def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = controllers.clinvar_export(store, institute_id, case_name,
variant_id)
if request.method == 'GET':
return data
else:
form_dict = request.form.to_dict()
variants_to_submit = get_submission_variants(
form_dict) # list of variants to be submitted
variant_header = get_submission_header(form_dict, variants_to_submit,
'variants')
variant_lines = get_submission_lines(form_dict, variants_to_submit,
variant_header)
casedata_header = get_submission_header(form_dict, variants_to_submit,
'casedata')
casedata_lines = get_submission_lines(form_dict, variants_to_submit,
casedata_header)
variant_types = {}
for var in variants_to_submit:
variant_types[var] = form_dict['variant-type_' + str(var)]
# create clinvar submission session object:
session['clinvar_submission'] = create_clinvar_submission_dict(
variant_header, variant_lines, casedata_header, casedata_lines,
variant_types)
data.update({
'variant_header': variant_header,
'variant_lines': variant_lines,
'casedata_header': casedata_header,
'casedata_lines': casedata_lines,
'form': request.form,
})
return data
def test_clinvar_submission_parser():
# GIVEN a clinvar form submission
test_clinvar_form_dict = get_submission_dict()
# call the parser to get a list of the variants IDs to be used in the submission
test_clinvars = get_submission_variants(test_clinvar_form_dict)
# assert that the form contains info for 2 variants
assert len(
test_clinvars
) == 2 # variant '3eecfca5efea445eec6c19a53299043b' and 'a3ec99657a128d14419563d77e1381bd'
# call the parser to get the header (a mini version of it actually, because of the shortened test form) of the .Variants csv file for the submission
test_variants_header = get_submission_header(test_clinvar_form_dict,
test_clinvars, 'variants')
# assert that the file header contains all the unique variant-related control fields (taken both from snv and sv variants):
variant_control_fields = [
'##Local ID', 'Linking ID', 'Chromosome', 'Start', 'Stop',
'Reference allele', 'Alternate allele', 'Variant type'
]
assert test_variants_header == variant_control_fields
# call the parser to get the lines of the .Variants csv file for the submission
test_variants_lines = get_submission_lines(test_clinvar_form_dict,
test_clinvars,
test_variants_header)
# assert that each variant (== each line of the file) contains the same number of elements specified in the file header
for variant_line in test_variants_lines:
assert len(variant_line) == len(test_variants_header)
# call the parser to get the header of the .Casedata csv file for the submission
test_casedata_header = get_submission_header(test_clinvar_form_dict,
test_clinvars, 'casedata')
# call the parser to get the lines of the .Casedata csv file for the submission
test_casedata_lines = get_submission_lines(test_clinvar_form_dict,
test_clinvars,
test_casedata_header)
# assert that there is casedata for one sample only
assert len(test_casedata_lines) == 1
# assert that the casedata line for that sample has three fields ('Linking ID', 'Individual ID', 'Affected status')
assert len(test_casedata_lines[0]) == 3
test_variant_types = {
'3eecfca5efea445eec6c19a53299043b': 'snv',
'a3ec99657a128d14419563d77e1381bd': 'sv'
}
# transform the text files values into a dictionary list. Each dictionary item of this list is a variant submission onject that is saved to scout db.
test_vars_dict_list = create_clinvar_submission_dict(
test_variants_header, test_variants_lines, test_casedata_header,
test_casedata_lines, test_variant_types)
# assert that two variant objects were created
assert len(test_vars_dict_list) == 2
def test_parse_clinvar_form():
"""Test create list of submission objects (variants and casedata) from clinvar page form"""
# Given a filled in form
form_fields_dict = get_submission_dict()
# Retrieve the IDs of variants in the form
variant_ids = get_submission_variants(form_fields_dict)
assert len(variant_ids) == 2
# obtain variant and casedata objects to include in submission
subm_objs = set_submission_objects(form_fields_dict)
assert len(subm_objs[0]) == 2 # one snv and one sv variant
assert len(subm_objs[1]) ==1 # one case data object