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Success! TranscriptToGenomicInfo now works without the delicate hacks that Ben had put in. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4232 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-09-08 18:06:00 +00:00
parent cd091d7309
commit 40283f6456
2 changed files with 35 additions and 144 deletions
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161
java/src/org/broadinstitute/sting/gatk/refdata/features/annotator/AnnotatorInputTableFeature.java
View File

@ -43,28 +43,13 @@ public class AnnotatorInputTableFeature implements Feature {
private String chr; private String chr;
private int start; private int start;
private int end; private int end;
private String strRep = null;
// Temporary attributes were added to make it easier to implement certain
// optimizations for RODs that span an interval. For example, if a Walker
// needs to do a time-consuming computation on data from a ROD, it would normally
// have to repeat this computation every time its map(..) method is called.
// If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
// However, many computations (including validation and parsing) are done per ROD rather than
// per position. Therefore, substantial optimizations are possible if the result
// of the first computation is cached and reused on subsequent map(..) calls.
// Temporary attributes provide a convenient place to store these results,
// freeing the Walkers from having to maintain their own ROD -> result hashmaps.
private Map<Object, Object> temporaryAttributes;
/** /**
* Constructor. * Constructor.
* @param chr The chromosome name. * @param chr The chromosome name.
* @param start * @param start The start position
* @param end * @param end The end position
*/ */
public AnnotatorInputTableFeature(String chr, int start, int end) { public AnnotatorInputTableFeature(String chr, int start, int end) {
this.chr = chr; this.chr = chr;
@ -85,8 +70,7 @@ public class AnnotatorInputTableFeature implements Feature {
/** /**
* Returns the list of column names from the file header. * @return the list of column names from the file header.
* @return
*/ */
public ArrayList<String> getHeader() { public ArrayList<String> getHeader() {
return columnNames; return columnNames;
@ -99,12 +83,12 @@ public class AnnotatorInputTableFeature implements Feature {
* @param columnName The column name as it appears in the file header. * @param columnName The column name as it appears in the file header.
* @return The value * @return The value
*/ */
public String getColumnValue(final Object columnName) { public String getColumnValue(final String columnName) {
return columnValues.get(columnName); return columnValues.get(columnName);
} }
public boolean containsColumnName(final Object columnName) { public boolean containsColumnName(final String columnName) {
return columnValues.containsKey(columnName); return columnValues.containsKey(columnName);
} }
@ -121,9 +105,7 @@ public class AnnotatorInputTableFeature implements Feature {
} }
/** /**
* Returns all values in this line, hashed by their column names. * @return all values in this line, hashed by their column names.
*
* @return
*/ */
public Map<String,String> getColumnValues() { public Map<String,String> getColumnValues() {
return Collections.unmodifiableMap(columnValues); return Collections.unmodifiableMap(columnValues);
@ -154,124 +136,23 @@ public class AnnotatorInputTableFeature implements Feature {
this.end = end; this.end = end;
} }
/**
* Checks whether an attribute has been set for the given key.
*
* Temporary attributes make it easier to implement certain
* optimizations for RODs that span an interval. For example, if a Walker
* needs to do a time-consuming computation on data from a ROD, it would normally
* have to repeat this computation every time its map(..) method is called.
* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
* However, many computations (including validation and parsing) are done per ROD rather than
* per position. Therefore, substantial optimizations are possible if the result
* of the first computation is cached and reused on subsequent map(..) calls.
* Temporary attributes provide a convenient place to store these results,
* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
*
* @param key key
* @return True if an attribute has been set for this key.
*/
public boolean containsTemporaryAttribute(Object key) {
if(temporaryAttributes != null) {
return temporaryAttributes.containsKey(key);
}
return false;
}
/**
* Sets the key to the given value, replacing any previous value. The previous
* value is returned.
*
* Temporary attributes make it easier to implement certain
* optimizations for RODs that span an interval. For example, if a Walker
* needs to do a time-consuming computation on data from a ROD, it would normally
* have to repeat this computation every time its map(..) method is called.
* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
* However, many computations (including validation and parsing) are done per ROD rather than
* per position. Therefore, substantial optimizations are possible if the result
* of the first computation is cached and reused on subsequent map(..) calls.
* Temporary attributes provide a convenient place to store these results,
* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
*
* @param key key
* @param value value
* @return attribute
*/
public Object setTemporaryAttribute(Object key, Object value) {
if(temporaryAttributes == null) {
temporaryAttributes = new HashMap<Object, Object>();
}
return temporaryAttributes.put(key, value);
}
/**
* Looks up the value associated with the given key.
*
* Temporary attributes make it easier to implement certain
* optimizations for RODs that span an interval. For example, if a Walker
* needs to do a time-consuming computation on data from a ROD, it would normally
* have to repeat this computation every time its map(..) method is called.
* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
* However, many computations (including validation and parsing) are done per ROD rather than
* per position. Therefore, substantial optimizations are possible if the result
* of the first computation is cached and reused on subsequent map(..) calls.
* Temporary attributes provide a convenient place to store these results,
* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
*
* @param key key
* @return The value, or null.
*/
public Object getTemporaryAttribute(Object key) {
if(temporaryAttributes != null) {
return temporaryAttributes.get(key);
}
return null;
}
/**
* Removes the attribute that has the given key.
*
* Temporary attributes make it easier to implement certain
* optimizations for RODs that span an interval. For example, if a Walker
* needs to do a time-consuming computation on data from a ROD, it would normally
* have to repeat this computation every time its map(..) method is called.
* If a ROD spans an interval, the Walker's map(..) method will be called for every position in ROD.
* However, many computations (including validation and parsing) are done per ROD rather than
* per position. Therefore, substantial optimizations are possible if the result
* of the first computation is cached and reused on subsequent map(..) calls.
* Temporary attributes provide a convenient place to store these results,
* freeing the Walkers from having to maintain their own ROD -> result hashmaps.
*
* @param key key
* @return The value that was associated with this key, or null.
*/
public Object removeTemporaryAttribute(Object key) {
if(temporaryAttributes != null) {
return temporaryAttributes.remove(key);
}
return null;
}
@Override @Override
public String toString() { public String toString() {
StringBuilder sb = new StringBuilder(); if ( strRep == null ) {
StringBuilder sb = new StringBuilder();
for(String columnName : columnNames ) { for(String columnName : columnNames ) {
if(sb.length() == 0) { if ( sb.length() == 0 )
sb.append("["); sb.append("[");
} else { else
sb.append(", "); sb.append(", ");
sb.append(columnName + "=" + columnValues.get(columnName));
} }
sb.append(columnName + "=" + columnValues.get(columnName)); sb.append("]");
strRep = sb.toString();
} }
sb.append("]");
return sb.toString(); return strRep;
} }
} }

