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Hernan Morales
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Add Haplotypes tests
Add Genepop wrapper + tests Rename BioParserTests -> BioParsers-Tests
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‎repository/BaselineOfBioSmalltalk/BaselineOfBioSmalltalk.class.st‎

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@@ -114,7 +114,7 @@ BaselineOfBioSmalltalk >> baselineCommonPackages: spec [
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includes: #('BioPharoCommon') ];
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package: 'BioToolsSamples' with: [ spec requires: #('BioTools' 'BioEntrez' 'BioParsers' ). ];
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package: 'BioTools-Tests' with: [ spec requires: #('BioTools' ). ];
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package: 'BioWrapperTests' with: [ spec requires: #('BioTools-Tests' ) ];
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package: 'BioWrappers-Tests' with: [ spec requires: #('BioTools-Tests' ) ];
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package: 'BioPhysics' with: [ spec requires: #('BioTools') ];
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package: 'BioPhysics-Tests' with: [ spec requires: #('BioPhysics') ];
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package: 'BioWrappers' with: [ spec requires: #('BioTools' ) ];
@@ -240,7 +240,7 @@ BaselineOfBioSmalltalk >> baselineTestsGroup: spec [
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'BioTools-Tests'
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'BioBlastTests'
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'BioWrapperTests'
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'BioWrappers-Tests'
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'BioParsers-Tests'
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'BioEntrezTests'
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'BioNCBITests'

‎repository/BioHaplotypes-Tests/BioHaplotypeIOTest.class.st‎

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Class {
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#name : 'BioHaplotypeIOTest',
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#superclass : 'TestCase',
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#category : 'BioHaplotypes-Tests-Core',
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#package : 'BioHaplotypes-Tests',
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#tag : 'Core'
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}
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{ #category : 'tests' }
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BioHaplotypeIOTest >> testAsBioHaplotypesReturnsCollection [
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| reader haps |
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reader := BioHaplotypePlinkReader new.
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haps := reader asBioHaplotypes.
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self assert: haps class equals: BioHaplotypes.
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self assert: haps size equals: 0
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]
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{ #category : 'tests' }
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BioHaplotypeIOTest >> testFromPedFileMapFileCreatesCollection [
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"Tests class-side factory exists and configuration works (no file I/O)."
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| reader |
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reader := BioHaplotypePlinkReader new.
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reader pedFile: 'test.ped'; mapFile: 'test.map'.
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self assert: reader pedFile equals: 'test.ped'.
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self assert: reader mapFile equals: 'test.map'
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]
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{ #category : 'tests' }
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BioHaplotypeIOTest >> testParseMapLines [
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| reader lines variants |
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reader := BioHaplotypePlinkReader new.
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lines := #( '1 rs111 0 100' '1 rs222 0 200' '1 rs333 0 300' ).
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variants := reader parseMapLines: lines.
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self assert: variants size equals: 3.
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self assert: (variants at: 1) rsID equals: 'rs111'.
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self assert: (variants at: 1) position equals: 100.
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self assert: (variants at: 1) chromosome equals: '1'.
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self assert: (variants at: 2) rsID equals: 'rs222'.
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self assert: (variants at: 3) rsID equals: 'rs333'
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]
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{ #category : 'tests' }
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BioHaplotypeIOTest >> testParsePedLines [
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| reader variants haps v1 v2 |
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v1 := BioVariant position: 100 referenceAllele: 'A' alternateAlleles: #('T') rsID: 'rs111' chromosome: '1'.
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v2 := BioVariant position: 200 referenceAllele: 'C' alternateAlleles: #('G') rsID: 'rs222' chromosome: '1'.
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variants := {v1 . v2}.
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reader := BioHaplotypePlinkReader new.
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haps := reader parsePedLines: #('FAM1 IND1 0 0 1 1 A T C G') variants: variants.
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self assert: haps size equals: 2.
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self assert: (haps at: 1) alleles equals: #('A' 'C').
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self assert: (haps at: 2) alleles equals: #('T' 'G').
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self assert: (haps at: 1) identifier equals: 'IND1_a'.
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self assert: (haps at: 2) identifier equals: 'IND1_b'
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]
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{ #category : 'tests' }
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BioHaplotypeIOTest >> testPlinkWrapperConfiguration [
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"Verify plinkWrapper can be set and retrieved."
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| reader plink |
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reader := BioHaplotypePlinkReader new.
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plink := BioPLINK1Wrapper new.
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reader plinkWrapper: plink.
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self assert: reader plinkWrapper equals: plink
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]

