Groups, groupMap->namesOfGroups); + vector allGroups = groupMap->getNamesOfGroups(); + util->setGroups(Groups, allGroups); delete util; if (m->control_pressed) { delete groupMap; return 0; } @@ -194,7 +211,7 @@ int RemoveOtusCommand::execute(){ //read through the list file keeping any otus that contain any sequence from the groups selected readListGroup(); - 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; } if (outputNames.size() != 0) { m->mothurOutEndLine(); @@ -228,14 +245,20 @@ int RemoveOtusCommand::readListGroup(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick." + label + m->getExtension(listfile); + map variables; + variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile)); + variables["[tag]"] = label; + variables["[extension]"] = m->getExtension(listfile); + string outputFileName = getOutputFileName("list", variables); ofstream out; m->openOutputFile(outputFileName, out); string GroupOutputDir = outputDir; if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); } - string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick." + label + m->getExtension(groupfile); + variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)); + variables["[extension]"] = m->getExtension(groupfile); + string outputGroupFileName = getOutputFileName("group", variables); ofstream outGroup; m->openOutputFile(outputGroupFileName, outGroup); @@ -257,7 +280,7 @@ int RemoveOtusCommand::readListGroup(){ //as long as you are not at the end of the file or done wih the lines you want while((list != NULL) && (userLabels.size() != 0)) { - if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str());return 0; } + if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; } if(labels.count(list->getLabel()) == 1){ processList(list, groupMap, out, outGroup, wroteSomething); @@ -291,7 +314,7 @@ int RemoveOtusCommand::readListGroup(){ } - if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); remove(outputFileName.c_str()); remove(outputGroupFileName.c_str()); return 0; } + if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; } //output error messages about any remaining user labels set::iterator it; @@ -405,30 +428,6 @@ int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstr } } //********************************************************************************************************************** -void RemoveOtusCommand::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(); - - } - catch(exception& e) { - m->errorOut(e, "RemoveOtusCommand", "readAccnos"); - exit(1); - } -} -//**********************************************************************************************************************