Package ubic.gemma.core.loader.association

Class NCBIGene2GOAssociationParser

java.lang.Object

ubic.gemma.core.loader.util.parser.BasicLineParser<Gene2GOAssociation>

ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser

All Implemented Interfaces:

LineParser<Gene2GOAssociation>, Parser<Gene2GOAssociation>, QueuingParser<Gene2GOAssociation>

public class NCBIGene2GOAssociationParser
extends BasicLineParser<Gene2GOAssociation>
implements QueuingParser<Gene2GOAssociation>

This parses GO annotations from NCBI. See readme.

 tax_id:
 the unique identifier provided by NCBI Taxonomy
 for the species or strain/isolate
 GeneID:
 the unique identifier for a gene
 --note:  for genomes previously available from LocusLink,
 the identifiers are equivalent
 GO ID:
 the GO ID, formatted as GO:0000000
 Evidence:
 the evidence code in the gene_association file
 Qualifier:
 a qualifier for the relationship between the gene
 and the GO term
 GO term:
 the term indicated by the GO ID
 PubMed:
 pipe-delimited set of PubMed uids reported as evidence
 for the association
 Category:
 the GO category (Function, Process, or Component)
 

Author:

keshav, pavlidis

Field Summary

Fields inherited from class ubic.gemma.core.loader.util.parser.BasicLineParser

log

Fields inherited from interface ubic.gemma.core.loader.util.parser.LineParser

MIN_PARSED_LINES_FOR_UPDATE, PARSE_ALERT_TIME_FREQUENCY_MS

Fields inherited from interface ubic.gemma.core.loader.util.parser.Parser

PARSE_ALERT_FREQUENCY

Constructor Summary

Constructors

Constructor	Description
NCBIGene2GOAssociationParser(Collection<Taxon> taxa)

Method Summary

Modifier and Type	Method	Description
protected void	addResult(Gene2GOAssociation obj)
int	getCount()
Collection<Gene2GOAssociation>	getResults()
Gene2GOAssociation	mapFromGene2GO(String line)	Note that "-" means a missing value, which in practice only occurs in the "qualifier" and "pubmed" columns.
void	parse(InputStream inputStream, BlockingQueue<Gene2GOAssociation> aqueue)	Parse an input stream, storing the results in the passed queue (which can be used by a consumer)
Gene2GOAssociation	parseOneLine(String line)	Handle the parsing of a single line from the input.

Methods inherited from class ubic.gemma.core.loader.util.parser.BasicLineParser

parse, parse, parse

Methods inherited from class java.lang.Object

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

Constructor Detail

NCBIGene2GOAssociationParser

public NCBIGene2GOAssociationParser(Collection<Taxon> taxa)

Parameters:

taxa - to consider (usually we pass in all)

Method Detail

getCount

public int getCount()

getResults

public Collection<Gene2GOAssociation> getResults()

Specified by:

getResults in interface Parser<Gene2GOAssociation>

Specified by:

getResults in class BasicLineParser<Gene2GOAssociation>

Returns:

the results of the parse.

addResult

protected void addResult(Gene2GOAssociation obj)

Specified by:

addResult in class BasicLineParser<Gene2GOAssociation>

mapFromGene2GO

public Gene2GOAssociation mapFromGene2GO(String line)

Note that "-" means a missing value, which in practice only occurs in the "qualifier" and "pubmed" columns.

Parameters:

line - line

Returns:

Object

parse

public void parse(InputStream inputStream,
                  BlockingQueue<Gene2GOAssociation> aqueue)
           throws IOException

Description copied from interface: QueuingParser

Parse an input stream, storing the results in the passed queue (which can be used by a consumer)

Specified by:

parse in interface QueuingParser<Gene2GOAssociation>

Parameters:

inputStream - input stream

aqueue - queue

Throws:

IOException - IO problems

parseOneLine

public Gene2GOAssociation parseOneLine(String line)

Description copied from interface: LineParser

Handle the parsing of a single line from the input.

Specified by:

parseOneLine in interface LineParser<Gene2GOAssociation>

Parameters:

line - line to parse

Returns:

parsed object