Package ubic.gemma.core.loader.genome.gene

Class ExternalFileGeneLoaderServiceImpl

java.lang.Object

ubic.gemma.core.loader.genome.gene.ExternalFileGeneLoaderServiceImpl

All Implemented Interfaces:

ExternalFileGeneLoaderService

@Component
public class ExternalFileGeneLoaderServiceImpl
extends Object
implements ExternalFileGeneLoaderService

Class to provide functionality to load genes from a tab delimited file. Typical usage is for non model organisms that do not have genes in NCBI. Supports loading genes against a non species taxon such as a family e.g Salmonids. File format is : Optional header which should be appended with a # to indicate not to process this line Then a line containing 3 fields which should be 'Gene Symbol' 'Gene Name' 'UniProt id' (last is optional) separated by tabs. The Class reads the file and looping through each line creates a gene (NCBI id is null) and one associated gene product. The gene is populated with gene symbol, gene name, gene official name (gene symbol) and a description indicating that this gene has been loaded from a text file. Then gene is associated with a gene product bearing the same name as the gene symbol and persisted.

Author:

ldonnison

Constructor Summary

Constructors

Constructor	Description
ExternalFileGeneLoaderServiceImpl()

Method Summary

Modifier and Type	Method	Description
int	load(InputStream geneInputStream, String taxonName)
int	load(String geneFile, String taxonName)	Work flow is: The file is first checked to see if readable, and the taxon checked to see it is in Gemma.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExternalFileGeneLoaderServiceImpl

public ExternalFileGeneLoaderServiceImpl()

Method Detail

load

public int load(InputStream geneInputStream,
                String taxonName)
         throws Exception

Specified by:

load in interface ExternalFileGeneLoaderService

Parameters:

geneInputStream - gene input stream

taxonName - taxon name

Returns:

number of genes loaded

Throws:

Exception - Thrown with a file format error or problem in persisting gene to database.

load

public int load(String geneFile,
                String taxonName)
         throws Exception

Description copied from interface: ExternalFileGeneLoaderService

Work flow is: The file is first checked to see if readable, and the taxon checked to see it is in Gemma. If validation passes the file is read line by line. Each line equates to a gene and its gene product, which is created from the file details. The gene is then persisted. If successfully loaded taxon flag isGenesLoaded is set to true to indicate that there are genes loaded for this taxon.

Specified by:

load in interface ExternalFileGeneLoaderService

Parameters:

geneFile - Full path to file containing genes details

taxonName - taxonName to be associated to this gene, does not have to be a species.

Returns:

number of genes loaded

Throws:

Exception - Thrown with a file format error or problem in persisting gene to database.