#include "getsharedotucommand.h"
-//**********************************************************************************************************************
-GetSharedOTUCommand::GetSharedOTUCommand(string option){
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSharedOTUCommand::GetSharedOTUCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"list","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getRequiredFiles");
+ 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 {
//valid paramters for this command
- string Array[] = {"label","groups","fasta","list","group","output"};
+ string Array[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
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 = ""; }
+
+ //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("fasta");
+ //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["fasta"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("list");
+ //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["list"] = 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; }
+ }
+ }
+
+
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { abort = true; }
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- if ((listfile == "") || (groupfile == "")) { mothurOut("The list and group parameters are required."); mothurOutEndLine(); abort = true; }
+ if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); 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 = ""; }
- groups = validParameter.validFile(parameters, "groups", false);
+ groups = validParameter.validFile(parameters, "unique", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ userGroups = "unique." + groups;
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+
+ }
+
+ groups = validParameter.validFile(parameters, "shared", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ userGroups = groups;
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
+ unique = false;
}
fastafile = validParameter.validFile(parameters, "fasta", true);
}
catch(exception& e) {
- errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
exit(1);
}
}
void GetSharedOTUCommand::help(){
try {
- mothurOut("The get.sharedseqs command parameters are list, group, label, groups, output and fasta. The list and group parameters are required.\n");
- mothurOut("The label parameter allows you to select what distance levels you would like output files for, and are separated by dashes.\n");
- mothurOut("The groups parameter allows you to select groups you would like to know the shared info for, and are separated by dashes.\n");
- 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");
- mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n");
- 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");
- 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");
- mothurOut("The get.sharedseqs command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
- mothurOut("Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n");
- mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n");
- mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
+ 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.sharedseqs(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) {
- errorOut(e, "GetSharedOTUCommand", "help");
+ m->errorOut(e, "GetSharedOTUCommand", "help");
exit(1);
}
}
int GetSharedOTUCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+ 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);
+ m->openInputFile(fastafile, inFasta);
while(!inFasta.eof()) {
- Sequence seq(inFasta);
+ 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();
set<string> userLabels = labels;
ifstream in;
- openInputFile(listfile, 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++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ delete groupMap; return 0;
+ }
+
list = new ListVector(in);
if(allLines == 1 || labels.count(list->getLabel()) == 1){
- mothurOut(list->getLabel());
+ m->mothurOut(list->getLabel());
process(list);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
- mothurOut(lastlist->getLabel());
+ m->mothurOut(lastlist->getLabel());
process(lastlist);
processedLabels.insert(lastlist->getLabel());
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
- mothurOut(lastlist->getLabel());
+ m->mothurOut(lastlist->getLabel());
process(lastlist);
processedLabels.insert(lastlist->getLabel());
globaldata->Groups.clear();
if (lastlist != NULL) { delete lastlist; }
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
+
+ //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); }
+ }
+
+ if (output == "accnos") {
+ itTypes = outputTypes.find("accnos");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+ }
+ }
+
+ 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();
+
+
return 0;
}
catch(exception& e) {
- errorOut(e, "GetSharedOTUCommand", "execute");
+ m->errorOut(e, "GetSharedOTUCommand", "execute");
exit(1);
}
}
/***********************************************************/
-void GetSharedOTUCommand::process(ListVector* shared) {
+int GetSharedOTUCommand::process(ListVector* shared) {
try {
map<string, string> fastaMap;
ofstream outNames;
string outputFileNames;
+
+ if (outputDir == "") { outputDir += m->hasPath(listfile); }
if (output != "accnos") {
- outputFileNames = getRootName(listfile) + shared->getLabel() + ".shared.seqs";
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
}else {
- outputFileNames = getRootName(listfile) + shared->getLabel() + ".accnos";
+ outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
}
- openOutputFile(outputFileNames, outNames);
+ 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; }
- bool sharedByAll = true;
+ bool uniqueOTU = true;
map<string, int> atLeastOne;
- for (int m = 0; m < Groups.size(); m++) {
- atLeastOne[Groups[m]] = 0;
+ for (int f = 0; f < Groups.size(); f++) {
+ atLeastOne[Groups[f]] = 0;
}
vector<string> namesOfSeqsInThisBin;
string names = shared->get(i);
- while ((names.find_first_of(',') != -1) && sharedByAll) {
+ 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());
-
+
//find group
string seqGroup = groupMap->getGroup(name);
if (output != "accnos") {
- namesOfSeqsInThisBin.push_back((name + "\t" + seqGroup + "\t" + toString(i+1)));
+ namesOfSeqsInThisBin.push_back((name + "|" + seqGroup + "|" + toString(i+1)));
}else { namesOfSeqsInThisBin.push_back(name); }
-
- if (seqGroup == "not found") { mothurOut(name + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1); }
+
+ if (seqGroup == "not found") { m->mothurOut(name + " 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()) { sharedByAll = false; } //you have a sequence from a group you don't want
+ if (it == groupFinder.end()) { uniqueOTU = false; } //you have a sequence from a group you don't want
else { atLeastOne[seqGroup]++; }
}
//get last name
- //find group
- if (sharedByAll) {
- string seqGroup = groupMap->getGroup(names);
- if (output != "accnos") {
- namesOfSeqsInThisBin.push_back((names + "\t" + seqGroup + "\t" + toString(i+1)));
- }else { namesOfSeqsInThisBin.push_back(names); }
-
- if (seqGroup == "not found") { mothurOut(names + " is not in your groupfile. Please correct."); mothurOutEndLine(); exit(1); }
+ 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]++; }
- //is this seq in one of hte groups we care about
- it = groupFinder.find(seqGroup);
- if (it == groupFinder.end()) { sharedByAll = 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;
for (it2 = atLeastOne.begin(); it2 != atLeastOne.end(); it2++) {
if (it2->second == 0) { sharedByAll = false; }
}
- //if shared, save names of seqs in that bin
- if (sharedByAll) {
+ //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++;
if (fastafile != "") {
if (output != "accnos") {
- string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('\t'));
- seqName = seqName.substr(0,seqName.find_last_of('\t'));
+ string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
+ seqName = seqName.substr(0,seqName.find_last_of('|'));
fastaMap[seqName] = namesOfSeqsInThisBin[j]; //fastaMap needs to contain just the seq name for output later
}else {
fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
}
}
}
-
-
-
}
outNames.close();
}
outputString += groupString + ".";
- mothurOut(outputString); mothurOutEndLine();
- }else { mothurOut("\t" + toString(num)); mothurOutEndLine(); }
+ 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); }
+ }
//if fasta file provided output new fasta file
- if ((fastafile != "") && wroteSomething) {
- string outputFileFasta = getRootName(fastafile) + shared->getLabel() + ".shared.fasta";
+ if ((fastafile != "") && wroteSomething) {
+ if (outputDir == "") { outputDir += m->hasPath(fastafile); }
+ string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
ofstream outFasta;
- openOutputFile(outputFileFasta, outFasta);
+ 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; }
+
//if this is a sequence we want, output it
it = fastaMap.find(seqs[k].getName());
if (it != fastaMap.end()) {
outFasta.close();
}
-
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "GetSharedOTUCommand", "process");
+ m->errorOut(e, "GetSharedOTUCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff