#include "sequence.hpp"
#include "listvector.hpp"
#include "sharedutilities.h"
+#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> RemoveGroupsCommand::getValidParameters(){
+vector<string> RemoveGroupsCommand::setParameters(){
try {
- string Array[] = {"fasta","name", "group", "accnos", "groups","list","taxonomy","outputdir","inputdir" };
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT","fasta",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "sharedGroup", "FNGLT","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "sharedGroup", "FNGLT","design",false,false); parameters.push_back(pdesign);
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT","list",false,false,true); parameters.push_back(plist);
+ CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT","taxonomy",false,false,true); 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<string> 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);
}
}
//**********************************************************************************************************************
-RemoveGroupsCommand::RemoveGroupsCommand(){
+string RemoveGroupsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["fasta"] = tempOutNames;
- outputTypes["taxonomy"] = tempOutNames;
- outputTypes["name"] = tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
+ 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, count, 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, design and groups. The group or count parameter is required, unless you have a current group or count 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";
+ 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", "RemoveGroupsCommand");
+ m->errorOut(e, "RemoveGroupsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> RemoveGroupsCommand::getRequiredParameters(){
- try {
- string Array[] = {"group"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveGroupsCommand", "getRequiredParameters");
- exit(1);
- }
+string RemoveGroupsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "list") { pattern = "[filename],pick,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[tag],pick,[extension]"; }
+ else if (type == "design") { pattern = "[filename],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, "RemoveGroupsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> RemoveGroupsCommand::getRequiredFiles(){
+RemoveGroupsCommand::RemoveGroupsCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["taxonomy"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ outputTypes["group"] = tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "RemoveGroupsCommand", "getRequiredFiles");
+ m->errorOut(e, "RemoveGroupsCommand", "RemoveGroupsCommand");
exit(1);
}
}
//allow user to run help
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<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
outputTypes["name"] = tempOutNames;
outputTypes["group"] = tempOutNames;
outputTypes["list"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ outputTypes["design"] = tempOutNames;
+ outputTypes["count"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = 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; }
+ }
+
+ 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; }
+ }
+
+ it = parameters.find("count");
+ //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["count"] = inputDir + it->second; }
+ }
}
//check for required parameters
accnosfile = validParameter.validFile(parameters, "accnos", true);
- if (accnosfile == "not open") { abort = true; }
+ if (accnosfile == "not open") { accnosfile = ""; abort = true; }
else if (accnosfile == "not found") { accnosfile = ""; }
+ 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); }
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; }
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
+ if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
+ 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); }
+
+ 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 = ""; }
else {
m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
+ }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
+
+
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
+
+ if ((sharedfile == "") && (groupfile == "") && (designfile == "") && (countfile == "")) {
+ //is there are current file available for any of these?
+ if ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")) {
+ //give priority to group, then shared
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else {
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
+ }else {
+ //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 {
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else {
+ countfile = m->getCountTableFile();
+ if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current groupfile, designfile, countfile or sharedfile and one is required."); m->mothurOutEndLine(); abort = true;
+ }
+
+ }
+ }
+ }
+ }
}
