def test_annotation(self):
annotation = Annotation("COG0001")
self.session.add(annotation)
self.session.commit()
assert Annotation.query.first() is annotation
#Test the many to many relationship
reference_assembly = ReferenceAssembly("version 1")
gene = Gene("gene1", reference_assembly)
gene2 = Gene("gene2", reference_assembly)
gene3 = Gene("gene3", reference_assembly)
annotation2 = Annotation("COG0002", description="This cog is really really good")
# Test having multiple genes to one annotation
annotation_source = AnnotationSource("Cog", "v1.0", "rpsblast", "e_value=0.000001")
gene_annotation1 = GeneAnnotation(annotation_source = annotation_source, e_value=0.0000001)
gene_annotation2 = GeneAnnotation(annotation_source = annotation_source)
gene_annotation1.gene = gene
gene_annotation2.gene = gene2
gene_annotation1.annotation = annotation
gene_annotation2.annotation = annotation
self.session.add(annotation)
self.session.add(gene3)
self.session.add(gene_annotation1)
self.session.add(gene_annotation2)
self.session.commit()
annotation_01 = Annotation.query.filter_by(type_identifier="COG0001").first()
assert len(annotation_01.genes) == 2
assert gene in annotation_01.genes
assert gene2 in annotation_01.genes
assert annotation in Gene.query.filter_by(name="gene1").first().annotations
assert annotation in Gene.query.filter_by(name="gene2").first().annotations
assert len(Gene.query.filter_by(name="gene3").first().annotations) == 0
# Genes for annotation method
genes_for_annotation = Annotation.genes_per_annotation([annotation.id])
assert len(genes_for_annotation) == 2
assert (gene, annotation) in genes_for_annotation
assert (gene2, annotation) in genes_for_annotation
# Add the second annotation
self.session.add(annotation2)
self.session.commit()
q = Annotation.query.filter(Annotation.description.contains("good"))
annotation_02 = q.all()
assert len(annotation_02) == 1
assert annotation_02[0] == annotation2
# Test having multiple annotations to one gene
gene_annotation3 = GeneAnnotation(annotation2, gene, annotation_source, e_value = 1e-14)
self.session.add(gene_annotation3)
self.session.commit()
assert len(Gene.query.filter_by(name="gene1").first().annotations) == 2
assert annotation in Gene.query.filter_by(name="gene1").first().annotations
assert annotation2 in Gene.query.filter_by(name="gene1").first().annotations
assert gene_annotation1.e_value > gene_annotation3.e_value
assert gene.e_value_for(annotation) > gene.e_value_for(annotation2)
# gene -> annotation
# gene2 -> annotation
# gene -> annotation2
# Genes for annotation method
genes_for_annotation = Annotation.genes_per_annotation([annotation.id])
assert len(genes_for_annotation) == 2
assert (gene, annotation) in genes_for_annotation
assert (gene2, annotation) in genes_for_annotation
genes_for_annotation = Annotation.genes_per_annotation([annotation2.id])
assert len(genes_for_annotation) == 1
assert (gene, annotation2) in genes_for_annotation
genes_for_annotation = Annotation.genes_per_annotation([annotation.id, annotation2.id])
assert len(genes_for_annotation) == 3
assert (gene, annotation) in genes_for_annotation
assert (gene, annotation2) in genes_for_annotation
assert (gene2, annotation) in genes_for_annotation
annotation3 = Annotation("COG0003", description=("This cog is really really good. I assure you, "
"really quite good. Among its capabilities I have to mention that its utterly suitable for "
"testing the description string, including the short description."))
assert len(annotation3.description) > 103
assert annotation3.short_description[-3:] == "..."
assert len(annotation3.short_description) == 103
assert annotation3.description[:100] == annotation3.short_description[:100]
