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A more general method for specifying samples to act on from the command-line. Supports samples specified individually on the console, a file of samples, or regular expressions to select multiple samples. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4945 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-01-06 14:54:56 +00:00
parent 48772a9d01
commit e9201b81d1
2 changed files with 58 additions and 66 deletions
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68
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -75,87 +75,25 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
private List<VariantContextUtils.JexlVCMatchExp> jexls = null;
private Set<String> samples = new HashSet<String>();
private Set<String> possibleSampleRegexs = new HashSet<String>();
private Set<String> sampleExpressionsThatDidNotWork = new HashSet<String>();
/**
* Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
*/
public void initialize() {
// Get list of samples to include in the output
ArrayList<String> rodNames = new ArrayList<String>();
rodNames.add("variant");
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
if (SAMPLE_EXPRESSIONS != null) {
// Let's first go through the list and see if we were given any files. We'll add every entry in the file to our
// sample list set, and treat the entries as if they had been specified on the command line.
Set<String> samplesFromFiles = new HashSet<String>();
for (String SAMPLE_EXPRESSION : SAMPLE_EXPRESSIONS) {
File sampleFile = new File(SAMPLE_EXPRESSION);
try {
XReadLines reader = new XReadLines(sampleFile);
List<String> lines = reader.readLines();
for (String line : lines) {
samplesFromFiles.add(line);
}
} catch (FileNotFoundException e) {
// ignore exception
}
}
SAMPLE_EXPRESSIONS.addAll(samplesFromFiles);
// Let's now assume that the values in SAMPLE_EXPRESSIONS are literal sample names and not regular
// expressions. Extract those samples specifically so we don't make the mistake of selecting more
// than what the user really wants.
for (String SAMPLE_EXPRESSION : SAMPLE_EXPRESSIONS) {
if (!(new File(SAMPLE_EXPRESSION).exists())) {
if (vcfSamples.contains(SAMPLE_EXPRESSION)) {
samples.add(SAMPLE_EXPRESSION);
} else {
possibleSampleRegexs.add(SAMPLE_EXPRESSION);
}
}
}
// Now, check the expressions that weren't used in the previous step, and use them as if they're regular expressions
for (String sampleRegex : possibleSampleRegexs) {
Pattern p = Pattern.compile(sampleRegex);
boolean patternWorked = false;
for (String vcfSample : vcfSamples) {
Matcher m = p.matcher(vcfSample);
if (m.find()) {
samples.add(vcfSample);
patternWorked = true;
}
}
if (!patternWorked) {
sampleExpressionsThatDidNotWork.add(sampleRegex);
}
}
// Finally, warn the user about any leftover sample expressions that had no effect
if (sampleExpressionsThatDidNotWork.size() > 0) {
for (String exp : sampleExpressionsThatDidNotWork) {
logger.warn("The sample expression '" + exp + "' had no effect (no matching sample or pattern match found). Skipping.");
}
}
} else {
samples.addAll(vcfSamples);
}
samples = SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS);
for (String sample : samples) {
logger.info("Including sample '" + sample + "'");
}
// Initialize VCF header
Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
headerLines.add(new VCFHeaderLine("source", "SelectVariants"));
vcfWriter.writeHeader(new VCFHeader(headerLines, samples));

56
java/src/org/broadinstitute/sting/utils/SampleUtils.java
View File

@ -215,5 +215,59 @@ public class SampleUtils {
return new ArrayList<String>();
}
public static Set<String> getSamplesFromCommandLineInput(Collection<String> vcfSamples, Collection<String> sampleExpressions) {
Set<String> samples = new HashSet<String>();
if (sampleExpressions != null) {
// Let's first go through the list and see if we were given any files. We'll add every entry in the file to our
// sample list set, and treat the entries as if they had been specified on the command line.
Set<String> samplesFromFiles = new HashSet<String>();
for (String sampleExpression : sampleExpressions) {
File sampleFile = new File(sampleExpression);
try {
XReadLines reader = new XReadLines(sampleFile);
List<String> lines = reader.readLines();
for (String line : lines) {
samplesFromFiles.add(line);
}
} catch (FileNotFoundException e) {
// ignore exception
}
}
sampleExpressions.addAll(samplesFromFiles);
// Let's now assume that the values in sampleExpressions are literal sample names and not regular
// expressions. Extract those samples specifically so we don't make the mistake of selecting more
// than what the user really wants.
Set<String> possibleSampleRegexs = new HashSet<String>();
for (String sampleExpression : sampleExpressions) {
if (!(new File(sampleExpression).exists())) {
if (vcfSamples.contains(sampleExpression)) {
samples.add(sampleExpression);
} else {
possibleSampleRegexs.add(sampleExpression);
}
}
}
// Now, check the expressions that weren't used in the previous step, and use them as if they're regular expressions
for (String sampleRegex : possibleSampleRegexs) {
Pattern p = Pattern.compile(sampleRegex);
for (String vcfSample : vcfSamples) {
Matcher m = p.matcher(vcfSample);
if (m.find()) {
samples.add(vcfSample);
}
}
}
} else {
samples.addAll(vcfSamples);
}
return samples;
}
}