org.molgenis.data.annotation.impl

Class SnpEffServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.impl.SnpEffServiceAnnotator

All Implemented Interfaces:

EventListener, RepositoryAnnotator, org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

@Component(value="SnpEffServiceAnnotator")
public class SnpEffServiceAnnotator
extends Object
implements RepositoryAnnotator, org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

new ANN field replacing EFF: ANN=A|missense_variant|MODERATE|NEXN|NEXN|transcript|NM_144573.3|Coding|8/13|c.733G>A|p.Gly245Arg|1030/3389|733/2028| 245/675|| -lof doesnt seem to work? would be great... http://snpeff.sourceforge.net/snpEff_lof_nmd.pdf

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SnpEffServiceAnnotator.impact

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANNOTATION
static String	C_DNA_POSITION
static String	CDS_POSITION
static String	DISTANCE_TO_FEATURE
static String	ERRORS
static String	FEATURE_ID
static String	FEATURE_TYPE
static String	GENE_ID
static String	GENE_NAME
static String	HGVS_C
static String	HGVS_P
static String	LOF
static String	NMD
static String	PROTEIN_POSITION
static String	PUTATIVE_IMPACT
static String	RANK_TOTAL
static String	SNPEFF_JAR_LOCATION_PROPERTY
static String	snpEffPath
static String	TRANSCRIPT_BIOTYPE

Fields inherited from interface org.molgenis.data.annotation.RepositoryAnnotator

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
SnpEffServiceAnnotator(File snpEffLocation, File inputVcfFile, File outputVCFFile)
SnpEffServiceAnnotator(MolgenisSettings molgenisSettings, AnnotationService annotatorService, DataService dataService)

Method Summary

Modifier and Type	Method and Description
Iterator<Entity>	annotate(Iterable<Entity> source)
String	canAnnotate(EntityMetaData repoMetaData)
String	getDescription()
String	getFullName()
EntityMetaData	getInputMetaData()
File	getInputTempFile(Iterable<Entity> source, String tempInputFileName)
EntityMetaData	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)
Entity	parseOutputLineToEntity(String line, String entityName)
void	runSnpEff(File tempInput, File tempOutput)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SNPEFF_JAR_LOCATION_PROPERTY

public static final String SNPEFF_JAR_LOCATION_PROPERTY

See Also:

Constant Field Values

snpEffPath

public static String snpEffPath

ANNOTATION

public static final String ANNOTATION

See Also:

Constant Field Values

PUTATIVE_IMPACT

public static final String PUTATIVE_IMPACT

See Also:

Constant Field Values

GENE_NAME

public static final String GENE_NAME

See Also:

Constant Field Values

GENE_ID

public static final String GENE_ID

See Also:

Constant Field Values

FEATURE_TYPE

public static final String FEATURE_TYPE

See Also:

Constant Field Values

FEATURE_ID

public static final String FEATURE_ID

See Also:

Constant Field Values

TRANSCRIPT_BIOTYPE

public static final String TRANSCRIPT_BIOTYPE

See Also:

Constant Field Values

RANK_TOTAL

public static final String RANK_TOTAL

See Also:

Constant Field Values

HGVS_C

public static final String HGVS_C

See Also:

Constant Field Values

HGVS_P

public static final String HGVS_P

See Also:

Constant Field Values

C_DNA_POSITION

public static final String C_DNA_POSITION

See Also:

Constant Field Values

CDS_POSITION

public static final String CDS_POSITION

See Also:

Constant Field Values

PROTEIN_POSITION

public static final String PROTEIN_POSITION

See Also:

Constant Field Values

DISTANCE_TO_FEATURE

public static final String DISTANCE_TO_FEATURE

See Also:

Constant Field Values

ERRORS

public static final String ERRORS

See Also:

Constant Field Values

LOF

public static final String LOF

See Also:

Constant Field Values

NMD

public static final String NMD

See Also:

Constant Field Values

Constructor Detail

SnpEffServiceAnnotator

@Autowired
public SnpEffServiceAnnotator(MolgenisSettings molgenisSettings,
                                         AnnotationService annotatorService,
                                         DataService dataService)
                                  throws IOException

Throws:

IOException

SnpEffServiceAnnotator

public SnpEffServiceAnnotator(File snpEffLocation,
                              File inputVcfFile,
                              File outputVCFFile)
                       throws Exception

Throws:

Exception

Method Detail

onApplicationEvent

public void onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Specified by:

onApplicationEvent in interface org.springframework.context.ApplicationListener<org.springframework.context.event.ContextRefreshedEvent>

getSimpleName

public String getSimpleName()

Specified by:

getSimpleName in interface RepositoryAnnotator

getFullName

public String getFullName()

Specified by:

getFullName in interface RepositoryAnnotator

getDescription

public String getDescription()

Specified by:

getDescription in interface RepositoryAnnotator

annotate

public Iterator<Entity> annotate(Iterable<Entity> source)

Specified by:

annotate in interface RepositoryAnnotator

runSnpEff

public void runSnpEff(File tempInput,
                      File tempOutput)
               throws IOException,
                      InterruptedException

Throws:

IOException

InterruptedException

getInputTempFile

public File getInputTempFile(Iterable<Entity> source,
                             String tempInputFileName)
                      throws IOException

Throws:

IOException

parseOutputLineToEntity

public Entity parseOutputLineToEntity(String line,
                                      String entityName)

getOutputMetaData

public EntityMetaData getOutputMetaData()

Specified by:

getOutputMetaData in interface RepositoryAnnotator

getInputMetaData

public EntityMetaData getInputMetaData()

Specified by:

getInputMetaData in interface RepositoryAnnotator

canAnnotate

public String canAnnotate(EntityMetaData repoMetaData)

Specified by:

canAnnotate in interface RepositoryAnnotator