18
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
View File

@ -66,7 +66,7 @@ import org.broadinstitute.sting.utils.StingException;
@By(DataSource.REFERENCE) @By(DataSource.REFERENCE)
@Requires(value={DataSource.REFERENCE}, referenceMetaData={ @RMD(name=TranscriptToGenomicInfo.ROD_NAME,type=AnnotatorInputTableFeature.class) } ) @Requires(value={DataSource.REFERENCE}, referenceMetaData={ @RMD(name=TranscriptToGenomicInfo.ROD_NAME,type=AnnotatorInputTableFeature.class) } )
public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> { public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
private static final String ROD_NAME = "transcripts"; public static final String ROD_NAME = "transcripts";
//@Argument(fullName="pass-through", shortName="t", doc="Optionally specifies which columns from the transcript table should be copied verbatim (aka. passed-through) to the records in the output table. For example, -B transcripts,AnnotatorInputTable,/data/refGene.txt -t id will cause the refGene id column to be copied to the output table.", required=false) //@Argument(fullName="pass-through", shortName="t", doc="Optionally specifies which columns from the transcript table should be copied verbatim (aka. passed-through) to the records in the output table. For example, -B transcripts,AnnotatorInputTable,/data/refGene.txt -t id will cause the refGene id column to be copied to the output table.", required=false)
//protected String[] PASS_THROUGH_COLUMNS = {}; //protected String[] PASS_THROUGH_COLUMNS = {};
@ -140,6 +140,11 @@ public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
intergenic, intron, utr5, CDS, utr3, non_coding_exon, non_coding_intron intergenic, intron, utr5, CDS, utr3, non_coding_exon, non_coding_intron
} }
/**
* Store rods until we hit their ends so that we don't have to recompute
* basic information every time we see them in map().
*/
private Map<String, TranscriptTableRecord> storedTranscriptInfo = new HashMap<String, TranscriptTableRecord>();
/** /**
* Prepare the output file and the list of available features. * Prepare the output file and the list of available features.
@ -219,10 +224,12 @@ public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
for ( Object transcriptRodObject : transcriptRODs ) { for ( Object transcriptRodObject : transcriptRODs ) {
//parse this ROD if it hasn't been already. //parse this ROD if it hasn't been already.
final AnnotatorInputTableFeature transcriptRod = (AnnotatorInputTableFeature) transcriptRodObject; final AnnotatorInputTableFeature transcriptRod = (AnnotatorInputTableFeature) transcriptRodObject;
TranscriptTableRecord parsedTranscriptRod = (TranscriptTableRecord) transcriptRod.getTemporaryAttribute("parsedTranscriptRod"); String featureKey = transcriptRod.toString();
if( parsedTranscriptRod == null ) {
TranscriptTableRecord parsedTranscriptRod = storedTranscriptInfo.get(featureKey);
if ( parsedTranscriptRod == null ) {
parsedTranscriptRod = new TranscriptTableRecord(transcriptRod, GENE_NAME_COLUMNS); parsedTranscriptRod = new TranscriptTableRecord(transcriptRod, GENE_NAME_COLUMNS);
transcriptRod.setTemporaryAttribute("parsedTranscriptRod", parsedTranscriptRod); storedTranscriptInfo.put(featureKey, parsedTranscriptRod);
} }
//populate parsedTranscriptRod.txSequence //populate parsedTranscriptRod.txSequence
@ -274,6 +281,9 @@ public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
throw new RuntimeException(Thread.currentThread().getName() + " - Unexpected error occurred at position: [" + parsedTranscriptRod.txChrom + ":" + position + "] in transcript: " + parsedTranscriptRod, e); throw new RuntimeException(Thread.currentThread().getName() + " - Unexpected error occurred at position: [" + parsedTranscriptRod.txChrom + ":" + position + "] in transcript: " + parsedTranscriptRod, e);
} }
// remove it from the cache
storedTranscriptInfo.put(featureKey, null);
transcriptsProcessedCounter++; transcriptsProcessedCounter++;
if ( transcriptsProcessedCounter % 100 == 0 ) if ( transcriptsProcessedCounter % 100 == 0 )
logger.info(new Date() + ": " + transcriptsProcessedCounter + " transcripts processed"); logger.info(new Date() + ": " + transcriptsProcessedCounter + " transcripts processed");