‎repository/BioHaplotypes-Tests/BioHaplotypeMatrixTest.class.st‎

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Class {
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#name : 'BioHaplotypeMatrixTest',
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#superclass : 'TestCase',
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#category : 'BioHaplotypes-Tests-Core',
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#package : 'BioHaplotypes-Tests',
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#tag : 'Core'
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}
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{ #category : 'running' }
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BioHaplotypeMatrixTest >> exampleMatrix [
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^ BioHaplotypes exampleSimple asHaplotypeMatrix
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]
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{ #category : 'tests' }
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BioHaplotypeMatrixTest >> testAccessing [
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| mat |
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mat := self exampleMatrix.
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self assert: (mat at: 1 at: 1) equals: 'A'.
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self assert: (mat at: 1 at: 2) equals: 'C'.
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self assert: (mat at: 2 at: 1) equals: 'T'.
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self assert: (mat at: 2 at: 2) equals: 'G'
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]
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{ #category : 'tests' }
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BioHaplotypeMatrixTest >> testDimensions [
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| mat |
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mat := self exampleMatrix.
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self assert: mat rows equals: 2.
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self assert: mat columns equals: 2
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]
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{ #category : 'tests' }
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BioHaplotypeMatrixTest >> testHammingDistances [
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| mat dist |
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mat := self exampleMatrix.
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dist := mat pairwiseHammingDistances.
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self assert: (dist at: 1 at: 1) equals: 0.
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self assert: (dist at: 1 at: 2) equals: 2
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]

‎repository/BioHaplotypes-Tests/BioHaplotypePanelTest.class.st‎

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Class {
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#name : 'BioHaplotypePanelTest',
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#superclass : 'TestCase',
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#category : 'BioHaplotypes-Tests-Core',
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#package : 'BioHaplotypes-Tests',
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#tag : 'Core'
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}
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{ #category : 'tests' }
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BioHaplotypePanelTest >> testRegistry [
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| panel v1 |
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BioHaplotypePanel resetRegistry.
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v1 := BioVariant
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position: 100
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referenceAllele: 'A'
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alternateAlleles: #( 'T' )
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rsID: 'rs1'.
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panel := BioHaplotypePanel new
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panelName: 'TestPanel';
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addVariant: v1;
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yourself.
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BioHaplotypePanel register: panel.
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self
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assert: (BioHaplotypePanel panelNamed: 'TestPanel')
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equals: panel.
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BioHaplotypePanel unregister: panel.
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self assert: (BioHaplotypePanel panelNamed: 'TestPanel') isNil
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]
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{ #category : 'tests' }
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BioHaplotypePanelTest >> testVariantAtRsID [
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| panel v1 v2 |
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panel := BioHaplotypePanel new panelName: 'RsTest'.
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v1 := BioVariant
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position: 100
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referenceAllele: 'A'
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alternateAlleles: #( 'T' )
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rsID: 'rs1'.
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v2 := BioVariant
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position: 200
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referenceAllele: 'C'
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alternateAlleles: #( 'G' )
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rsID: 'rs2'.
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panel
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addVariant: v1;
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addVariant: v2.
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self assert: (panel variantAtRsID: 'rs1') equals: v1.
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self assert: (panel variantAtRsID: 'rs2') equals: v2.
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self assert: (panel variantAtRsID: 'rs999') isNil
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]

