def main():
# Get data from config
config = ConfigParser(
'config/config.txt'
) # To run by pressing play in pycharm, use ../config/config.txt
consensus_table = config.prefix + config.consensus
comments_table = config.prefix + config.comments
history_file = f'{config.input}{config.prefix}{config.history}.tsv'
previous_exports = config.previous
if type(previous_exports) != list:
previous_exports = [previous_exports]
output = config.output
labs = config.labs
# Retrieve data
retriever = DataRetriever(labs, config.prefix, history_file, config.output)
retriever.retrieve_all_data()
lab_data = retriever.all_lab_data
# Sort history on export
history = retriever.history
history_sorter = HistorySorter(history, previous_exports)
sorted_history = history_sorter.sorted_history
alternative_history = history_sorter.alternative_history
# Generate consensus table in memory
consensus_generator = ConsensusTableGenerator(lab_data)
consensus = consensus_generator.process_variants()
# Generate and upload CSV with consensus table
file_generator = ConsensusFileGenerator(
data={
'consensus': consensus,
'history': {
'history': sorted_history,
'alternative': alternative_history
}
},
tables={
'consensus_table': output + consensus_table,
'comments_table': output + comments_table
},
labs=labs,
incorrect_variant_history_file=output +
'incorrect_variant_history.csv')
file_generator.generate_consensus_files()
# Generate reports
prefix = config.prefix
csv = '{}/{}consensus.csv'.format(output, prefix)
public = prefix + 'public_consensus'
ConsensusReporter(csv, config.labs, public, prefix,
output).process_consensus()
print('Added incorrect variants in history to [{}]'.format(
colored('{}incorrect_variant_history.csv'.format(output), 'blue')))
def test_create_consensus_header(self):
labs = ['lab1', 'lab2', 'lab3']
observed = ConsensusFileGenerator.create_consensus_header(labs)
expected = 'id\tchromosome\tstart\tstop\tref\talt\tgene\tc_dna\ttranscript\tprotein\thgvs\t' \
'consensus_classification\tlab1_link\tlab1\tlab2_link\tlab2\tlab3_link\tlab3\tmatches\thistory\t' \
'disease\tcomments\n'
self.assertEqual(expected, observed)
def test__check_alternative_history(self):
transcript = 'NM_000702.2'
c_dna = 'c.2841-19delTinsCT'
gene = 'ATP1A2'
export = {'ATP1A2_NM_000702.2:c.2841-19delTinsCT': 'f2941cd0ea'}
observed = ConsensusFileGenerator._check_alternative_history(
transcript, c_dna, gene, export)
self.assertEqual(observed, 'f2941cd0ea')
def test__get_history_ids_for_variant(self, _, variant_info, expected):
variant_id = variant_info['variant_id']
chromosome = variant_info['chromosome']
pos = variant_info['pos']
gene = variant_info['gene']
ref = variant_info['ref']
alt = variant_info['alt']
variant_type = variant_info['variant_type']
file_generator = ConsensusFileGenerator(data={
'consensus': {},
'history': {
'history': {},
'alternative': {}
}
},
tables={
'consensus_table': '',
'comments_table': ''
},
labs=[])
observed = file_generator._get_history_ids_for_variant(
variant_id, chromosome, pos, ref, alt, gene, variant_type)
self.assertEqual(observed, expected)
def test__get_lab_classification(self):
variant_classifications = {"LAB1": "b", "LAB2": "v", "LAB3": ""}
variant = {
"chromosome": "11",
"start": "108167858",
"ref": "T",
"alt": "A",
"gene": "ATM"
}
expected_string = '\tLAB1_4d11f6c3b0\tBenign'
