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Little changes in recognized annotation terms; columns in annotated maf are now prioritized and multiple alternatives do not cause 'i don't know what to do' crash: e.g. if Chromosome and chr columns are both present, then Chromosome is taken (has a priority). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5302 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-02-24 16:19:06 +00:00
parent 255cc246a2
commit abf3fcbb72
3 changed files with 64 additions and 37 deletions
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1
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -359,6 +359,7 @@ public class VariantContextAdaptors {
case Flank5: attrs.put("VC","5'flank"); break;
case Promoter: attrs.put("VC","5'flank"); break;
case De_novo_start: attrs.put("VC","De_novo_start"); break;
case De_novo_start_out_of_frame: attrs.put("VC","De_novo_start_out_of_frame"); break;
case Silent: attrs.put("VC","Silent"); break;
case Missense: attrs.put("VC","Missense"); break;
case Nonsense: attrs.put("VC","Nonsense"); break;

80
java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafCodec.java
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@ -34,10 +34,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import java.io.IOException;
import java.util.Map;
import java.util.HashMap;
import java.util.List;
import java.util.ArrayList;
import java.util.*;
import java.lang.reflect.Field;
/**
@ -53,20 +50,20 @@ public class MafCodec implements FeatureCodec {
private int expectedTokenCount = -1;
private Column BUILD_COL = new Column("NCBI_Build",true);
private Column CHR_COL = new Column("Chromosome",true);
private Column START_COL = new Column("Start_position",true);
private Column END_COL = new Column("End_position",true);
private Column REF_ALLELE_COL = new Column("Reference_Allele",true);
private Column TUMOR_ALLELE1_COL = new Column("Tumor_Seq_Allele1",true);
private Column TUMOR_ALLELE2_COL = new Column("Tumor_Seq_Allele2",true);
private Column TUMOR_SAMPLE_COL = new Column("Tumor_Sample_Barcode",true);
private Column NORMAL_SAMPLE_COL = new Column("Matched_Norm_Sample_Barcode",true);
private Column BUILD_COL = new Column(new String[]{"NCBI_Build","build"},true);
private Column CHR_COL = new Column(new String[] {"Chromosome","chr"},true);
private Column START_COL = new Column(new String[] {"Start_position","start"},true);
private Column END_COL = new Column(new String[]{"End_position","end"},true);
private Column REF_ALLELE_COL = new Column(new String[] {"Reference_Allele","ref_allele"},true);
private Column TUMOR_ALLELE1_COL = new Column(new String[] {"Tumor_Seq_Allele1","tum_allele1"},true);
private Column TUMOR_ALLELE2_COL = new Column(new String[] {"Tumor_Seq_Allele2","tum_allele2"},true);
private Column TUMOR_SAMPLE_COL = new Column(new String[] {"Tumor_Sample_Barcode","tumor_barcode"},true);
private Column NORMAL_SAMPLE_COL = new Column(new String[]{"Matched_Norm_Sample_Barcode","normal_barcode"},true);
// optional fields (absent from maf lite):
private Column VARTYPE_COL = new Column("Variant_Type",false);
private Column STRAND_COL = new Column("Strand",false);
private Column HUGO_GENE_COL = new Column("Hugo_Symbol",false);
private Column VARCLASS_COL = new Column("Variant_Classification",false);
private Column VARTYPE_COL = new Column(new String[]{"Variant_Type","classification"},false);
private Column STRAND_COL = new Column(new String[]{"Strand","strand"},false);
private Column HUGO_GENE_COL = new Column(new String[]{"Hugo_Symbol","gene"},false);
private Column VARCLASS_COL = new Column(new String[]{"Variant_Classification","type"},false);
public enum MAF_TYPE {
@ -151,7 +148,8 @@ public class MafCodec implements FeatureCodec {
log.info("MAF file has "+expectedTokenCount +" columns in first line, unknown file type");
}
}
if ( line.contains("Chromosome") && line.contains("Start") && line.contains("Build")) {
if ( line.contains("Chromosome") && line.contains("Start") && line.contains("Build") ||
line.contains("build") && line.contains("start") && line.contains("ref_allele") ) {
// a naive way to detect the line with column names
setColumnsFromHeader(tokens);
@ -181,7 +179,7 @@ public class MafCodec implements FeatureCodec {
}
}
if ( tokens[CHR_COL.getIndex()].equals("Chromosome") ) return null; // if someone uses this codec manually and feeds it the header line multiple times...
if ( tokens[CHR_COL.getIndex()].equals("Chromosome") || tokens[CHR_COL.getIndex()].equals("chr")) return null; // if someone uses this codec manually and feeds it the header line multiple times...
// create a new feature from the line:
int start = 0;
@ -339,23 +337,38 @@ public class MafCodec implements FeatureCodec {
class Column {
int index ;
String name;
List<String> names;
boolean required;
Column(String name, boolean required) {
this.name = name;
this.names = new ArrayList<String>();
this.names.add(name);
this.required = required;
this.index = -1;
}
public String getName() { return name; }
public void setName(String name) { this.name = name; }
Column(String [] names, boolean required) {
this.names = new ArrayList<String>();
for ( int i = 0 ; i < names.length ; i++ ) this.names.add(names[i]);
this.required = required;
this.index = -1;
}
public String getName() { return names.get(0); }
public Collection<String> getNames() { return names; }
public void setName(String name) {
for ( String n : names ) {
if ( n.equals(name) ) return;
}
this.names.add( name );
}
public int getIndex() { return index; }
public void setIndex(int index) { this.index = index; }
public String getValue(String[] fields) {
if ( index < fields.length ) return fields[index];
if ( required ) throw new UserException.MalformedFile("In MAF file: required column "+name+" has index "+index+
if ( required ) throw new UserException.MalformedFile("In MAF file: required column "+getName()+" has index "+index+
", but only "+fields.length+ " fields are present in maf line");
return null;
}
@ -367,13 +380,20 @@ class Column {
* @param throw_exception
*/
public void setFromMap(Map<String,Integer> m, boolean throw_exception) {
Integer i = m.get(this.name);
if ( i == null ) {
if ( this.required && throw_exception ) throw new UserException.MalformedFile("Required column "+this.name+" is missing from the maf file");
index = -1;
return; // not found
// Integer i = null;
for ( String n : names ) {
if ( m.containsKey(n) ) {
// if ( i != null )
// throw new UserException.MalformedFile("MAF file contains multiple columns with name or alternative names registered for single data field "+getName());
// go with the first column name found; we assume here that column names have priorities:
// for instance, if the file has both 'Chromosome' and 'chr' columns, we will just take
// Chromosome and run with that
this.index = m.get(n);
return;
}
}
this.index = i.intValue(); // found and set.
if ( this.required && throw_exception ) throw new UserException.MalformedFile("Required column "+getName()+" is missing from the maf file");
this.index = -1;
}
/** Sets this column's index from the provided name->index map (i.e. searches for itself in the map).

