inst/unitTests/test_Filters.R

In jotsetung/ensembldb-old: Utilities to create and use an Ensembl based annotation database

library( "EnsDb.Hsapiens.v75" )

## testing GeneidFilter
test_GeneidFilter <- function(){
    GF <- GeneidFilter( "ENSG0000001" )
    ## check if column matches the present database.
    checkEquals( column( GF, EnsDb.Hsapiens.v75 ), "gene.gene_id" )
    ## check error if value is not as expected.
    checkException( GeneidFilter( "ENSG000001", ">" ) )
    ## expect the filter to change the condition if lenght of values
    ## is > 1
    checkMultiValsIn( GeneidFilter( c( "a", "b" ), "=" ) )
    checkMultiValsNotIn( GeneidFilter( c( "a", "b" ), "!=" ) )
}

test_GenebiotypeFilter <- function(){
    Filt <- GenebiotypeFilter( "protein_coding" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "gene.gene_biotype" )
    checkException( GenebiotypeFilter( "protein_coding", ">" ) )
    ## expect the filter to change the condition if lenght of values
    ## is > 1
    checkMultiValsIn( GenebiotypeFilter( c( "a", "b" ), "=" ) )
    checkMultiValsNotIn( GenebiotypeFilter( c( "a", "b" ), "!=" ) )

}

test_GenenameFilter <- function(){
    Filt <- GenenameFilter( "genename" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "gene.gene_name" )
    checkException( GenenameFilter( "genename", ">" ) )
    ## expect the filter to change the condition if lenght of values
    ## is > 1
    checkMultiValsIn( GenenameFilter( c( "a", "b" ), "=" ) )
    checkMultiValsNotIn( GenenameFilter( c( "a", "b" ), "!=" ) )
    ## check if we're escaping correctly!
    Filt <- GenenameFilter( "I'm a gene" )
    checkEquals( where( Filt, EnsDb.Hsapiens.v75 ), "gene.gene_name = 'I''m a gene'" )
}

test_TxidFilter <- function(){
    Filt <- TxidFilter( "a" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "tx.tx_id" )
    checkException( TxidFilter( "a", ">" ) )
    ## expect the filter to change the condition if lenght of values
    ## is > 1
    checkMultiValsIn( TxidFilter( c( "a", "b" ), "=" ) )
    checkMultiValsNotIn( TxidFilter( c( "a", "b" ), "!=" ) )
}

test_TxbiotypeFilter <- function(){
    Filt <- TxbiotypeFilter( "a" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "tx.tx_biotype" )
    checkException( TxbiotypeFilter( "a", ">" ) )
    ## expect the filter to change the condition if lenght of values
    ## is > 1
    checkMultiValsIn( TxbiotypeFilter( c( "a", "b" ), "=" ) )
    checkMultiValsNotIn( TxbiotypeFilter( c( "a", "b" ), "!=" ) )
}

test_ExonidFilter <- function(){
    Filt <- ExonidFilter( "a" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "tx2exon.exon_id" )
    checkException( ExonidFilter( "a", ">" ) )
    ## expect the filter to change the condition if lenght of values
    ## is > 1
    checkMultiValsIn( ExonidFilter( c( "a", "b" ), "=" ) )
    checkMultiValsNotIn( ExonidFilter( c( "a", "b" ), "!=" ) )
}

## SeqnameFilter
test_SeqnameFilter <- function(){
    Filt <- SeqnameFilter( "a" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "gene.seq_name" )
    checkException( SeqnameFilter( "a", ">" ) )
}

## SeqstrandFilter
test_SeqstrandFilter <- function(){
    checkException( SeqstrandFilter( "a" ) )
    Filt <- SeqstrandFilter( "-" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "gene.seq_strand" )
}

## SeqstartFilter, feature
test_SeqstartFilter <- function(){
    Filt <- SeqstartFilter( 123, feature="gene" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "gene.gene_seq_start" )
    Filt <- SeqstartFilter( 123, feature="transcript" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "tx.tx_seq_start" )
}

## SeqendFilter
test_SeqendFilter <- function(){
    Filt <- SeqendFilter( 123, feature="gene" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "gene.gene_seq_end" )
    Filt <- SeqendFilter( 123, feature="transcript" )
    checkEquals( column( Filt, EnsDb.Hsapiens.v75 ), "tx.tx_seq_end" )
}



## checks if "condition" of the filter is "in"
checkMultiValsIn <- function( filt ){
    checkEquals( condition( filt ), "in" )
}
## checks if "condition" of the filter is "in"
checkMultiValsNotIn <- function( filt ){
    checkEquals( condition( filt ), "not in" )
}