com.milaboratory.mitcr.statistics.CloneSetQualityControl Maven / Gradle / Ivy
/*
* MiTCR
*
* Copyright (c) 2010-2013:
* Bolotin Dmitriy
* Chudakov Dmitriy
*
* MiTCR is free software: you can redistribute it and/or modify it
* under the terms of the GNU General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option)
* any later version.
*
* This program is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
* more details.
*
* You should have received a copy of the GNU General Public License along
* with this program. If not, see goodVCombinations;
private final long oofSequences;
private final int oofClones;
private final long jNotDetermined;
private final int jNotDeterminedClones;
private final long vNotDetermined;
private final int vNotDeterminedClones;
private final int withStopsClones;
private final long withStopsSequences;
private final long m1, p1;
private final int m1c, p1c;
/**
* Creates an instance of a class that performs several quality controls on a clone set
*
* @param library parent library of segments
* @param species parent species
* @param gene parent gene
* @param cloneSet clone set to check
*/
public CloneSetQualityControl(SegmentLibrary library, Species species, Gene gene, CloneSet cloneSet, long totalReads) {
this.totalReads = totalReads;
this.library = library;
this.species = species;
this.gene = gene;
if (gene == Gene.TRB && species == Species.HomoSapiens) {
BitArray good12 = new BitArray(library.getGroup(species, gene, SegmentGroupType.Variable).getSegmentCount());
good12.set(library.getGroup(species, gene, SegmentGroupType.Variable).getSegmentByName("TRBV12-3").getIndex());
good12.set(library.getGroup(species, gene, SegmentGroupType.Variable).getSegmentByName("TRBV12-4").getIndex());
BitArray good6 = new BitArray(library.getGroup(species, gene, SegmentGroupType.Variable).getSegmentCount());
good6.set(library.getGroup(species, gene, SegmentGroupType.Variable).getSegmentByName("TRBV6-2").getIndex());
good6.set(library.getGroup(species, gene, SegmentGroupType.Variable).getSegmentByName("TRBV6-3").getIndex());
goodVCombinations = new HashSet<>();
goodVCombinations.add(good12);
goodVCombinations.add(good6);
} else {
goodVCombinations = Collections.EMPTY_SET;
}
long oofSequences = 0;
int oofClones = 0;
long jNotDetermined = 0;
int jNotDeterminedClones = 0;
long vNotDetermined = 0;
int vNotDeterminedClones = 0;
int withStopsClones = 0;
long withStopsSequences = 0;
long m1 = 0, p1 = 0;
int m1c = 0, p1c = 0;
this.clones = cloneSet.getClones().size();
this.totalGoodReads = cloneSet.getTotalCount();
for (Clone clone : cloneSet.getClones()) {
int rem = clone.getCDR3().size() % 3;
if (rem != 0) {
oofClones++;
oofSequences += clone.getCount();
}
if (rem == 1) {
p1 += clone.getCount();
p1c++;
}
if (rem == 2) {
m1 += clone.getCount();
m1c++;
}
if (clone.getCDR3AA().containStops()) {
withStopsClones++;
withStopsSequences += clone.getCount();
}
if (clone.getVSegments().size() > 1 && !goodVCombinations.contains(clone.getVSegments().getBitArrayCopy())) {
vNotDetermined += clone.getCount();
++vNotDeterminedClones;
}
if (clone.getJSegments().size() > 1) {
jNotDetermined += clone.getCount();
++jNotDeterminedClones;
}
}
this.oofClones = oofClones;
this.oofSequences = oofSequences;
this.jNotDetermined = jNotDetermined;
this.jNotDeterminedClones = jNotDeterminedClones;
this.vNotDetermined = vNotDetermined;
this.vNotDeterminedClones = vNotDeterminedClones;
this.withStopsClones = withStopsClones;
this.withStopsSequences = withStopsSequences;
this.m1 = m1;
this.p1 = p1;
this.m1c = m1c;
this.p1c = p1c;
if (cloneSet instanceof CloneSetClustered) {
int cc = 0;
long rc = 0;
