*/
#include "getsharedotucommand.h"
+#include "sharedutilities.h"
//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::setParameters(){
+ try {
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "sharedFasta", "none", "none","fasta",false,false); parameters.push_back(pfasta);
+ CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "groupList","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter plist("list", "InputTypes", "", "", "sharedList", "sharedList", "groupList","sharedseq",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "sharedList-sharedFasta", "sharedList", "none","sharedseq",false,false,true); parameters.push_back(pshared);
+ CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter puniquegroups("uniquegroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(puniquegroups);
+ CommandParameter psharedgroups("sharedgroups", "String", "", "", "", "", "","",false,false,true); parameters.push_back(psharedgroups);
+ 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, "GetSharedOTUCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetSharedOTUCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.sharedseqs command parameters are list, group, shared, label, uniquegroups, sharedgroups, output and fasta. The list and group or shared parameters are required, unless you have valid current files.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n";
+ helpString += "The uniquegroups and sharedgroups parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n";
+ helpString += "If you enter your groups under the uniquegroups parameter mothur will return the otus that contain ONLY sequences from those groups.\n";
+ helpString += "If you enter your groups under the sharedgroups parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n";
+ helpString += "If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group or shared file.\n";
+ helpString += "The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified. It can only be used with a list and group file not the shared file input.\n";
+ helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
+ helpString += "With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n";
+ helpString += "The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n";
+ helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, uniquegroups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+ helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=amazon.groups, uniquegroups=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+ helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
+ helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetSharedOTUCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+ if (type == "fasta") { pattern = "[filename],[distance],[group],shared.fasta"; }
+ else if (type == "accnos") { pattern = "[filename],[distance],[group],accnos"; }
+ else if (type == "sharedseqs") { pattern = "[filename],[distance],[group],shared.seqs"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSharedOTUCommand::GetSharedOTUCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
unique = true;
allLines = 1;
- labels.clear();
//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[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
+
//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 = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("list");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["list"] = 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("group");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ 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; }
}
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { globaldata->setListFile(listfile); globaldata->setFormat("list"); }
+ else if (listfile == "not found") { listfile = ""; }
+ else { format = "list"; m->setListFile(listfile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
-
- if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
-
+ else { m->setGroupFile(groupfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { m->setSharedFile(sharedfile); }
+
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; }
+ else { m->setFastaFile(fastafile); }
+
+
+ if ((sharedfile == "") && (listfile == "")) { //look for currents
+ //is there are current file available for either of these?
+ //give priority to shared, then list
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ listfile = m->getListFile();
+ if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a shared or list file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }else if ((sharedfile != "") && (listfile != "")) {
+ m->mothurOut("You may enter ONLY ONE of the following: shared or list."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if (listfile != "") {
+ if (groupfile == ""){
+ groupfile = m->getGroupFile();
+ if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You need to provide a group file if you are going to use the list format."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
+
+ if ((sharedfile != "") && (fastafile != "")) { m->mothurOut("You cannot use the fasta file with the shared file."); m->mothurOutEndLine(); abort = true; }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
output = validParameter.validFile(parameters, "output", false);
if (output == "not found") { output = ""; }
+ else if (output == "default") { output = ""; }
- groups = validParameter.validFile(parameters, "unique", false);
+ groups = validParameter.validFile(parameters, "uniquegroups", false);
if (groups == "not found") { groups = ""; }
else {
userGroups = "unique." + groups;
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
-
+ m->splitAtDash(groups, Groups);
}
- groups = validParameter.validFile(parameters, "shared", false);
+ groups = validParameter.validFile(parameters, "sharedgroups", false);
if (groups == "not found") { groups = ""; }
else {
userGroups = groups;
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->splitAtDash(groups, Groups);
unique = false;
}
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; }
-
- }
+ }
}
catch(exception& e) {
}
//**********************************************************************************************************************
-void GetSharedOTUCommand::help(){
- try {
- m->mothurOut("The get.sharedseqs command parameters are list, group, label, unique, shared, output and fasta. The list and group parameters are required.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
- m->mothurOut("The unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n");
- m->mothurOut("If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n");
- m->mothurOut("If you enter your groups under the shared parameter mothur will return the otus that contain sequences from those groups and may also contain sequences from other groups.\n");
- m->mothurOut("If you do not enter any groups then the get.sharedseqs command will return sequences that are unique to all groups in your group file.\n");
- m->mothurOut("The fasta parameter allows you to input a fasta file and outputs a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified.\n");
- m->mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n");
- m->mothurOut("With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n");
- m->mothurOut("The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n");
- m->mothurOut("The get.sharedseqs command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
- m->mothurOut("Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n");
- m->mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n");
- m->mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "GetSharedOTUCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetSharedOTUCommand::~GetSharedOTUCommand(){}
-
-//**********************************************************************************************************************
-
int GetSharedOTUCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- groupMap = new GroupMap(groupfile);
- int error = groupMap->readMap();
- if (error == 1) { delete groupMap; return 0; }
-
- if (m->control_pressed) { delete groupMap; return 0; }
-
- globaldata->gGroupmap = groupMap;
-
- if (Groups.size() == 0) {
- Groups = groupMap->namesOfGroups;
-
- //make string for outputfile name
- userGroups = "unique.";
- for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
- userGroups = userGroups.substr(0, userGroups.length()-1);
- }
-
- //put groups in map to find easier
- for(int i = 0; i < Groups.size(); i++) {
- groupFinder[Groups[i]] = Groups[i];
- }
-
- if (fastafile != "") {
- ifstream inFasta;
- openInputFile(fastafile, inFasta);
-
- while(!inFasta.eof()) {
- if (m->control_pressed) { inFasta.close(); delete groupMap; return 0; }
-
- Sequence seq(inFasta); gobble(inFasta);
- if (seq.getName() != "") { seqs.push_back(seq); }
- }
- inFasta.close();
- }
-
- ListVector* lastlist = NULL;
- string lastLabel = "";
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = labels;
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- ifstream in;
- openInputFile(listfile, in);
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) {
- if (lastlist != NULL) { delete lastlist; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- delete groupMap; return 0;
- }
-
- list = new ListVector(in);
-
- if(allLines == 1 || labels.count(list->getLabel()) == 1){
- m->mothurOut(list->getLabel());
- process(list);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- }
-
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
-
- m->mothurOut(lastlist->getLabel());
- process(lastlist);
-
- processedLabels.insert(lastlist->getLabel());
- userLabels.erase(lastlist->getLabel());
-
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
- }
+ if ( sharedfile != "") { runShared(); }
+ else {
+ m->setGroups(Groups);
+ groupMap = new GroupMap(groupfile);
+ int error = groupMap->readMap();
+ if (error == 1) { delete groupMap; return 0; }
+
+ if (m->control_pressed) { delete groupMap; return 0; }
+
+ if (Groups.size() == 0) {
+ Groups = groupMap->getNamesOfGroups();
+
+ //make string for outputfile name
+ userGroups = "unique.";
+ for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
+ userGroups = userGroups.substr(0, userGroups.length()-1);
+ }else{
+ //sanity check for group names
+ SharedUtil util;
+ vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+ util.setGroups(Groups, namesOfGroups);
+ groupMap->setNamesOfGroups(namesOfGroups);
+ }
+
+ //put groups in map to find easier
+ for(int i = 0; i < Groups.size(); i++) {
+ groupFinder[Groups[i]] = Groups[i];
+ }
+
+ if (fastafile != "") {
+ ifstream inFasta;
+ m->openInputFile(fastafile, inFasta);
+
+ while(!inFasta.eof()) {
+ if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
+
+ Sequence seq(inFasta); m->gobble(inFasta);
+ if (seq.getName() != "") { seqs.push_back(seq); }
+ }
+ inFasta.close();
+ }
+
+ ListVector* lastlist = NULL;
+ string lastLabel = "";
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ ifstream in;
+ m->openInputFile(listfile, in);
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) {
+ if (lastlist != NULL) { delete lastlist; }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
+ delete groupMap; return 0;
+ }
+
+ list = new ListVector(in);
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+ m->mothurOut(list->getLabel());
+ process(list);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ m->mothurOut(lastlist->getLabel());
+ process(lastlist);
+
+ processedLabels.insert(lastlist->getLabel());
+ userLabels.erase(lastlist->getLabel());
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
- lastLabel = list->getLabel();
-
- if (lastlist != NULL) { delete lastlist; }
- lastlist = list;
+ lastLabel = list->getLabel();
+
+ if (lastlist != NULL) { delete lastlist; }
+ lastlist = list;
+ }
+
+ in.close();
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ m->mothurOut(lastlist->getLabel());
+ process(lastlist);
+
+ processedLabels.insert(lastlist->getLabel());
+ userLabels.erase(lastlist->getLabel());
+ }
+
+
+ //reset groups parameter
+ m->clearGroups();
+
+ if (lastlist != NULL) { delete lastlist; }
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete groupMap; return 0; }
}
-
- in.close();
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); 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); }
}
- //run last label if you need to
- if (needToRun == true) {
- m->mothurOut(lastlist->getLabel());
- process(lastlist);
-
- processedLabels.insert(lastlist->getLabel());
- userLabels.erase(lastlist->getLabel());
+ if (output == "accnos") {
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
}
-
- //reset groups parameter
- globaldata->Groups.clear();
-
- if (lastlist != NULL) { delete lastlist; }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
-
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
ofstream outNames;
string outputFileNames;
- if (outputDir == "") { outputDir += hasPath(listfile); }
- if (output != "accnos") {
- outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
- }else {
- outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
- }
- openOutputFile(outputFileNames, outNames);
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[distance]"] = shared->getLabel();
+ variables["[group]"] = userGroups;
+ if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
+ else { outputFileNames = getOutputFileName("accnos", variables); }
+
+ m->openOutputFile(outputFileNames, outNames);
bool wroteSomething = false;
int num = 0;
//go through each bin, find out if shared
for (int i = 0; i < shared->getNumBins(); i++) {
- if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
+ if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
bool uniqueOTU = true;
vector<string> namesOfSeqsInThisBin;
- string names = shared->get(i);
- while ((names.find_first_of(',') != -1)) {
- string name = names.substr(0,names.find_first_of(','));
- names = names.substr(names.find_first_of(',')+1, names.length());
+ string names = shared->get(i);
+ vector<string> binNames;
+ m->splitAtComma(names, binNames);
+ for(int j = 0; j < binNames.size(); j++) {
+ string name = binNames[j];
//find group
string seqGroup = groupMap->getGroup(name);
else { atLeastOne[seqGroup]++; }
}
- //get last name
- string seqGroup = groupMap->getGroup(names);
- if (output != "accnos") {
- namesOfSeqsInThisBin.push_back((names + "|" + seqGroup + "|" + toString(i+1)));
- }else { namesOfSeqsInThisBin.push_back(names); }
-
- if (seqGroup == "not found") { m->mothurOut(names + " is not in your groupfile. Please correct."); m->mothurOutEndLine(); exit(1); }
-
- //is this seq in one of hte groups we care about
- it = groupFinder.find(seqGroup);
- if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
- else { atLeastOne[seqGroup]++; }
-
-
//make sure you have at least one seq from each group you want
bool sharedByAll = true;
map<string, int>::iterator it2;
outNames.close();
if (!wroteSomething) {
- remove(outputFileNames.c_str());
+ m->mothurRemove(outputFileNames);
string outputString = "\t" + toString(num) + " - No otus shared by groups";
string groupString = "";
}else {
m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
outputNames.push_back(outputFileNames);
+ if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
