Package ubic.gemma.core.loader.util.biomart

Class BioMartEnsemblNcbiObjectGeneratorTest

java.lang.Object

ubic.gemma.core.loader.util.biomart.BioMartEnsemblNcbiObjectGeneratorTest

public class BioMartEnsemblNcbiObjectGeneratorTest
extends Object

Class to test BioMartEnsemblNcbiObjectGeneration. Simple class but there is some logic connected to the many to many relationship between ensembl genes and entrez genes and map manipulation. Using awk on the file validate the numbers.

Author:

ldonnison

Constructor Summary

Constructors

Constructor	Description
BioMartEnsemblNcbiObjectGeneratorTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
void	testGenerate()	Tests that given a taxon biomart file a BioMartEnsembleNcbi can be returned and that the genes are correctly mapped.

Methods inherited from class java.lang.Object

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

Constructor Details

BioMartEnsemblNcbiObjectGeneratorTest

public BioMartEnsemblNcbiObjectGeneratorTest()

Method Details

setUp

public void setUp()
           throws URISyntaxException,
IOException

Throws:

URISyntaxException

IOException

testGenerate

public void testGenerate()
                  throws IOException

Tests that given a taxon biomart file a BioMartEnsembleNcbi can be returned and that the genes are correctly mapped. Could be done through parser but thought do a quick test here. AWk commands are given to help give the counts to check validity of the numbers

Throws:

IOException