Skip to content

Commit

Permalink
Added proper filtering and warning messages for alleles with wildcard…
Browse files Browse the repository at this point in the history 
… symbols in `featureToAlign` region. (#281)

This fixes #260
  • Loading branch information
@dbolotin
dbolotin committed Nov 22, 2017
1 parent 78d83b9 commit 80704b4
Show file tree
Hide file tree
Showing 3 changed files with 60 additions and 30 deletions.
1 change: 1 addition & 0 deletions CHANGELOG_CURRENT
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
minor: Added proper filtering for alleles with wildcard symbols in `featureToAlign` region
79 changes: 51 additions & 28 deletions src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,11 @@ public class ActionAlign implements Action {
@Override
@SuppressWarnings("unchecked")
public void go(ActionHelper helper) throws Exception {
// FIXME remove in 2.2
if (actionParameters.printNonFunctionalWarnings())
System.out.println("WARNING: -wf / --non-functional-warnings option is deprecated, will be removed in 2.2 " +
"release. Use -v / --verbose instead.");

// Saving initial timestamp
long beginTimestamp = System.currentTimeMillis();

Expand All @@ -92,6 +97,7 @@ public void go(ActionHelper helper) throws Exception {
throw new ProcessException("Failed to override some parameter.");
}

// FIXME remove in 2.2
if (actionParameters.allowDifferentVJLoci != null && actionParameters.allowDifferentVJLoci) {
System.out.println("Warning: usage of --diff-loci is deprecated. Use -OallowChimeras=true instead.");
alignerParameters.setAllowChimeras(true);
Expand All @@ -112,14 +118,13 @@ public void go(ActionHelper helper) throws Exception {
System.out.println("Reference library: " + library.getLibraryId());

for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
if (gene.getGeneType() == GeneType.Variable)
if (gene.getGeneType() == GeneType.Variable) {
totalV++;
else
continue;
if (!alignerParameters.containsRequiredFeature(gene)) {
totalVErrors++;
if (gene.getPartitioning().isAvailable(correctingFeature))
hasVRegion++;
if (!alignerParameters.containsRequiredFeature(gene)) {
totalVErrors++;
if (gene.getPartitioning().isAvailable(correctingFeature))
hasVRegion++;
}
}
}

Expand All @@ -131,41 +136,45 @@ public void go(ActionHelper helper) throws Exception {
alignerParameters.getVAlignerParameters().setGeneFeatureToAlign(correctingFeature);
}

//boolean warnings = false;

int numberOfExcludedNFGenes = 0;
int numberOfExcludedFGenes = 0;
for (VDJCGene gene : library.getGenes(actionParameters.getChains())) {
if (!alignerParameters.containsRequiredFeature(gene)) {
if (params().printWarnings() && (gene.isFunctional() || params().printNonFunctionalWarnings())) {
NucleotideSequence featureSequence = alignerParameters.extractFeatureToAlign(gene);

// exclusionReason is null ==> gene is not excluded
String exclusionReason = null;
if (featureSequence == null)
exclusionReason = "absent " + GeneFeature.encode(alignerParameters.getFeatureToAlign(gene.getGeneType()));
else if (featureSequence.containsWildcards())
exclusionReason = "wildcard symbols in " + GeneFeature.encode(alignerParameters.getFeatureToAlign(gene.getGeneType()));

if (exclusionReason == null)
aligner.addGene(gene); // If there are no reasons to exclude the gene, adding it to aligner
else {
if (gene.isFunctional()) {
++numberOfExcludedFGenes;
if (numberOfExcludedFGenes < 2)
System.out.println("WARNING: " + (gene.isFunctional() ? "Functional gene" : "Gene") + " " + gene.getName() +
" doesn't contain full " + GeneFeature.encode(alignerParameters
.getFeatureToAlign(gene.getGeneType())) + " (excluded)");
//warnings = true;
}
if (!gene.isFunctional())
if (actionParameters.verbose())
System.out.println("WARNING: Functional gene " + gene.getName() +
" excluded due to " + exclusionReason);
} else
++numberOfExcludedNFGenes;
continue;
}
aligner.addGene(gene);
}

if (numberOfExcludedFGenes > 1)
System.out.println("WARNING: ... " + (numberOfExcludedFGenes - 1) + " more functional genes excluded due to absent " +
"\"featureToAlign\".");
if (actionParameters.printWarnings() && numberOfExcludedFGenes > 0)
System.out.println("WARNING: " + numberOfExcludedFGenes + " functional genes were excluded, re-run " +
"with -v option to see the list of excluded genes and exclusion reason.");