‎repository/BioHaplotypes-Tests/BioHaplotypeTest.class.st‎

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Class {
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#name : 'BioHaplotypeTest',
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#superclass : 'TestCase',
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#category : 'BioHaplotypes-Tests-Core',
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#package : 'BioHaplotypes-Tests',
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#tag : 'Core'
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}
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{ #category : 'running' }
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BioHaplotypeTest >> exampleHaplotype [
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| v1 v2 |
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v1 := BioVariant
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position: 100
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referenceAllele: 'A'
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alternateAlleles: #( 'T' )
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rsID: 'rs1'
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chromosome: '1'.
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v2 := BioVariant
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position: 200
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referenceAllele: 'C'
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alternateAlleles: #( 'G' )
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rsID: 'rs2'
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chromosome: '1'.
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^ BioHaplotype
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withAlleles: #( 'A' 'C' )
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atVariants: {
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v1.
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v2 }
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identifier: 'hap1'
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]
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{ #category : 'running' }
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BioHaplotypeTest >> exampleHaplotype2 [
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| v1 v2 |
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v1 := BioVariant
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position: 100
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referenceAllele: 'A'
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alternateAlleles: #( 'T' )
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rsID: 'rs1'
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chromosome: '1'.
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v2 := BioVariant
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position: 200
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referenceAllele: 'C'
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alternateAlleles: #( 'G' )
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rsID: 'rs2'
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chromosome: '1'.
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^ BioHaplotype
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withAlleles: #( 'T' 'G' )
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atVariants: {
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v1.
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v2 }
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identifier: 'hap2'
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testAlleleAtRsID [
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| h |
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h := self exampleHaplotype.
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self assert: (h alleleAtRsID: 'rs1') equals: 'A'.
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self assert: (h alleleAtRsID: 'rs2') equals: 'C'
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testAsAlleleString [
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| h |
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h := self exampleHaplotype.
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self assert: h asAlleleString equals: 'A-C'
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testAt [
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| h |
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h := self exampleHaplotype.
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self assert: (h at: 1) equals: 'A'.
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self assert: (h at: 2) equals: 'C'
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testCreation [
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| h |
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h := self exampleHaplotype.
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self assert: h alleles equals: #( 'A' 'C' ).
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self assert: h identifier equals: 'hap1'.
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self assert: h size equals: 2
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testDynamicRsIDAccess [
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| h |
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h := self exampleHaplotype.
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self assert: (h perform: #rs1) equals: 'A'.
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self assert: (h perform: #rs2) equals: 'C'
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testHammingDistance [
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| h1 h2 |
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h1 := self exampleHaplotype.
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h2 := self exampleHaplotype2.
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self assert: (h1 hammingDistanceTo: h2) equals: 2.
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self assert: (h1 hammingDistanceTo: h1) equals: 0
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testImmutability [
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| h |
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h := self exampleHaplotype.
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self assert: h isImmutable.
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self should: [ h at: 1 put: 'T' ] raise: Error
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testMatchesAtLocus [
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| h1 h2 |
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h1 := self exampleHaplotype.
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h2 := self exampleHaplotype2.
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self deny: (h1 matches: h2 atLocus: 1).
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self deny: (h1 matches: h2 atLocus: 2)
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testPrintOn [
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| h |
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h := self exampleHaplotype.
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self assert: h printString equals: 'BioHaplotype(hap1)[A|C]'
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]
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{ #category : 'tests' }
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BioHaplotypeTest >> testVariantAt [
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| h v1 |
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h := self exampleHaplotype.
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v1 := BioVariant
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position: 100
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referenceAllele: 'A'
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alternateAlleles: #( 'T' )
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rsID: 'rs1'
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chromosome: '1'.
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self assert: (h variantAt: 1) position equals: 100
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]

‎repository/BioHaplotypes-Tests/BioHaplotypesTest.class.st‎

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Class {
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#name : 'BioHaplotypesTest',
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#superclass : 'TestCase',
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#category : 'BioHaplotypes-Tests-Core',
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#package : 'BioHaplotypes-Tests',
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#tag : 'Core'
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}
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{ #category : 'running' }
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BioHaplotypesTest >> exampleHaplotypes [
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^ BioHaplotypes exampleSimple
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]
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{ #category : 'tests' }
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BioHaplotypesTest >> testCountAllelesAtLocus [
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| hs |
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hs := self exampleHaplotypes.
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self assert: ((hs countAllelesAtLocus: 1) occurrencesOf: 'A') equals: 1.
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self assert: ((hs countAllelesAtLocus: 1) occurrencesOf: 'T') equals: 1
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]
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{ #category : 'tests' }
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BioHaplotypesTest >> testHaplotypeDiversity [
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| hs |
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hs := self exampleHaplotypes.
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self assert: hs haplotypeDiversity closeTo: 1.0
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]
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{ #category : 'tests' }
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BioHaplotypesTest >> testPairwiseDistances [
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| hs dist |
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hs := self exampleHaplotypes.
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dist := hs pairwiseDistances.
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self assert: (dist at: 1 at: 1) equals: 0.
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self assert: (dist at: 1 at: 2) equals: 2.
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self assert: (dist at: 2 at: 1) equals: 2.
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self assert: (dist at: 2 at: 2) equals: 0
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]
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{ #category : 'tests' }
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BioHaplotypesTest >> testSelect [
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| hs selected |
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hs := self exampleHaplotypes.
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selected := hs select: [ :h | h identifier = 'h1' ].
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self assert: selected size equals: 1
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]
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{ #category : 'tests' }
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BioHaplotypesTest >> testSize [
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| hs |
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hs := self exampleHaplotypes.
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self assert: hs size equals: 2
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]
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{ #category : 'tests' }
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BioHaplotypesTest >> testUniqueHaplotypes [
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| hs |
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hs := self exampleHaplotypes.
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self assert: hs uniqueHaplotypes size equals: 2
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]

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