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Major effort to unify pathway analysis using KEGG MEDICUS for variant
and diff exp datatypes.
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Jun 22, 2024
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| package edu.utah.kohli; | ||
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| import util.gen.Misc; | ||
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| public class AccuGenProbe { | ||
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| private String originalInput; | ||
| private String chr; | ||
| private int pos; //this is 1 base space so subtract one before using is queries | ||
| private String ref; | ||
| private String alt; | ||
| private String gene; | ||
| private boolean ok = true; | ||
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| public AccuGenProbe (String rep) { | ||
| //Chr_POS_REF_ALT_GENE | ||
| originalInput = rep; | ||
| String[] f = Misc.UNDERSCORE.split(rep); | ||
| chr = f[0]; | ||
| pos = Integer.parseInt(f[1]); | ||
| ref = f[2]; | ||
| alt = f[3]; | ||
| gene = f[4]; | ||
| } | ||
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| public String getOriginalInput() { | ||
| return originalInput; | ||
| } | ||
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| public String getChr() { | ||
| return chr; | ||
| } | ||
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| public int getPos() { | ||
| return pos; | ||
| } | ||
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| public String getRef() { | ||
| return ref; | ||
| } | ||
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| public String getAlt() { | ||
| return alt; | ||
| } | ||
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| public String getGene() { | ||
| return gene; | ||
| } | ||
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| public boolean isOk() { | ||
| return ok; | ||
| } | ||
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| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| package edu.utah.kohli; | ||
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| import util.gen.Num; | ||
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| public class AccuGenProbeCounts { | ||
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| private int refCounts; | ||
| private int altCounts; | ||
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| public AccuGenProbeCounts(int refCounts, int altCounts) { | ||
| this.refCounts = refCounts; | ||
| this.altCounts = altCounts; | ||
| } | ||
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| public int getReadDepth(){ | ||
| return refCounts+ altCounts; | ||
| } | ||
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| public double getAlleleFraction() { | ||
| return (double) altCounts/ (double)(refCounts+ altCounts); | ||
| } | ||
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| public String toString() { | ||
| return refCounts+":"+altCounts+":"+getReadDepth()+":"+Num.formatNumber(getAlleleFraction(), 3); | ||
| } | ||
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| } |
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