for (CloneCluster cluster : ((CloneSetClustered) cloneSet).getClones()) {
cc += cluster.getChildClones().size();
for (Clone clone : cluster.getChildClones())
rc += clone.getCount();
}
clonesClusterized = cc;
readsClusterized = rc;
} else {
clonesClusterized = 0;
readsClusterized = 0;
}
coreClones = clones + clonesClusterized;
}
/**
* Gets number of sequences with frame shift in CDR3
*/
public long getOutOfFrameSequences() {
return oofSequences;
}
/**
* Gets number of clones with frame shift in CDR3
*/
public int getOutOfFrameClones() {
return oofClones;
}
/**
* Gets number of sequences with J not determined
*/
public long getJNotDeterminedSequences() {
return jNotDetermined;
}
/**
* Gets number of clones with J not determined
*/
public int getJNotDeterminedClones() {
return jNotDeterminedClones;
}
/**
* Gets number of sequences with V not determined
*/
public long getVNotDeterminedSequences() {
return vNotDetermined;
}
/**
* Gets number of clones with V not determined
*/
public int getVNotDeterminedClones() {
return vNotDeterminedClones;
}
/**
* Gets number of clones with stop codon in CDR3
*/
public int getWithStopsClones() {
return withStopsClones;
}
/**
* Gets number of sequences with stop codon in CDR3
*/
public long getWithStopsSequences() {
return withStopsSequences;
}
/**
* Gets number of sequences with -1 frame shift in CDR3
*/
public long getM1() {
return m1;
}
/**
* Gets number of sequences with +1 frame shift in CDR3
*/
public long getP1() {
return p1;
}
/**
* Gets number of clones with -1 frame shift in CDR3
*/
public int getM1Clones() {
return m1c;
}
/**
* Gets number of clones with +1 frame shift in CDR3
*/
public int getP1Clones() {
return p1c;
}
public long getTotalGoodReads() {
return totalGoodReads;
}
public long getTotalReads() {
return totalReads;
}
public int getClones() {
return clones;
}
public long getReadsClusterized() {
return readsClusterized;
}
public int getClonesClusterized() {
return clonesClusterized;
}
//TODO rename?
public int getCoreClones() {
return coreClones;
}
/*public void process(CloneSet input) {
input.getMetadataContainer().add("qual.outOfFrameSequences", oofSequences);
input.getMetadataContainer().add("qual.outOfFrameClones", oofClones);
input.getMetadataContainer().add("qual.p1", p1);
input.getMetadataContainer().add("qual.m1", m1);
input.getMetadataContainer().add("qual.withStopsClones", withStopsClones);
input.getMetadataContainer().add("qual.withStopsSequences", withStopsSequences);
input.getMetadataContainer().add("qual.vNotDeterminedInClones", vNotDetermined);
input.getMetadataContainer().add("qual.jNotDeterminedInClones", jNotDetermined);
input.getMetadataContainer().add("qual.vNotDetermined", perSeqVNotDetermined.get());
input.getMetadataContainer().add("qual.jNotDetermined", perSeqJNotDetermined.get());
}*/
/*@Override
public void put(SExtractorResult object) throws InterruptedException {
if (object != null && object.isGood()) { //Such clones will be accepted by GoodCDR3Filter on next step (in SAnalyser).
BitArray vBarcodeSegments = library.getGroup(species, gene, SegmentGroupType.Variable).converToSegments(object.barcode(SegmentGroupType.Variable));
if (vBarcodeSegments.bitCount() > 1) {
boolean combFound = false;
for (BitArray good : goodVCombinations)
if (vBarcodeSegments.equals(good)) {
combFound = true;
break;
}
if (!combFound)
perSeqVNotDetermined.incrementAndGet();
}
BitArray jBarcodeSegments = library.getGroup(species, gene, SegmentGroupType.Joining).converToSegments(object.barcode(SegmentGroupType.Joining));
if (jBarcodeSegments.bitCount() > 1)
perSeqJNotDetermined.incrementAndGet();
}
}*/
}
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