expected_bool = True
observed_string, observed_bool = ConsensusFileGenerator._get_lab_classification(
variant_classifications, 'LAB1', variant)
self.assertEqual(expected_string, observed_string)
self.assertEqual(expected_bool, observed_bool)
def test__add_simple_column(self, _, variant, column, expected):
line = ''
observed = ConsensusFileGenerator._add_simple_column(
line, variant, column)
self.assertEqual(expected, observed)
class ConsensusFileGeneratorTest(TestCase):
file_generator = ConsensusFileGenerator(data={
'consensus': {},
'history': {
'history': {
'1912':
['1912_00299bb101', '1912_001759607f', '1912_f2941cd0ea']
},
'alternative': {
'1912': {
'ATP1A2_NM_000702.2:c.2841-20_2841-19insC':
'1912_f2941cd0ea',
'PALB2_NM_024675.3:c.2928G>T': '1912_00299bb101'
}
}
}
},
tables={
'consensus_table': '',
'comments_table': ''
},
labs=[])
def test__get_lab_classification(self):
variant_classifications = {"LAB1": "b", "LAB2": "v", "LAB3": ""}
variant = {
"chromosome": "11",
"start": "108167858",
"ref": "T",
"alt": "A",
"gene": "ATM"
}
expected_string = '\tLAB1_4d11f6c3b0\tBenign'
expected_bool = True
observed_string, observed_bool = ConsensusFileGenerator._get_lab_classification(
variant_classifications, 'LAB1', variant)
self.assertEqual(expected_string, observed_string)
self.assertEqual(expected_bool, observed_bool)
def test_create_consensus_header(self):
labs = ['lab1', 'lab2', 'lab3']
observed = ConsensusFileGenerator.create_consensus_header(labs)
expected = 'id\tchromosome\tstart\tstop\tref\talt\tgene\tc_dna\ttranscript\tprotein\thgvs\t' \
'consensus_classification\tlab1_link\tlab1\tlab2_link\tlab2\tlab3_link\tlab3\tmatches\thistory\t' \
'disease\tcomments\n'
self.assertEqual(expected, observed)
def test__get_variant(self):
observed = ConsensusFileGenerator._get_variant(1, 123, 'A', 'C',
'ABC1')
expected = '1_123_A_C_ABC1'
self.assertEqual(expected, observed)
def test_create_consensus_line(self):
variant_id = 'cfd99f1bea'
variant = {
'id': variant_id,
'chromosome': '1',
'start': 123,
'stop': 124,
'ref': 'A',
'alt': 'C',
'gene': 'ABC1',
'consensus_classification': '(Likely) benign',
'type': 'sub'
}
observed = self.file_generator._create_consensus_line(
'cfd99f1bea', variant, {
'lab1': 'lb',
'lab2': 'b',
'lab3': ''
}, ['lab1', 'lab2', 'lab3'])
expected = 'cfd99f1bea\t1\t123\t124\tA\tC\tABC1\t\t\t\t\t(Likely) benign\tLAB1_cfd99f1bea\tLikely benign\t' \
'LAB2_cfd99f1bea\tBenign\t\t\t2\t\t\tcfd99f1bea\n'
self.assertEqual(expected, observed)
@parameterized.expand([('empty', {}, 'test', '\t'),
('column', {
'column': 'value'
}, 'column', '\tvalue')])
def test__add_simple_column(self, _, variant, column, expected):
line = ''
observed = ConsensusFileGenerator._add_simple_column(
line, variant, column)
self.assertEqual(expected, observed)
@parameterized.expand([('vus', 'VUS', 3, '\t3'),
('no consensus', 'No consensus', 0, '\t'),
('benign', '(Likely) benign', 5, '\t5'),
('1lab', 'Classified by one lab', 1, '\t1')])
def test__get_match_count_if_consensus(self, _, classification, matches,
expected):
observed = ConsensusFileGenerator._get_match_count_if_consensus(
matches, classification)
self.assertEqual(expected, observed)
@parameterized.expand([
('sub', {
'variant_id': '5d0cf0e376',
'chromosome': '10',
'pos': '112540884',
'gene': 'RBM20',
'ref': 'C',
'alt': 'A',
