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added rarepercent and keepties parameters to the filter.shared command.
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SarahsWork committed Apr 8, 2013
1 parent a54ba61 commit feb0fbe
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Showing 3 changed files with 63 additions and 4 deletions.
1 change: 0 additions & 1 deletion classifyseqscommand.cpp
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Expand Up @@ -258,7 +258,6 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option) {

namefile = validParameter.validFile(parameters, "name", false);
if (namefile == "not found") { namefile = ""; }

else {
m->splitAtDash(namefile, namefileNames);

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62 changes: 61 additions & 1 deletion filtersharedcommand.cpp
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Expand Up @@ -15,10 +15,12 @@ vector<string> FilterSharedCommand::setParameters(){
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
CommandParameter pminpercent("minpercent", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pminpercent);
CommandParameter prarepercent("rarepercent", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(prarepercent);
CommandParameter pminabund("minabund", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pminabund);
CommandParameter pmintotal("mintotal", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pmintotal);
CommandParameter pminnumsamples("minnumsamples", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pminnumsamples);
CommandParameter pminpercentsamples("minpercentsamples", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pminpercentsamples);
CommandParameter pkeepties("keepties", "Boolean", "", "T", "", "", "","",false,false,true); parameters.push_back(pkeepties);
CommandParameter pmakerare("makerare", "Boolean", "", "T", "", "", "","",false,false,true); parameters.push_back(pmakerare);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
Expand All @@ -37,12 +39,14 @@ string FilterSharedCommand::getHelpString(){
try {
string helpString = "";
helpString += "The filter.shared command is used to remove OTUs based on various critieria.\n";
helpString += "The filter.shared command parameters are shared, minpercent, minabund, mintotal, minnumsamples, minpercentsamples, makerare, groups and label. You must provide a shared file.\n";
helpString += "The filter.shared command parameters are shared, minpercent, minabund, mintotal, minnumsamples, minpercentsamples, rarepercent, makerare, keepties, groups and label. You must provide a shared file.\n";
helpString += "The groups parameter allows you to specify which of the groups you would like included. The group names are separated by dashes.\n";
helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";

helpString += "The minabund parameter allows you indicate the minimum abundance required for each sample in a given OTU. If any samples abundance falls below the minimum, the OTU is removed. Default=0\n";
helpString += "The minpercent parameter allows you indicate the minimum relative abundance of an OTU. For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1. The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed. Default=0.\n";
helpString += "The rarepercent parameter allows you indicate the percentage of otus to remove. The OTUs chosen to be removed are the rarest. For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance. Default=0.\n";
helpString += "The keepties parameter is used with the rarepercent parameter. It allows you indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU. For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU, but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10. Default=T\n";
helpString += "The minnumsamples parameter allows you indicate the minimum number of samples present in an OTU. If the number of samples present falls below the minimum, the OTU is removed. Default=0.\n";
helpString += "The minpercentsamples parameter allows you indicate the minimum percent of sample present in an OTU. For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333, the minimum is 0.50, so the OTU will be removed. Default=0.\n";
helpString += "The mintotal parameter allows you indicate the minimum abundance required for a given OTU. If abundance across all samples falls below the minimum, the OTU is removed. Default=0.\n";
Expand Down Expand Up @@ -183,6 +187,14 @@ FilterSharedCommand::FilterSharedCommand(string option) {
if (minPercent < 1) {} //already in percent form
else { minPercent = minPercent / 100.0; } //user gave us a whole number version so convert to %

temp = validParameter.validFile(parameters, "rarepercent", false);
if (temp == "not found"){ temp = "-1"; }
else { setSomething = true; }

m->mothurConvert(temp, rarePercent);
if (rarePercent < 1) {} //already in percent form
else { rarePercent = rarePercent / 100.0; } //user gave us a whole number version so convert to %

temp = validParameter.validFile(parameters, "minpercentsamples", false);
if (temp == "not found"){ temp = "-1"; }
else { setSomething = true; }
Expand All @@ -194,6 +206,9 @@ FilterSharedCommand::FilterSharedCommand(string option) {
temp = validParameter.validFile(parameters, "makerare", false); if (temp == "not found"){ temp = "T"; }
makeRare = m->isTrue(temp);

temp = validParameter.validFile(parameters, "keepties", false); if (temp == "not found"){ temp = "T"; }
keepties = m->isTrue(temp);

if (!setSomething) { m->mothurOut("\nYou did not set any parameters. I will filter using minabund=1.\n\n"); minAbund = 1; }
}

Expand Down Expand Up @@ -332,6 +347,45 @@ int FilterSharedCommand::processShared(vector<SharedRAbundVector*>& thislookup)
filteredLookup.push_back(temp);
}

//you want to remove a percentage of OTUs
set<string> removeLabels;
if (rarePercent != -0.01) {
vector<spearmanRank> otus;
//rank otus by abundance
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
float otuTotal = 0.0;
for (int j = 0; j < thislookup.size(); j++) {
otuTotal += thislookup[j]->getAbundance(i);
}
spearmanRank temp(saveBinLabels[i], otuTotal);
otus.push_back(temp);
}

//sort by abundance
sort(otus.begin(), otus.end(), compareSpearman);

//find index of cutoff
int indexFirstNotRare = ceil(rarePercent * (float)thislookup[0]->getNumBins());

//handle ties
if (keepties) { //adjust indexFirstNotRare if needed
if (indexFirstNotRare != 0) { //not out of bounds
if (otus[indexFirstNotRare].score == otus[indexFirstNotRare-1].score) { //you have a tie
bool tie = true;
for (int i = indexFirstNotRare-1; i >=0; i--) {
if (otus[indexFirstNotRare].score != otus[i].score) { //found value below tie
indexFirstNotRare = i+1; tie = false; break;
}
}
if (tie) { if (m->debug) { m->mothurOut("For distance " + thislookup[0]->getLabel() + " all rare OTUs abundance tie with first 'non rare' OTU, not removing any for rarepercent parameter.\n"); }indexFirstNotRare = 0; }
}
}
}

//saved labels for OTUs above rarepercent
for (int i = 0; i < indexFirstNotRare; i++) { removeLabels.insert(otus[i].name); }
}

bool filteredSomething = false;
int numRemoved = 0;
for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
Expand Down Expand Up @@ -383,6 +437,12 @@ int FilterSharedCommand::processShared(vector<SharedRAbundVector*>& thislookup)
if (percent < minPercentSamples) { okay = false; }
}

if (okay && (rarePercent != -0.01)) {
if (removeLabels.count(saveBinLabels[i]) != 0) { //are we on the 'bad' list
okay = false;
}
}

//did this OTU pass the filter criteria
if (okay) {
filteredLabels.push_back(saveBinLabels[i]);
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4 changes: 2 additions & 2 deletions filtersharedcommand.h
View file
Expand Up @@ -34,12 +34,12 @@ class FilterSharedCommand : public Command {
void help() { m->mothurOut(getHelpString()); }

private:
bool abort, pickedGroups, allLines, makeRare;
bool abort, pickedGroups, allLines, makeRare, keepties;
set<string> labels; //holds labels to be used
string groups, label, outputDir, sharedfile;
vector<string> Groups, outputNames;
int minAbund, minTotal, minSamples;
float minPercent, minPercentSamples;
float minPercent, minPercentSamples, rarePercent;

int processShared(vector<SharedRAbundVector*>&);

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