globaldata = GlobalData::getInstance();
abort = false;
+ unique = true;
allLines = 1;
labels.clear();
else {
//valid paramters for this command
- string Array[] = {"label","groups","fasta","list","group","output"};
+ string Array[] = {"label","unique","shared","fasta","list","group","output"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
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);
globaldata->Groups = Groups;
+
+ }
+
+ groups = validParameter.validFile(parameters, "shared", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ unique = false;
}
fastafile = validParameter.validFile(parameters, "fasta", true);
void GetSharedOTUCommand::help(){
try {
- mothurOut("The get.sharedotu command parameters are list, group, label, groups, output and fasta. The list and group parameters are required.\n");
+ 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 groups parameter allows you to select groups you would like to know the shared info 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.sharedotu 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.sharedotu command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
- mothurOut("Example get.sharedotu(label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, 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");
}
if (Groups.size() == 0) {
Groups = groupMap->namesOfGroups;
}
-
+
//put groups in map to find easier
for(int i = 0; i < Groups.size(); i++) {
groupFinder[Groups[i]] = Groups[i];
while(!inFasta.eof()) {
Sequence seq(inFasta);
- seqs.push_back(seq);
+ if (seq.getName() != "") { seqs.push_back(seq); }
}
inFasta.close();
}
}
if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
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();
map<string, string> fastaMap;
ofstream outNames;
- string outputFileNames = getRootName(listfile) + shared->getLabel() + ".names";
+ string outputFileNames;
+ if (output != "accnos") {
+ outputFileNames = getRootName(listfile) + shared->getLabel() + ".shared.seqs";
+ }else {
+ outputFileNames = getRootName(listfile) + shared->getLabel() + ".accnos";
+ }
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++) {
- bool sharedByAll = true;
+ bool uniqueOTU = true;
map<string, int> atLeastOne;
for (int m = 0; m < Groups.size(); m++) {
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 + "|" + seqGroup + "|" + toString(i)));
+ 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); }
//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 + "|" + seqGroup + "|" + toString(i)));
- }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 + "\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); }
+
+ //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++;
//output list of names
for (int j = 0; j < namesOfSeqsInThisBin.size(); j++) {
if (fastafile != "") {
if (output != "accnos") {
- string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('|'));
- seqName = seqName.substr(0,seqName.find_last_of('|'));
+ string seqName = namesOfSeqsInThisBin[j].substr(0,namesOfSeqsInThisBin[j].find_last_of('\t'));
+ seqName = seqName.substr(0,seqName.find_last_of('\t'));
fastaMap[seqName] = namesOfSeqsInThisBin[j]; //fastaMap needs to contain just the seq name for output later
}else {
fastaMap[namesOfSeqsInThisBin[j]] = namesOfSeqsInThisBin[j];
}
}
}
-
-
-
}
outNames.close();
if (!wroteSomething) {
remove(outputFileNames.c_str());
- string outputString = " - No otus shared by groups";
+ string outputString = "\t" + toString(num) + " - No otus shared by groups";
string groupString = "";
for (int h = 0; h < Groups.size(); h++) {
outputString += groupString + ".";
mothurOut(outputString); mothurOutEndLine();
- }else { mothurOutEndLine(); }
+ }else { mothurOut("\t" + toString(num)); mothurOutEndLine(); }
//if fasta file provided output new fasta file
if ((fastafile != "") && wroteSomething) {
- string outputFileFasta = getRootName(fastafile) + shared->getLabel() + ".fasta";
+ string outputFileFasta = getRootName(fastafile) + shared->getLabel() + ".shared.fasta";
ofstream outFasta;
openOutputFile(outputFileFasta, outFasta);
projects / mothur.git / blobdiff