- 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 ((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 == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group or list."); m->mothurOutEndLine(); abort = true; }
+ if ((fastafile == "") && (namefile == "") && (countfile == "") && (groupfile == "") && (designfile == "") && (sharedfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared, design, count or list."); m->mothurOutEndLine(); abort = true; }
+ if (((groupfile == "") && (countfile == "")) && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != ""))) { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group or count file."); m->mothurOutEndLine(); abort = true; }
+
+ if (countfile == "") {
+ if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+ vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+ parser.getNameFile(files);
+ }
+ }
}
}
}
//**********************************************************************************************************************
-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) { if (calledHelp) { return 0; } return 2; }
- groupMap = new GroupMap(groupfile);
- 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);
- delete util;
-
- //fill names with names of sequences that are from the groups we want to remove
- fillNames();
-
- if (m->control_pressed) { delete groupMap; return 0; }
+ if (groupfile != "") {
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+
+ //make sure groups are valid
+ //takes care of user setting groupNames that are invalid or setting groups=all
+ vector<string> namesGroups = groupMap->getNamesOfGroups();
+ vector<string> checkedGroups;
+ for (int i = 0; i < Groups.size(); i++) {
+ if (m->inUsersGroups(Groups[i], namesGroups)) { checkedGroups.push_back(Groups[i]); }
+ else { m->mothurOut("[WARNING]: " + Groups[i] + " is not a valid group in your groupfile, ignoring.\n"); }
+ }
+
+ if (checkedGroups.size() == 0) { m->mothurOut("[ERROR]: no valid groups, aborting.\n"); delete groupMap; return 0; }
+ else {
+ Groups = checkedGroups;
+ m->setGroups(Groups);
+ }
+
+ //fill names with names of sequences that are from the groups we want to remove
+ fillNames();
+
+ delete groupMap;
+ }else if (countfile != ""){
+ if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
+ m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
+ }
+ CountTable ct;
+ ct.readTable(countfile, true);
+ if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
+
+ vector<string> gNamesOfGroups = ct.getNamesOfGroups();
+ SharedUtil util;
+ util.setGroups(Groups, gNamesOfGroups);
+ vector<string> namesOfSeqs = ct.getNamesOfSeqs();
+ sort(Groups.begin(), Groups.end());
+
+ for (int i = 0; i < namesOfSeqs.size(); i++) {
+ vector<string> thisSeqsGroups = ct.getGroups(namesOfSeqs[i]);
+ if (m->isSubset(Groups, thisSeqsGroups)) { //you only have seqs from these groups so remove you
+ names.insert(namesOfSeqs[i]);
+ }
+ }
+ }
+
+
+ if (m->control_pressed) { return 0; }
//read through the correct file and output lines you want to keep
if (namefile != "") { readName(); }
if (fastafile != "") { readFasta(); }
if (groupfile != "") { readGroup(); }
+ if (countfile != "") { readCount(); }
if (listfile != "") { readList(); }
if (taxfile != "") { readTax(); }
+ if (sharedfile != "") { readShared(); }
+ if (designfile != "") { readDesign(); }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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(); }
- m->mothurOutEndLine();
-
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
if (outputNames.size() != 0) {
m->mothurOutEndLine();
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); }
+ }
+
+ itTypes = outputTypes.find("shared");
+ 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); }
+ }
+
+ itTypes = outputTypes.find("count");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+ }
}
return 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string name;
bool wroteSomething = false;
+ int removedCount = 0;
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();
//if this name is in the accnos file
if (names.count(name) == 0) {
wroteSomething = true;
-
- currSeq.printSequence(out);
+ currSeq.printSequence(out);
+ }else {
+ //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(name);
+ if (it != uniqueToRedundant.end()) {
+ wroteSomething = true;
+ currSeq.setName(it->second);
+ currSeq.printSequence(out);
+ }else { removedCount++; }
}
}
m->gobble(in);
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
outputTypes["fasta"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
+
return 0;
}
exit(1);
}
}
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readShared(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
+
+ //get group names from sharedfile so we can set Groups to the groupNames we want to keep
+ //that way we can take advantage of the reads in inputdata and sharedRabundVector
+ InputData* tempInput = new InputData(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = tempInput->getSharedRAbundVectors();
+
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+
+ //save m->Groups
+ vector<string> allGroupsNames = m->getAllGroups();
+ vector<string> mothurOutGroups = m->getGroups();
+
+ vector<string> groupsToKeep;
+ for (int i = 0; i < allGroupsNames.size(); i++) {
+ if (!m->inUsersGroups(allGroupsNames[i], m->getGroups())) {
+ groupsToKeep.push_back(allGroupsNames[i]);
+ }
+ }
+
+ if (allGroupsNames.size() == groupsToKeep.size()) { m->mothurOut("Your file does not contain any groups you wish to remove."); m->mothurOutEndLine(); m->setGroups(mothurOutGroups); delete tempInput; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+
+ //reset read
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ delete tempInput;
+ m->setGroups(groupsToKeep);
+ m->clearAllGroups();
+ m->saveNextLabel = "";
+ m->printedHeaders = false;
+ m->currentBinLabels.clear();
+ m->binLabelsInFile.clear();
+
+ InputData input(sharedfile, "sharedfile");
+ lookup = input.getSharedRAbundVectors();
+ bool wroteSomething = false;
+
+ while(lookup[0] != NULL) {
+
+ variables["[tag]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ if (m->control_pressed) { out.close(); m->mothurRemove(outputFileName); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+
+ lookup[0]->printHeaders(out);
+
+ for (int i = 0; i < lookup.size(); i++) {
+ out << lookup[i]->getLabel() << '\t' << lookup[i]->getGroup() << '\t';
+ lookup[i]->print(out);
+ wroteSomething = true;
+
+ }
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors();
+
+ out.close();
+ }
+
+
+ m->setGroups(mothurOutGroups);
+
+ if (wroteSomething == false) { m->mothurOut("Your file contains only the groups you wish to remove."); m->mothurOutEndLine(); }
+
+ string groupsString = "";
+ for (int i = 0; i < Groups.size()-1; i++) { groupsString += Groups[i] + ", "; }
+ groupsString += Groups[Groups.size()-1];
+
+ m->mothurOut("Removed groups: " + groupsString + " from your shared file."); m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readShared");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
int RemoveGroupsCommand::readList(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
m->openInputFile(listfile, in);
bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
+
+ removedCount = 0;
+
//read in list vector
ListVector list(in);
//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);
//if that name is in the .accnos file, add it
if (names.count(name) == 0) { newNames += name + ","; }
+ else {
+ //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(name);
+ if (it != uniqueToRedundant.end()) {
+ newNames += it->second + ",";
+ }else { removedCount++; }
+ }
}
//get last name
if (names.count(binnames) == 0) { newNames += binnames + ","; }
+ else { //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(binnames);
+ if (it != uniqueToRedundant.end()) {
+ newNames += it->second + ",";
+ }else { removedCount++; }
+ }
//if there are names in this bin add to new list
if (newNames != "") {
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();
+
return 0;
}
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
-
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string name, firstCol, secondCol;
bool wroteSomething = false;
+ int removedCount = 0;
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;
}
}
+ removedCount += parsedNames.size()-validSecond.size();
//if the name in the first column is in the set then print it and any other names in second column also in set
if (names.count(firstCol) == 0) {
//you know you have at least one valid second since first column is valid
for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
out << validSecond[validSecond.size()-1] << endl;
+ uniqueToRedundant[firstCol] = validSecond[0];
}
}
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
outputTypes["name"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your name file."); m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
-
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string name, group;
bool wroteSomething = false;
+ int removedCount = 0;
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
if (names.count(name) == 0) {
wroteSomething = true;
out << name << '\t' << group << endl;
- }
+ }else { removedCount++; }
m->gobble(in);
}
if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your group file."); m->mothurOutEndLine();
+
+
return 0;
}
catch(exception& e) {
}
}
//**********************************************************************************************************************
-int RemoveGroupsCommand::readTax(){
+int RemoveGroupsCommand::readCount(){
try {
string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
+ if (outputDir == "") { thisOutputDir += m->hasPath(countfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string outputFileName = getOutputFileName("count", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
ifstream in;
- m->openInputFile(taxfile, in);
