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_rpkm_table(self):
annotation_types = [("Cog", {'class': Cog}),
("Pfam", {'class': Pfam}),
("TigrFam", {'class': TigrFam}),
("EcNumber", {'class': EcNumber})]
nr_annotation_types = len(annotation_types)
annotation_sources = {}
for annotation_type, type_d in annotation_types:
annotation_sources[annotation_type]= AnnotationSource(
annotation_type,
"v1.0",
"rpsblast",
"e_value=0.000001"
)
sample1 = Sample("P1993_101", None, None)
sample2 = Sample("P1993_102", None, None)
nr_samples = 2
for i in range(50):
gene1 = Gene("gene1{}".format(i), None)
gene2 = Gene("gene2{}".format(i), None)
gene_count1 = GeneCount(gene1, sample1, 0.001)
gene_count2 = GeneCount(gene1, sample2, 0.01)
gene_count3 = GeneCount(gene2, sample1, 0.002)
gene_count4 = GeneCount(gene2, sample2, 0.02)
for annotation_type, type_d in annotation_types:
if annotation_type == 'Cog':
type_id = str(i)
type_id = "0"*(4-len(type_id))+type_id
annotation = type_d['class'](annotation_type.upper() + type_id, "H")
elif annotation_type == 'EcNumber':
if i > 25:
type_id = "0.0.2.{}".format(i)
else:
type_id = "0.0.0.{}".format(i)
annotation = type_d['class'](type_id)
else:
type_id = str(i)
type_id = "0"*(4-len(type_id))+type_id
annotation = type_d['class'](annotation_type.upper() + type_id)
annotation_mode = i % 3
gene_annotations = []
if annotation_mode in [0,1]:
gene_annotations.append(GeneAnnotation(
annotation,
gene1,
annotation_sources[annotation_type]
))
if annotation_mode in [1,2]:
gene_annotations.append(GeneAnnotation(
annotation,
gene2,
annotation_sources[annotation_type]
))
self.session.add_all(gene_annotations)
self.session.add(gene1)
self.session.add(gene2)
self.session.commit()
refresh_all_mat_views()
samples, rows = Annotation.rpkm_table()
assert len(samples) == 2
assert len(rows) == 20 # Default limit
samples, rows = Annotation.rpkm_table(limit=100)
assert len(samples) == 2
assert len(rows) == 100
samples, rows = Annotation.rpkm_table(limit=None)
assert len(samples) == 2
assert len(rows) == nr_annotation_types * 50
for annotation, sample_d in rows.items():
# sample_d should be a ordered dict
assert ["P1993_101", "P1993_102"] == [sample.scilifelab_code for sample in sample_d.keys()]
rpkms = [[rpkm for sample, rpkm in sample_d.items()] for annotation, sample_d in rows.items()]
rpkms_flat = []
for rpkm_row in rpkms:
rpkms_flat += rpkm_row
assert len(rpkms_flat) == nr_annotation_types * nr_samples * 50
# Annotations sorted by total rpkm over all samples
# and the rpkm values should be summed over all genes for that annotation
# there should be roughly equal numbers of the three different counts
for i, row in enumerate(rpkms[:67]):
assert row == [0.003, 0.03]
for row in rpkms[69:130]:
assert row == [0.002, 0.02]
for row in rpkms[150:200]:
assert row == [0.001, 0.01]
# possible to filter on function classes
for annotation_type, type_d in annotation_types:
samples, rows = Annotation.rpkm_table(limit=None, function_class=annotation_type.lower())
assert len(rows) == 50
for key in rows.keys():
assert annotation_type[:3].lower() == key.annotation_type[:3]
# possible to filter on samples
for sample in [sample1, sample2]:
samples, rows = Annotation.rpkm_table(samples=[sample.scilifelab_code], limit=None)
assert len(rows) == 200
assert len(samples) == 1
assert samples[0] == sample
for annotation, sample_d in rows.items():
assert list(sample_d.keys()) == [sample]
rpkms = [[rpkm for sample, rpkm in sample_d.items()] for annotation, sample_d in rows.items()]
if sample.scilifelab_code == "P1993_101":
for i, row in enumerate(rpkms[:65]):
assert row == [0.003]
for row in rpkms[69:130]:
assert row == [0.002]
for row in rpkms[150:200]:
assert row == [0.001]
else:
for row in rpkms[:67]:
assert row == [0.03]
for row in rpkms[69:130]:
assert row == [0.02]
for row in rpkms[150:200]:
assert row == [0.01]
# possible to filter on sample and function class at the same time
for annotation_type, type_d in annotation_types:
for sample in [sample1, sample2]:
samples, rows = Annotation.rpkm_table(limit=None, function_class=annotation_type.lower(), samples=[sample.scilifelab_code])
assert len(rows) == 50
for key in rows.keys():
assert annotation_type.lower()[:3] == key.annotation_type[:3]
assert len(samples) == 1
assert samples[0] == sample
for annotation, sample_d in rows.items():
assert list(sample_d.keys()) == [sample]
rpkms = [[rpkm for sample, rpkm in sample_d.items()] for annotation, sample_d in rows.items()]
if sample.scilifelab_code == "P1993_101":
for row in rpkms[:9]:
assert row == [0.003]
for row in rpkms[19:29]:
assert row == [0.002]
for row in rpkms[39:]:
assert row == [0.001]
else:
for row in rpkms[:9]:
assert row == [0.03]
for row in rpkms[19:29]:
assert row == [0.02]
for row in rpkms[39:]:
assert row == [0.01]
# possible to filter on individual annotations
annotation_ids = ["COG0001", "TIGRFAM0004", "COG0003", "PFAM0002", "0.0.2.26"]
for r in range(5):
for type_identifiers in itertools.combinations(annotation_ids, r+1):
samples, rows = Annotation.rpkm_table(limit=None, type_identifiers=list(type_identifiers))
assert len(samples) == 2
assert len(rows) == len(type_identifiers)
assert set([key.type_identifier for key in rows.keys()]) == set(type_identifiers)
