def functional_table():
form = FunctionClassFilterForm()
form.function_class.choices = [('cog', 'Cog'),
('pfam', 'Pfam'),
('tigrfam', 'TigrFam'),
('all', 'All')
]
form.select_sample_groups.choices = [(sample_set.name, sample_set.name) for sample_set in SampleSet.query.all()]
type_identifiers = []
if form.validate_on_submit():
function_class = form.function_class.data
if function_class == 'all':
function_class = None
limit = form.limit.data
if limit == 'all':
limit = None
else:
limit = int(limit)
filter_alternative = form.filter_alternative.data
if filter_alternative == 'filter_with_type_identifiers':
for type_identifier in form.type_identifiers.entries:
if type_identifier.data != '':
type_identifiers.append(type_identifier.data)
elif filter_alternative == 'filter_with_search':
search_string = form.search_annotations
if search_string.data != '':
q = _search_query(search_string.data)
type_identifiers = [a.type_identifier for a in q.all()]
sample_sets = form.select_sample_groups.data
if len(sample_sets) > 0:
samples = [sample.scilifelab_code for sample in Sample.all_from_sample_sets(sample_sets)]
else:
samples = None
download_action = False
if form.submit_download.data:
download_action = True
download_select = form.download_select.data
else:
function_class=None
limit=20
samples = None
download_action = False
if len(form.type_identifiers) == 0:
form.type_identifiers.append_entry()
if type_identifiers == []:
type_identifiers = None
samples, table = Annotation.rpkm_table(limit=limit, samples=samples, function_class=function_class, type_identifiers=type_identifiers)
samples = sorted(samples, key=lambda x: x.scilifelab_code)
sample_scilifelab_codes = [sample.scilifelab_code for sample in samples]
if download_action:
if download_select == 'Gene List':
# Fetch all contributing genes for all the annotations in the table
annotation_ids = [annotation.id for annotation, sample in table.items()]
genes_per_annotation = Annotation.genes_per_annotation(annotation_ids)
csv_output = '\n'.join(
[','.join([gene.name, annotation.type_identifier]) \
for gene, annotation in genes_per_annotation])
r = make_response(csv_output)
r.headers["Content-Disposition"] = "attachment; filename=gene_list.csv"
r.headers["Content-Type"] = "text/csv"
return r
return render_template('functional_table.html',
table=table,
samples=samples,
sample_scilifelab_codes = sample_scilifelab_codes,
form=form
)
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]