- string name, tax;
+ m->openInputFile(countfile, in);
+
+ bool wroteSomething = false;
+ int removedCount = 0;
+
+ string headers = m->getline(in); m->gobble(in);
+ vector<string> columnHeaders = m->splitWhiteSpace(headers);
+
+ vector<string> groups;
+ map<int, string> originalGroupIndexes;
+ map<string, int> GroupIndexes;
+ set<int> indexOfGroupsChosen;
+ for (int i = 2; i < columnHeaders.size(); i++) { groups.push_back(columnHeaders[i]); originalGroupIndexes[i-2] = columnHeaders[i]; }
+ //sort groups to keep consistent with how we store the groups in groupmap
+ sort(groups.begin(), groups.end());
+ for (int i = 0; i < groups.size(); i++) { GroupIndexes[groups[i]] = i; }
+
+ vector<string> groupsToKeep;
+ for (int i = 0; i < groups.size(); i++) {
+ if (!m->inUsersGroups(groups[i], Groups)) { groupsToKeep.push_back(groups[i]); }
+ }
+ sort(groupsToKeep.begin(), groupsToKeep.end());
+ out << "Representative_Sequence\ttotal\t";
+ for (int i = 0; i < groupsToKeep.size(); i++) { out << groupsToKeep[i] << '\t'; indexOfGroupsChosen.insert(GroupIndexes[groupsToKeep[i]]); }
+ out << endl;
+
+ string name; int oldTotal;
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
+
+ in >> name; m->gobble(in); in >> oldTotal; m->gobble(in);
+ if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + toString(oldTotal) + "\n"); }
+
+ if (names.count(name) == 0) {
+ //if group info, then read it
+ vector<int> selectedCounts; int thisTotal = 0; int temp;
+ for (int i = 0; i < groups.size(); i++) {
+ int thisIndex = GroupIndexes[originalGroupIndexes[i]];
+ in >> temp; m->gobble(in);
+ if (indexOfGroupsChosen.count(thisIndex) != 0) { //we want this group
+ selectedCounts.push_back(temp); thisTotal += temp;
+ }
+ }
+
+ out << name << '\t' << thisTotal << '\t';
+ for (int i = 0; i < selectedCounts.size(); i++) { out << selectedCounts[i] << '\t'; }
+ out << endl;
+
+ wroteSomething = true;
+ removedCount+= (oldTotal - thisTotal);
+ }else { m->getline(in); removedCount += oldTotal; }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething == false) { m->mothurOut("Your file does NOT contain sequences from the groups you wish to get."); m->mothurOutEndLine(); }
+ outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your count file."); m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RemoveGroupsCommand", "readCount");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int RemoveGroupsCommand::readDesign(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(designfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(designfile));
+ variables["[extension]"] = m->getExtension(designfile);
+ string outputFileName = getOutputFileName("design", variables);
+
+ 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(); 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
+ in >> group; //read from second column
//if this name is in the accnos file
- if (names.count(name) == 0) {
+ if (!(m->inUsersGroups(name, Groups))) {
wroteSomething = true;
- out << name << '\t' << tax << endl;
- }
+ out << name << '\t' << group << endl;
+ }else { removedCount++; }
m->gobble(in);
}
in.close();
out.close();
- if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
- outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ 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", "readTax");
+ m->errorOut(e, "RemoveGroupsCommand", "readDesign");
exit(1);
}
}
+
//**********************************************************************************************************************
-void RemoveGroupsCommand::readAccnos(){
+int RemoveGroupsCommand::readTax(){
try {
- Groups.clear();
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
ifstream in;
- m->openInputFile(accnosfile, in);
- string name;
+ m->openInputFile(taxfile, in);
+ string name, tax;
+
+ bool wroteSomething = false;
+ int removedCount = 0;
while(!in.eof()){
- in >> name;
+ 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
- Groups.push_back(name);
+ //if this name is in the accnos file
+ if (names.count(name) == 0) {
+ wroteSomething = true;
+ out << name << '\t' << tax << endl;
+ }else { //if you are not in the accnos file check if you are a name that needs to be changed
+ map<string, string>::iterator it = uniqueToRedundant.find(name);
+ if (it != uniqueToRedundant.end()) {
+ wroteSomething = true;
+ out << it->second << '\t' << tax << endl;
+ }else { removedCount++; } }
m->gobble(in);
}
- in.close();
+ in.close();
+ out.close();
+ if (wroteSomething == false) { m->mothurOut("Your file contains only sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
+ outputTypes["taxonomy"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ m->mothurOut("Removed " + toString(removedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
+
+ return 0;
}
catch(exception& e) {
- m->errorOut(e, "RemoveGroupsCommand", "readAccnos");
+ m->errorOut(e, "RemoveGroupsCommand", "readTax");
exit(1);
}
}
projects / mothur.git / blobdiff