//if (numberOfExcludedNFGenes > 0 && !params().printNonFunctionalWarnings())
// System.out.println("WARNING: " + numberOfExcludedNFGenes + " non-functional genes excluded due to absent \"featureToAlign\".");
if (actionParameters.verbose() && numberOfExcludedNFGenes > 0)
System.out.println("WARNING: " + numberOfExcludedNFGenes + " non-functional genes excluded.");

if (aligner.getVGenesToAlign().isEmpty())
throw new ProcessException("No V genes to align. Aborting execution. See warnings for more info " +
"(turn warnings by adding -w option).");
"(turn on verbose warnings by adding --verbose option).");

if (aligner.getJGenesToAlign().isEmpty())
throw new ProcessException("No J genes to align. Aborting execution. See warnings for more info " +
"(turn warnings by adding -w option).");
"(turn on verbose warnings by adding --verbose option).");

AlignerReport report = new AlignerReport();
aligner.setEventsListener(report);
Expand Down Expand Up @@ -287,10 +296,15 @@ public static class AlignParameters extends ActionParametersWithOutput {
names = {"-b", "--library"})
public String library = "default";

// TODO remove in 2.2 release
@Parameter(description = "Print warnings for non-functional V/D/J/C genes",
names = {"-wf", "--non-functional-warnings"})
public Boolean nonFunctionalWarnings = null;

@Parameter(description = "Verbose warning messages.",
names = {"--verbose"})
public Boolean verbose = null;

@Parameter(description = "Don't print warnings",
names = {"-nw", "--no-warnings"})
public Boolean noWarnings = null;
Expand Down Expand Up @@ -385,10 +399,17 @@ public Boolean getSaveOriginalReads() {
return saveOriginalReads != null && saveOriginalReads;
}

@Deprecated
public boolean printNonFunctionalWarnings() {
return nonFunctionalWarnings != null && nonFunctionalWarnings;
}

public boolean verbose() {
return (verbose != null && verbose) ||
// FIXME remove in 2.2
(nonFunctionalWarnings != null && nonFunctionalWarnings);
}

public boolean printWarnings() {
return noWarnings == null || !noWarnings;
}
Expand Down Expand Up @@ -426,7 +447,7 @@ public SequenceReaderCloseable<? extends SequenceRead> createReader() throws IOE

@Override
protected List<String> getOutputFiles() {
return Arrays.asList(getOutputName());
return Collections.singletonList(getOutputName());
}

@Override
Expand All @@ -439,6 +460,8 @@ public void validate() {
throw new ParameterException("Wrong input for --not-aligned-R1,2");
if (failedReadsR1 != null && (failedReadsR2 != null) != isInputPaired())
throw new ParameterException("Option --not-aligned-R2 is not set.");
if (!printWarnings() && verbose())
throw new ParameterException("-nw/--no-warnings and -v/--verbose options are not compatible.");
super.validate();
}
}
Expand Down
10 changes: 8 additions & 2 deletions src/main/java/com/milaboratory/mixcr/vdjaligners/VDJCAlignerParameters.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
import com.fasterxml.jackson.databind.annotation.JsonSerialize;
import com.milaboratory.core.PairedEndReadsLayout;
import com.milaboratory.core.merger.MergerParameters;
import com.milaboratory.core.sequence.NucleotideSequence;
import com.milaboratory.mixcr.basictypes.HasFeatureToAlign;
import com.milaboratory.primitivio.annotations.Serializable;
import io.repseq.core.GeneFeature;
Expand Down Expand Up @@ -209,6 +210,11 @@ public boolean containsRequiredFeature(VDJCGene gene) {
return featureToAlign != null && gene.getPartitioning().isAvailable(featureToAlign);
}

public NucleotideSequence extractFeatureToAlign(VDJCGene gene) {
GeneFeature featureToAlign = getFeatureToAlign(gene.getGeneType());
return featureToAlign == null ? null : gene.getFeature(featureToAlign);
}

@JsonProperty("minSumScore")
public float getMinSumScore() {
return minSumScore;
Expand Down Expand Up @@ -260,10 +266,10 @@ public GeneFeature getFeatureToAlign(GeneType type) {
return params == null ? null : params.getGeneFeatureToAlign();
}

public EnumMap<GeneType, GeneFeature> getFeaturesToAlignMap(){
public EnumMap<GeneType, GeneFeature> getFeaturesToAlignMap() {
EnumMap<GeneType, GeneFeature> res = new EnumMap<>(GeneType.class);
for (GeneType gt : GeneType.VDJC_REFERENCE)
res.put(gt,getFeatureToAlign(gt));
res.put(gt, getFeatureToAlign(gt));
return res;
}

Expand Down

0 comments on commit 80704b4

Please sign in to comment.