+ else { outputTypes["accnos"].push_back(outputFileNames); }
}
//if fasta file provided output new fasta file
if ((fastafile != "") && wroteSomething) {
- if (outputDir == "") { outputDir += hasPath(fastafile); }
- string outputFileFasta = outputDir + getRootName(getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
+ if (outputDir == "") { outputDir += m->hasPath(fastafile); }
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileFasta = getOutputFileName("fasta", variables);
ofstream outFasta;
- openOutputFile(outputFileFasta, outFasta);
- outputNames.push_back(outputFileFasta);
+ m->openOutputFile(outputFileFasta, outFasta);
+ outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
for (int k = 0; k < seqs.size(); k++) {
if (m->control_pressed) { outFasta.close(); return 0; }
exit(1);
}
}
+/***********************************************************/
+int GetSharedOTUCommand::runShared() {
+ try {
+ InputData input(sharedfile, "sharedfile");
+ vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ if (Groups.size() == 0) {
+ Groups = m->getGroups();
+
+ //make string for outputfile name
+ userGroups = "unique.";
+ for(int i = 0; i < Groups.size(); i++) { userGroups += Groups[i] + "-"; }
+ userGroups = userGroups.substr(0, userGroups.length()-1);
+ }else {
+ //sanity check for group names
+ SharedUtil util;
+ vector<string> allGroups = m->getAllGroups();
+ util.setGroups(Groups, allGroups);
+ }
+
+ //put groups in map to find easier
+ for(int i = 0; i < Groups.size(); i++) {
+ groupFinder[Groups[i]] = Groups[i];
+ }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0;
+ }
+
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ m->mothurOut(lookup[0]->getLabel());
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel());
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input.getSharedRAbundVectors();
+ }
+
+ if (m->control_pressed) {
+ outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input.getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel());
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
+ //reset groups parameter
+ m->clearGroups();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "runShared");
+ exit(1);
+ }
+}
+/***********************************************************/
+int GetSharedOTUCommand::process(vector<SharedRAbundVector*>& lookup) {
+ try {
+
+ string outputFileNames;
+ if (outputDir == "") { outputDir += m->hasPath(sharedfile); }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[distance]"] = lookup[0]->getLabel();
+ variables["[group]"] = userGroups;
+ if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
+ else { outputFileNames = getOutputFileName("accnos", variables); }
+
+ ofstream outNames;
+ m->openOutputFile(outputFileNames, outNames);
+
+ bool wroteSomething = false;
+ int num = 0;
+
+ //go through each bin, find out if shared
+ for (int i = 0; i < lookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
+
+ bool uniqueOTU = true;
+ map<string, int> atLeastOne;
+ for (int f = 0; f < Groups.size(); f++) { atLeastOne[Groups[f]] = 0; }
+
+ set<string> namesOfGroupsInThisBin;
+
+ for(int j = 0; j < lookup.size(); j++) {
+ string seqGroup = lookup[j]->getGroup();
+ string name = m->currentBinLabels[i];
+
+ if (lookup[j]->getAbundance(i) != 0) {
+ if (output != "accnos") {
+ namesOfGroupsInThisBin.insert(name + "|" + seqGroup + "|" + toString(lookup[j]->getAbundance(i)));
+ }else { namesOfGroupsInThisBin.insert(name); }
+
+ //is this seq in one of the groups we care about
+ it = groupFinder.find(seqGroup);
+ if (it == groupFinder.end()) { uniqueOTU = false; } //you have sequences from a group you don't want
+ else { atLeastOne[seqGroup]++; }
+ }
+ }
+
+ //make sure you have at least one seq from each group you want
+ bool sharedByAll = true;
+ map<string, int>::iterator it2;
+ for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
+ if (it2->second == 0) { sharedByAll = false; }
+ }
+
+ //if the user wants unique bins and this is unique then print
+ //or this the user wants shared bins and this bin is shared then print
+ if ((unique && uniqueOTU && sharedByAll) || (!unique && sharedByAll)) {
+
+ wroteSomething = true;
+ num++;
+
+ //output list of names
+ for (set<string>::iterator itNames = namesOfGroupsInThisBin.begin(); itNames != namesOfGroupsInThisBin.end(); itNames++) {
+ outNames << (*itNames) << endl;
+ }
+ }
+ }
+ outNames.close();
+
+ if (!wroteSomething) {
+ m->mothurRemove(outputFileNames);
+ string outputString = "\t" + toString(num) + " - No otus shared by groups";
+
+ string groupString = "";
+ for (int h = 0; h < Groups.size(); h++) {
+ groupString += " " + Groups[h];
+ }
+
+ outputString += groupString + ".";
+ m->mothurOut(outputString); m->mothurOutEndLine();
+ }else {
+ m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
+ outputNames.push_back(outputFileNames);
+ if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
+ else { outputTypes["accnos"].push_back(outputFileNames); }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "process");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
projects / mothur.git / blobdiff