org.molgenis.data.annotation.impl

Class DbnsfpVariantServiceAnnotator

java.lang.Object

org.molgenis.data.annotation.AbstractRepositoryAnnotator

org.molgenis.data.annotation.LocusAnnotator

org.molgenis.data.annotation.VariantAnnotator

org.molgenis.data.annotation.impl.DbnsfpVariantServiceAnnotator

All Implemented Interfaces:

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

@Component(value="dbnsfpVariantService")
public class DbnsfpVariantServiceAnnotator
extends VariantAnnotator

This class uses a chromosome to approach a dbNSFP chromosome variant file, it then checks all locations recorded for a chromosome in the data set, for every line, and uses a matching line to add annotation to the data set variant.

dbNSFP variant returns: chr pos(1-coor) ref alt aaref aaalt hg18_pos(1-coor) genename Uniprot_acc Uniprot_id Uniprot_aapos Interpro_domain cds_strand refcodon SLR_test_statistic codonpos fold-degenerate Ancestral_allele Ensembl_geneid Ensembl_transcriptid aapos aapos_SIFT aapos_FATHMM SIFT_score SIFT_score_converted SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV_pred Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score LRT_score_converted LRT_pred MutationTaster_score MutationTaster_score_converted MutationTaster_pred MutationAssessor_score MutationAssessor_score_converted MutationAssessor_pred FATHMM_score FATHMM_score_converted FATHMM_pred RadialSVM_score RadialSVM_score_converted RadialSVM_pred LR_score LR_pred Reliability_index GERP++_NR GERP++_RS phyloP 29way_pi 29way_logOdds LRT_Omega UniSNP_ids 1000Gp1_AC 1000Gp1_AF 1000Gp1_AFR_AC 1000Gp1_AFR_AF 1000Gp1_EUR_AC 1000Gp1_EUR_AF 1000Gp1_AMR_AC 1000Gp1_AMR_AF 1000Gp1_ASN_AC 1000Gp1_ASN_AF ESP6500_AA_AF ESP6500_EA_AF

Version:

dbNSFP version 2.3 downloaded January 26, 2014

Author:

mdehaan

Field Summary

Fields

Modifier and Type	Field and Description
static String	CHROMOSOME_FILE_LOCATION_PROPERTY

Fields inherited from class org.molgenis.data.annotation.VariantAnnotator

ALTERNATIVE, REFERENCE

Fields inherited from class org.molgenis.data.annotation.LocusAnnotator

CHROMOSOME, POSITION

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

ANNOTATOR_PREFIX

Constructor Summary

Constructors

Constructor and Description
DbnsfpVariantServiceAnnotator(MolgenisSettings molgenisSettings, AnnotationService annotatorService)

Method Summary

Modifier and Type	Method and Description
List<Entity>	annotateEntity(Entity entity)
boolean	annotationDataExists() Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached
EntityMetaData	getOutputMetaData()
String	getSimpleName()
void	onApplicationEvent(org.springframework.context.event.ContextRefreshedEvent event)

Methods inherited from class org.molgenis.data.annotation.VariantAnnotator

getInputMetaData

Methods inherited from class org.molgenis.data.annotation.AbstractRepositoryAnnotator

annotate, canAnnotate, getFullName

Methods inherited from class java.lang.Object

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

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

annotate, canAnnotate, getDescription, getFullName

Field Detail

CHROMOSOME_FILE_LOCATION_PROPERTY

public static final String CHROMOSOME_FILE_LOCATION_PROPERTY

See Also:

Constant Field Values

Constructor Detail

DbnsfpVariantServiceAnnotator

@Autowired
public DbnsfpVariantServiceAnnotator(MolgenisSettings molgenisSettings,
                                                AnnotationService annotatorService)

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>

Overrides:

onApplicationEvent in class AbstractRepositoryAnnotator

getSimpleName

public String getSimpleName()

annotationDataExists

public boolean annotationDataExists()

Description copied from class: AbstractRepositoryAnnotator

Checks if folder and files that were set with a runtime property actually exist, or if a webservice can be reached

Specified by:

annotationDataExists in class AbstractRepositoryAnnotator

Returns:

boolean

annotateEntity

public List<Entity> annotateEntity(Entity entity)
                            throws IOException

Specified by:

annotateEntity in class AbstractRepositoryAnnotator

Throws:

IOException

getOutputMetaData

public EntityMetaData getOutputMetaData()