'variant_type': 'sub'
}, ['5d0cf0e376', '10_112540884_C_A_RBM20']),
('del', {
'variant_id': '5ef356611e',
'chromosome': '8',
'pos': '41573267',
'gene': 'ANK1',
'ref': 'GCGGTGGTGGC',
'alt': 'G',
'variant_type': 'del'
}, [
'5ef356611e', '8_41573267_GCGGTGGTGGC_G_ANK1',
'8_41573268_CGGTGGTGGC_._ANK1'
]),
('ins', {
'variant_id': '609ab27375',
'chromosome': '3',
'pos': '38627166',
'gene': 'SCN5A',
'ref': 'C',
'alt': 'CGTGTGTGTGTGTGG',
'variant_type': 'ins'
}, [
'609ab27375', '3_38627166_C_CGTGTGTGTGTGTGG_SCN5A',
'3_38627166_._GTGTGTGTGTGTGG_SCN5A'
]),
('delins', {
'variant_id': '3e69715481',
'chromosome': '9',
'pos': '135786871',
'gene': 'TSC1',
'ref': 'GGGGAACTCAGAGT',
'alt': 'AACTGC',
'variant_type': 'delins'
}, [
'3e69715481', '9_135786871_GGGGAACTCAGAGT_AACTGC_TSC1',
'4dd6e4fad5', '4b70f6a705', 'ae3fae1fd2', 'c3d04968bc'
])
])
def test__get_history_ids_for_variant(self, _, variant_info, expected):
variant_id = variant_info['variant_id']
chromosome = variant_info['chromosome']
pos = variant_info['pos']
gene = variant_info['gene']
ref = variant_info['ref']
alt = variant_info['alt']
variant_type = variant_info['variant_type']
file_generator = ConsensusFileGenerator(data={
'consensus': {},
'history': {
'history': {},
'alternative': {}
}
},
tables={
'consensus_table': '',
'comments_table': ''
},
labs=[])
observed = file_generator._get_history_ids_for_variant(
variant_id, chromosome, pos, ref, alt, gene, variant_type)
self.assertEqual(observed, expected)
def test__check_alternative_history(self):
transcript = 'NM_000702.2'
c_dna = 'c.2841-19delTinsCT'
gene = 'ATP1A2'
export = {'ATP1A2_NM_000702.2:c.2841-19delTinsCT': 'f2941cd0ea'}
observed = ConsensusFileGenerator._check_alternative_history(
transcript, c_dna, gene, export)
self.assertEqual(observed, 'f2941cd0ea')
@parameterized.expand([
('variant correct and has transcript:cDNA -> variant is correct', {
'id': '00299bb101',
'ref': 'C',
'alt': 'A',
'start': 23634358,
'chromosome': '16',
'gene': 'PALB2',
'type': 'sub',
'transcript': 'NM_024675.3',
'c_dna': 'c.2928G>T'
}, ['1912_00299bb101']),
('variant correct and has no transcript:cDNA -> variant is correct', {
'id': '001759607f',
'ref': 'G',
'alt': 'C',
'start': '108921331',
'chromosome': 'X',
'gene': 'ACSL4',
'type': 'sub'
}, ['1912_001759607f']),
# f2941cd0ea
('variant incorrect and has transcript:cDNA -> merged with correct existing variant',
{
'id': '6a550d807b',
'ref': 'A',
'alt': 'AC',
'start': '160109408',
'chromosome': '1',
'gene': 'ATP1A2',
'type': 'dup',
'transcript': 'NM_000702.2',
'c_dna': 'c.2841-20_2841-19insC'
}, ['1912_f2941cd0ea']),
('variant incorrect and has no transcript:cDNA -> new variant', {
'id': '6a550d807b',
'ref': 'A',
'alt': 'AC',
'start': '160109408',
'chromosome': '1',
'gene': 'ATP1A2',
'type': 'dup'
}, [])
])
def test___get_matching_history(self, _, variant, expected):
observed = self.file_generator._get_matching_history(variant)
self.assertEqual(observed, expected)
def test__get_variant(self):
observed = ConsensusFileGenerator._get_variant(1, 123, 'A', 'C',
'ABC1')
expected = '1_123_A_C_ABC1'
self.assertEqual(expected, observed)
def test__get_match_count_if_consensus(self, _, classification, matches,
expected):
observed = ConsensusFileGenerator._get_match_count_if_consensus(
matches, classification)
self.assertEqual(expected, observed)