//**********************************************************************************************************************
-GetSharedOTUCommand::GetSharedOTUCommand(string option){
+GetSharedOTUCommand::GetSharedOTUCommand(string option) {
try {
globaldata = GlobalData::getInstance();
else {
//valid paramters for this command
- string Array[] = {"label","unique","shared","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; }
}
+ //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 = 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);
+ //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 = 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...
groups = validParameter.validFile(parameters, "unique", false);
if (groups == "not found") { groups = ""; }
else {
+ userGroups = "unique." + groups;
splitAtDash(groups, Groups);
globaldata->Groups = Groups;
groups = validParameter.validFile(parameters, "shared", false);
if (groups == "not found") { groups = ""; }
else {
+ userGroups = groups;
splitAtDash(groups, Groups);
globaldata->Groups = Groups;
unique = false;
}
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, unique, shared, 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 unique and shared parameters allow you to select groups you would like to know the shared info for, and are separated by dashes.\n");
- mothurOut("If you enter your groups under the unique parameter mothur will return the otus that contain ONLY sequences from those groups.\n");
- 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");
- 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");
- 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.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) {
- errorOut(e, "GetSharedOTUCommand", "help");
+ m->errorOut(e, "GetSharedOTUCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+ int error = groupMap->readMap();
+ if (error == 1) { 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
openInputFile(fastafile, inFasta);
while(!inFasta.eof()) {
- Sequence seq(inFasta);
+ Sequence seq(inFasta); gobble(inFasta);
if (seq.getName() != "") { seqs.push_back(seq); }
}
inFasta.close();
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());
if ((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; }
+
+
+ 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);
}
}
ofstream outNames;
string outputFileNames;
+
+ if (outputDir == "") { outputDir += hasPath(listfile); }
if (output != "accnos") {
- outputFileNames = getRootName(listfile) + shared->getLabel() + ".shared.seqs";
+ outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".shared.seqs";
}else {
- outputFileNames = getRootName(listfile) + shared->getLabel() + ".accnos";
+ outputFileNames = outputDir + getRootName(getSimpleName(listfile)) + shared->getLabel() + userGroups + ".accnos";
}
openOutputFile(outputFileNames, outNames);
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;
namesOfSeqsInThisBin.push_back((name + "\t" + seqGroup + "\t" + 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);
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); }
+ 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);
}
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 fasta file provided output new fasta file
- if ((fastafile != "") && wroteSomething) {
- string outputFileFasta = getRootName(fastafile) + shared->getLabel() + ".shared.fasta";
+ if ((fastafile != "") && wroteSomething) {
+ if (outputDir == "") { outputDir += hasPath(fastafile); }
+ string outputFileFasta = outputDir + getRootName(getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
ofstream outFasta;
openOutputFile(outputFileFasta, outFasta);
+ outputNames.push_back(outputFileFasta);
for (int k = 0; k < seqs.size(); k++) {
//if this is a sequence we want, output it
}
catch(exception& e) {
- errorOut(e, "GetSharedOTUCommand", "process");
+ m->errorOut(e, "GetSharedOTUCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff