Add BioSummarizedExperiment with tests.

repository/BaselineOfBioSmalltalk/BaselineOfBioSmalltalk.class.st

@@ -115,7 +115,9 @@ BaselineOfBioSmalltalk >> baselineCommonPackages: spec [
 			package: 'BioTools-Tests' 			with: [ spec requires: #('BioTools' ). ];
 			package: 'BioWrapperTests' 			with: [ spec requires: #('BioTools-Tests' ) ];
 			package: 'BioPhysics'        	with: [ spec requires: #('BioTools') ];
-			package: 'BioWrappers' 				with: [ spec requires: #('BioTools' ) ]
+			package: 'BioWrappers' 				with: [ spec requires: #('BioTools' ) ];
+			package: 'BioSummarizedExperiment' with: [ spec requires: #('BioTools' 'DataFrame') ];
+			package: 'BioSummarizedExperiment-Tests' with: [ spec requires: #('BioSummarizedExperiment') ]
 
 ]
 

repository/BioSummarizedExperiment-Tests/BioRangedSummarizedExperimentTest.class.st

@@ -0,0 +1,128 @@
+Class {
+	#name : 'BioRangedSummarizedExperimentTest',
+	#superclass : 'TestCase',
+	#category : 'BioSummarizedExperiment-Tests',
+	#package : 'BioSummarizedExperiment-Tests'
+}
+
+{ #category : 'instance creation' }
+BioRangedSummarizedExperimentTest >> newTestRSE [
+	"Create a test RangedSummarizedExperiment with DataFrame."
+
+	| matrix rowData colData ranges |
+	matrix := Array2D rows: 3 columns: 2.
+	matrix at: 1 at: 1 put: 100.
+	matrix at: 1 at: 2 put: 150.
+	matrix at: 2 at: 1 put: 200.
+	matrix at: 2 at: 2 put: 250.
+	matrix at: 3 at: 1 put: 50.
+	matrix at: 3 at: 2 put: 75.
+	rowData := DataFrame
+		           withRows: #( #( 1 'BRCA1' ) #( 2 'TP53' ) #( 3 'EGFR' ) )
+		           columnNames: #( 'id' 'gene' ).
+	colData := DataFrame
+		           withRows: #( #( 1 'S1' ) #( 2 'S2' ) )
+		           columnNames: #( 'id' 'sample' ).
+	ranges := BioGenomicRanges new
+		          ranges: (BioIRanges starts: #( 1000 3000 5000 ) ends: #( 2000 4000 6000 ));
+		          seqnames: { 'chr1' . 'chr2' . 'chr3' };
+		          strands: #( $+ $- $+ ).
+	^ BioRangedSummarizedExperiment new
+		assay: matrix;
+		rowRanges: ranges;
+		rowData: rowData;
+		colData: colData;
+		yourself
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testByChromosome [
+
+	| rse chr1 |
+	rse := self newTestRSE.
+	chr1 := rse byChromosome: 'chr1'.
+	self assert: chr1 notNil
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testCreation [
+
+	| rse |
+	rse := BioRangedSummarizedExperiment new.
+	self assert: rse assays notNil.
+	self assert: rse rowRanges isNil
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testGranges [
+
+	| rse gr |
+	rse := self newTestRSE.
+	gr := rse granges.
+	self assert: gr notNil.
+	self assert: gr size equals: 3
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testInheritsFromSummarizedExperiment [
+
+	| rse |
+	rse := BioRangedSummarizedExperiment new.
+	self assert: (rse isKindOf: BioSummarizedExperiment)
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testOverlaps [
+
+	| rse overlaps |
+	rse := self newTestRSE.
+	overlaps := rse overlaps: 'chr1' from: 1500 to: 2500.
+	self assert: overlaps notNil
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testPythonExampleSize [
+
+	| rse |
+	rse := BioRangedSummarizedExperiment new.
+	self assert: rse dim key equals: 0.
+	self assert: rse dim value equals: 0
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testRowRanges [
+
+	| rse ranges |
+	rse := self newTestRSE.
+	ranges := rse rowRanges.
+	self assert: ranges notNil.
+	self assert: ranges size equals: 3
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testSeqnames [
+
+	| rse seqs |
+	rse := self newTestRSE.
+	seqs := rse seqnames.
+	self assert: seqs size equals: 3
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testStartEndWidth [
+
+	| rse |
+	rse := self newTestRSE.
+	self assert: rse start size equals: 3.
+	self assert: rse end size equals: 3.
+	self assert: rse width size equals: 3
+]
+
+{ #category : 'tests' }
+BioRangedSummarizedExperimentTest >> testStrand [
+
+	| rse strands |
+	rse := self newTestRSE.
+	strands := rse strand.
+	self assert: strands size equals: 3
+]

repository/BioSummarizedExperiment-Tests/BioSummarizedExperimentTest.class.st

@@ -0,0 +1,168 @@
+Class {
+	#name : 'BioSummarizedExperimentTest',
+	#superclass : 'TestCase',
+	#category : 'BioSummarizedExperiment-Tests',
+	#package : 'BioSummarizedExperiment-Tests'
+}
+
+{ #category : 'instance creation' }
+BioSummarizedExperimentTest >> newTestSE [
+	"Create a test SummarizedExperiment with 4 genes x 3 samples."
+
+	| se matrix rowData colData |
+	matrix := Array2D rows: 4 columns: 3.
+	matrix at: 1 at: 1 put: 10.
+	matrix at: 1 at: 2 put: 20.
+	matrix at: 1 at: 3 put: 30.
+	matrix at: 2 at: 1 put: 15.
+	matrix at: 2 at: 2 put: 25.
+	matrix at: 2 at: 3 put: 35.
+	matrix at: 3 at: 1 put: 5.
+	matrix at: 3 at: 2 put: 10.
+	matrix at: 3 at: 3 put: 15.
+	matrix at: 4 at: 1 put: 8.
+	matrix at: 4 at: 2 put: 16.
+	matrix at: 4 at: 3 put: 24.
+	rowData := DataFrame 
+		withRows: #( #( 1 'BRCA1' ) #( 2 'TP53' ) #( 3 'EGFR' ) #( 4 'MYC' ) )
+		columnNames: #( 'id' 'gene' ).
+	colData := DataFrame
+		withRows: #( #( 1 'S1' 'control' ) #( 2 'S2' 'treated' ) #( 3 'S3' 'treated' ) )
+		columnNames: #( 'id' 'sample' 'condition' ).
+	se := BioSummarizedExperiment
+		      assay: matrix
+		      rowData: rowData
+		      colData: colData.
+	^ se
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testAssay [
+
+	| se matrix |
+	se := BioSummarizedExperiment new.
+	matrix := Array2D rows: 2 columns: 2.
+	matrix atRow: 1 put: #( 1 2 ).
+	matrix atRow: 2 put: #( 3 4 ).
+	se assay: matrix.
+	self assert: se assay notNil.
+	self deny: se assays isEmpty
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testAssayAtPut [
+
+	| se matrix |
+	se := BioSummarizedExperiment new.
+	matrix := Array2D rows: 2 columns: 2.
+	se assayAt: 'counts' put: matrix.
+	se assayAt: 'logcounts' put: matrix.
+	self assert: (se assayAt: 'counts') notNil.
+	self assert: (se assayAt: 'logcounts') notNil.
+	self assert: se assayNames size equals: 2
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testColData [
+
+	| se |
+	se := self newTestSE.
+	self assert: se colCount equals: 3.
+	self assert: (se colData first at: 'condition') equals: 'control'
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testColNames [
+
+	| se names |
+	se := self newTestSE.
+	names := se colNames.
+	self assert: names size equals: 3
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testCreation [
+
+	| se |
+	se := BioSummarizedExperiment new.
+	self assert: se assays notNil.
+	self assertEmpty: se assays.
+	self assert: se rowCount equals: 0.
+	self assert: se colCount equals: 0
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testDim [
+
+	| se |
+	se := self newTestSE.
+	self assert: se dim key equals: 4. "rows"
+	self assert: se dim value equals: 3 "cols"
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testFactoryMethod [
+
+	| se matrix rowData colData |
+	matrix := Array2D rows: 2 columns: 2.
+	rowData := DataFrame
+		           withRows: #( #( 1 'gene1' ) #( 2 'gene2' ) )
+		           columnNames: #( 'id' 'name' ).
+	colData := DataFrame
+		           withRows: #( #( 1 'sample1' ) #( 2 'sample2' ) )
+		           columnNames: #( 'id' 'name' ).
+	se := BioSummarizedExperiment
+		      assay: matrix
+		      rowData: rowData
+		      colData: colData.
+	self assert: se rowCount equals: 2.
+	self assert: se colCount equals: 2
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testMetadata [
+
+	| se |
+	se := BioSummarizedExperiment new.
+	se metadata at: 'experiment' put: 'RNA-seq'.
+	se metadata at: 'date' put: '2024-01-15'.
+	self assert: (se metadata at: 'experiment') equals: 'RNA-seq'
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testRowData [
+
+	| se |
+	se := self newTestSE.
+	self assert: se rowCount equals: 4.
+	self assert: (se rowData first at: 'gene') equals: 'BRCA1'
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testRowNames [
+
+	| se names |
+	se := self newTestSE.
+	names := se rowNames.
+	self assert: names size equals: 4
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testSubetByRowIndex [
+
+	| se subset |
+	se := self newTestSE.
+	subset := se atRowIndex: 1 to: 2.
+	self assert: subset rowCount equals: 2.
+	self assert: subset colCount equals: 3
+]
+
+{ #category : 'tests' }
+BioSummarizedExperimentTest >> testSubsetByColIndex [
+
+	| se subset |
+	se := self newTestSE.
+	subset := se atColIndex: 2 to: 3.
+	self assert: subset rowCount equals: 4.
+	self assert: subset colCount equals: 2
+]

repository/BioSummarizedExperiment-Tests/package.st

@@ -0,0 +1 @@
+Package { #name : 'BioSummarizedExperiment-Tests' }