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Merged
hernanmd merged 1 commit into from
Apr 28, 2026
Merged

Add utility methods to BioSequence #17

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285 changes: 285 additions & 0 deletions repository/BioTools-Tests/BioSequenceAnalysisTest.class.st
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Class {
#name : 'BioSequenceAnalysisTest',
#superclass : 'BioAbstractTest',
#category : 'BioTools-Tests-Core',
#package : 'BioTools-Tests',
#tag : 'Core'
}

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> dnaSequence: aString [

^ BioSequence newDNA: aString
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> newSeqRecord [

^ BioSeqRecord new
sequence: (self dnaSequence: 'ATCGATCG');
id: 'TEST001';
yourself
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> proteinSequence: aString [

^ BioSequence newProtein: aString
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> rnaSequence: aString [

^ BioSequence newRNA: aString
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testATRatio [

| seq |
seq := self dnaSequence: 'AATT'.
self assert: seq atRatio equals: 1.0.
seq := self dnaSequence: 'GGCC'.
self assert: seq atRatio equals: 0.0
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testAnnotationPreservesAll [

| rec |
rec := self newSeqRecord.
rec
seqVersion: 1;
keywords: #( 'keyword1' );
dates: #( '01-JAN-2024' );
species: 'Homo sapiens';
primaryAccession: 'NM_001';
secondaryAccessions: #( 'NM_001.1' );
division: 'PRI';
taxonomy: #( 'Eukaryota' ).
self assert: rec seqVersion equals: 1.
self assert: rec keywords first equals: 'keyword1'.
self assert: rec dates first equals: '01-JAN-2024'.
self assert: rec species equals: 'Homo sapiens'.
self assert: rec primaryAccession equals: 'NM_001'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testComposition [

| seq comp |
seq := self dnaSequence: 'ATCGATCG'.
comp := seq composition.
self assert: (comp at: $A) equals: 2.
self assert: (comp at: $T) equals: 2.
self assert: (comp at: $C) equals: 2.
self assert: (comp at: $G) equals: 2
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testCompositionWithFrequencies [

| seq comp |
seq := self dnaSequence: 'AATT'.
comp := seq compositionWithFrequencies.
self assert: ((comp at: $A) at: #count) equals: 2.
self assert: ((comp at: $A) at: #frequency) equals: 0.5
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testDates [

| rec |
rec := self newSeqRecord.
self assert: rec dates isEmpty.
rec dates: #( '01-JAN-2024' '15-FEB-2024' ).
self assert: rec dates size equals: 2
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testDefinition [

| rec |
rec := self newSeqRecord.
rec definition: 'Test sequence for unit testing'.
self assert: rec definition equals: 'Test sequence for unit testing'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testDivision [

| rec |
rec := self newSeqRecord.
rec division: 'PRI'.
self assert: rec division equals: 'PRI'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testFeatureCount [

| rec |
rec := self newSeqRecord.
self assert: rec featureCount equals: 0.
rec addSeqFeature: (BioSequenceFeature new primaryTag: 'gene').
rec addSeqFeature: (BioSequenceFeature new primaryTag: 'CDS').
self assert: rec featureCount equals: 2
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testGCRatio [

| seq |
seq := self dnaSequence: 'GGCC'.
self assert: seq gcRatio equals: 1.0.
seq := self dnaSequence: 'AATT'.
self assert: seq gcRatio equals: 0.0.
seq := self dnaSequence: 'ATGC'.
self assert: seq gcRatio equals: 0.5
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testKeywords [

| rec |
rec := self newSeqRecord.
self assert: rec keywords isEmpty.
rec keywords: #( 'hypothetical protein' 'complete cds' ).
self assert: rec keywords size equals: 2.
self assert: rec keywords first equals: 'hypothetical protein'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testNucleotideComposition [

| seq comp |
seq := self dnaSequence: 'AATTTGGC'.
comp := seq nucleotideComposition.
self assert: (comp at: $A) equals: 2.
self assert: (comp at: $T) equals: 3.
self assert: (comp at: $G) equals: 2.
self assert: (comp at: $C) equals: 1
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testNucleotideCompositionRNA [

| seq comp |
seq := self rnaSequence: 'AAUUUGGC'.
comp := seq nucleotideComposition.
self assert: (comp at: $A) equals: 2.
self assert: (comp at: $U) equals: 3.
self assert: (comp at: $G) equals: 2.
self assert: (comp at: $C) equals: 1
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testOrganism [

| rec |
rec := self newSeqRecord.
rec organism: 'Drosophila melanogaster'.
self assert: rec organism equals: 'Drosophila melanogaster'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testPrimaryAccession [

| rec |
rec := self newSeqRecord.
rec primaryAccession: 'NM_12345'.
self assert: rec primaryAccession equals: 'NM_12345'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testPrimaryAccessionDefaultsToId [

| rec |
rec := self newSeqRecord.
"When no accession set, should return id"
self assert: rec primaryAccession equals: 'TEST001'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSecondaryAccessions [

| rec |
rec := self newSeqRecord.
self assert: rec secondaryAccessions isEmpty.
rec secondaryAccessions: #( 'NM_12345.1' 'NM_12345.2' ).
self assert: rec secondaryAccessions size equals: 2
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSeqVersion [

| rec |
rec := self newSeqRecord.
self assert: rec seqVersion isNil.
rec seqVersion: 1.
self assert: rec seqVersion equals: 1.
rec seqVersion: 2.
self assert: rec seqVersion equals: 2
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSequenceTypeDNA [

| seq |
seq := self dnaSequence: 'ATCG'.
self assert: seq sequenceType equals: #DNA
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSequenceTypeProtein [

| seq |
seq := self proteinSequence: 'MVLSP'.
self assert: seq sequenceType equals: #Protein
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSequenceTypeRNA [

| seq |
seq := self rnaSequence: 'AUCG'.
self assert: seq sequenceType equals: #RNA
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSpecies [

| rec |
rec := self newSeqRecord.
self assert: rec species isNil.
rec species: 'Homo sapiens'.
self assert: rec species equals: 'Homo sapiens'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSpeciesName [

| rec |
rec := self newSeqRecord.
rec speciesName: 'Mus musculus'.
self assert: rec speciesName equals: 'Mus musculus'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testSpeciesNameFromOrganism [

| rec |
rec := self newSeqRecord.
rec organism: 'Escherichia coli'.
self assert: rec speciesName equals: 'Escherichia coli'
]

{ #category : 'as yet unclassified' }
BioSequenceAnalysisTest >> testTaxonomy [

| rec |
rec := self newSeqRecord.
rec taxonomy:
#( 'Eukaryota' 'Metazoa' 'Chordata' 'Craniata' 'Mammalia' ).
self assert: rec taxonomy size equals: 5.
self assert: rec taxonomy first equals: 'Eukaryota'
]
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