efischer/BiGpairSEQ
1
0
Fork 0
Code Issues Pull Requests Projects Releases 13 Wiki Activity

Add real sequence collision rate

Browse Source
This commit is contained in:
eugenefischer
2022-09-28 17:45:09 -05:00
parent 0b36e2b742
commit 22faad3414
1 changed files with 6 additions and 4 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
src/main/java/Simulator.java
View File

@@ -27,7 +27,8 @@ public class Simulator implements GraphModificationFunctions {
public static GraphWithMapData makeCDR3Graph(CellSample cellSample, Plate samplePlate, int readDepth, public static GraphWithMapData makeCDR3Graph(CellSample cellSample, Plate samplePlate, int readDepth,
double readErrorRate, double errorCollisionRate, boolean verbose) { double readErrorRate, double errorCollisionRate,
double realSequenceCollisionRate, boolean verbose) {
//start timing //start timing
Instant start = Instant.now(); Instant start = Instant.now();
int[] alphaIndices = {SequenceType.CDR3_ALPHA.ordinal()}; int[] alphaIndices = {SequenceType.CDR3_ALPHA.ordinal()};
@@ -44,11 +45,11 @@ public class Simulator implements GraphModificationFunctions {
//Make linkedHashMap keyed to sequences, values are SequenceRecords reflecting plate statistics //Make linkedHashMap keyed to sequences, values are SequenceRecords reflecting plate statistics
if(verbose){System.out.println("Making sample plate sequence maps");} if(verbose){System.out.println("Making sample plate sequence maps");}
Map<String, SequenceRecord> alphaSequences = samplePlate.countSequences(readDepth, readErrorRate, Map<String, SequenceRecord> alphaSequences = samplePlate.countSequences(readDepth, readErrorRate,
errorCollisionRate, alphaIndices); errorCollisionRate, realSequenceCollisionRate, alphaIndices);
int alphaCount = alphaSequences.size(); int alphaCount = alphaSequences.size();
if(verbose){System.out.println("Alphas sequences read: " + alphaCount);} if(verbose){System.out.println("Alphas sequences read: " + alphaCount);}
Map<String, SequenceRecord> betaSequences = samplePlate.countSequences(readDepth, readErrorRate, Map<String, SequenceRecord> betaSequences = samplePlate.countSequences(readDepth, readErrorRate,
errorCollisionRate, betaIndices); errorCollisionRate, realSequenceCollisionRate, betaIndices);
int betaCount = betaSequences.size(); int betaCount = betaSequences.size();
if(verbose){System.out.println("Betas sequences read: " + betaCount);} if(verbose){System.out.println("Betas sequences read: " + betaCount);}
if(verbose){System.out.println("Sample plate sequence maps made");} if(verbose){System.out.println("Sample plate sequence maps made");}
@@ -131,7 +132,7 @@ public class Simulator implements GraphModificationFunctions {
Duration time = Duration.between(start, stop); Duration time = Duration.between(start, stop);
//create GraphWithMapData object //create GraphWithMapData object
GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey, GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey,
alphaCount, betaCount, readDepth, readErrorRate, errorCollisionRate, time); alphaCount, betaCount, readDepth, readErrorRate, errorCollisionRate, realSequenceCollisionRate, time);
//Set source file name in graph to name of sample plate //Set source file name in graph to name of sample plate
output.setSourceFilename(samplePlate.getFilename()); output.setSourceFilename(samplePlate.getFilename());
//return GraphWithMapData object //return GraphWithMapData object
@@ -307,6 +308,7 @@ public class Simulator implements GraphModificationFunctions {
metadata.put("sequence read depth", data.getReadDepth().toString()); metadata.put("sequence read depth", data.getReadDepth().toString());
metadata.put("sequence read error rate", data.getReadErrorRate().toString()); metadata.put("sequence read error rate", data.getReadErrorRate().toString());
metadata.put("read error collision rate", data.getErrorCollisionRate().toString()); metadata.put("read error collision rate", data.getErrorCollisionRate().toString());
metadata.put("real sequence collision rate", data.getRealSequenceCollisionRate().toString());
metadata.put("total alphas read from plate", data.getAlphaCount().toString()); metadata.put("total alphas read from plate", data.getAlphaCount().toString());
metadata.put("total betas read from plate", data.getBetaCount().toString()); metadata.put("total betas read from plate", data.getBetaCount().toString());
//HARD CODED, PARAMETERIZE LATER //HARD CODED, PARAMETERIZE LATER