20
java/src/org/broadinstitute/sting/playground/gatk/features/maf/MafFeature.java
View File

@ -57,7 +57,7 @@ public class MafFeature implements Feature {
public enum Classification {
Unclassified, Intergenic,Intron,Noncoding_transcript,UTR3,UTR5,Flank5,Silent,Missense, Nonsense, Splice_site, miRNA,
Frameshift, Inframe, Stop_deletion, Promoter,De_novo_start
Frameshift, Inframe, Stop_deletion, Promoter,De_novo_start, De_novo_start_out_of_frame
}
private Type type = Type.UNKNOWN;
@ -111,8 +111,13 @@ public class MafFeature implements Feature {
return hugoSymbol;
}
public String setHugoGeneSymbol(String genename) {
return hugoSymbol = genename;
public void setHugoGeneSymbol(String genename) {
int pos = genename.indexOf('|');
if ( pos < 0 ) {
hugoSymbol = genename;
} else {
hugoSymbol = genename.substring(0,pos);
}
}
/**
@ -214,13 +219,13 @@ public class MafFeature implements Feature {
public void setVariantClassification(String s) {
if ( s.equals("IGR") ) { classification = Classification.Intergenic ; return; }
if ( s.equals("Intron") ) { classification = Classification.Intron ; return; }
if ( s.equals("3'UTR") ) { classification = Classification.UTR3 ; return; }
if ( s.equals("5'UTR") ) { classification = Classification.UTR5 ; return; }
if ( s.equals("3'UTR") || s.equals("3'-UTR")) { classification = Classification.UTR3 ; return; }
if ( s.equals("5'UTR") || s.equals("5'-UTR")) { classification = Classification.UTR5 ; return; }
if ( s.equals("5'-Flank") ) { classification = Classification.Flank5 ; return; }
if ( s.equals("Silent") ) { classification = Classification.Silent ; return; }
if ( s.equals("Silent") || s.equals("Synonymous")) { classification = Classification.Silent ; return; }
if ( s.equals("Non-coding_Transcript")) { classification = Classification.Noncoding_transcript; return; }
if ( s.equals("Missense") || s.equals("Missense_Mutation") ) { classification = Classification.Missense ; return; }
if ( s.equals("Nonsense_Mutation") ) { classification = Classification.Nonsense ; return; }
if ( s.equals("Nonsense_Mutation") || s.equals("Nonsense") ) { classification = Classification.Nonsense ; return; }
if ( s.equals("Splice_Site") ) { classification = Classification.Splice_site ; return; }
if ( s.equals("miRNA") ) { classification = Classification.miRNA ; return; }
if ( s.equals("Frame_Shift_Ins") ) { classification = Classification.Frameshift ; return; }
@ -233,6 +238,7 @@ public class MafFeature implements Feature {
if ( s.equals("Splice_Site_SNP") ) { classification = Classification.Splice_site ; return; }
if ( s.equals("Promoter") ) { classification = Classification.Promoter ; return; }
if ( s.equals("De_novo_Start") ) { classification = Classification.De_novo_start ; return; }
if ( s.equals("De_novo_Start_OutOfFrame") ) { classification = Classification.De_novo_start_out_of_frame ; return; }
if ( s.equals("TX-REF-MISMATCH") ) { classification = Classification.Unclassified ; return; }
throw new UserException.MalformedFile("Unknown variant classification: " + s);
}