def test_dict_two_variants(self):
var1 = Variant('var1')
var2 = Variant('var2')
obj = ValOutput([var1, var2], self.vv)
res = obj.format_as_dict(with_meta=False)
self.assertIsInstance(res, dict)
self.assertEqual(list(res), ['flag', 'validation_warning_1', 'validation_warning_2'])
self.assertEqual(res['flag'], 'warning')
self.assertEqual(res['validation_warning_1']['submitted_variant'], 'var1')
self.assertEqual(res['validation_warning_2']['submitted_variant'], 'var2')
def test_table_intergenic(self):
var1 = Variant('var1')
var1.output_type_flag = 'intergenic'
obj = ValOutput([var1], self.vv)
res = obj.format_as_table(with_meta=False)
print(res)
self.assertIsInstance(res, list)
self.assertEqual(res[1], ['var1', '', None, None, None, None, None, None, None, '', '', '', '', '', '', '',
'', '', '', '', '', '', '', '', '', ''])
self.assertEqual(len(res), 2)
def test_dict_one_intergenic(self):
var1 = Variant('var1')
var1.output_type_flag = 'intergenic'
var2 = Variant('var2')
obj = ValOutput([var1, var2], self.vv)
res = obj.format_as_dict(with_meta=False)
print(res)
self.assertIsInstance(res, dict)
self.assertEqual(list(res), ['flag', 'intergenic_variant_1', 'validation_warning_1'])
self.assertEqual(res['flag'], 'intergenic')
self.assertEqual(res['intergenic_variant_1']['submitted_variant'], 'var1')
self.assertEqual(res['validation_warning_1']['submitted_variant'], 'var2')
def test_dict_one_variant(self):
var = Variant('')
obj = ValOutput([var], self.vv)
res = obj.format_as_dict(with_meta=False)
self.assertIsInstance(res, dict)
self.assertEqual(list(res), ['flag', 'validation_warning_1'])
self.assertEqual(res['flag'], 'warning')
def test_json(self):
var = Variant('')
obj = ValOutput([var], self.vv)
res = obj.format_as_json(with_meta=False)
self.assertIsInstance(res, str)
self.assertIn('"flag": "warning"', res)
self.assertIn('"validation_warning_1": {"selected_assembly": false, "submitted_variant": ""', res)
self.assertEqual(json.loads(res), obj.format_as_dict(with_meta=False))
def test_table_one_gene(self):
var1 = Variant('var1')
var1.output_type_flag = 'gene'
obj = ValOutput([var1], self.vv)
res = obj.format_as_table(with_meta=False)
print(res)
self.assertIsInstance(res, list)
self.assertEqual(res[0], ['Input', 'Warnings', 'Select transcript', 'HGVS_transcript',
'HGVS_intronic_chr_context',
'HGVS_intronic_rsg_context', 'HGVS_RefSeqGene', 'HGVS_LRG',
'HGVS_LRG_transcript', 'HGVS_Predicted_Protein', 'HGVS_Genomic_GRCh37', 'GRCh37_CHR',
'GRCh37_POS', 'GRCh37_ID', 'GRCh37_REF', 'GRCh37_ALT', 'HGVS_Genomic_GRCh38',
'GRCh38_CHR', 'GRCh38_POS', 'GRCh38_ID', 'GRCh38_REF', 'GRCh38_ALT',
'Gene_Symbol', 'HGNC_Gene_ID', 'Transcript_description', 'Alt_genomic_loci'])
self.assertEqual(res[1], ['var1', '', None, None, None, None, None, None, None, '', '', '', '', '', '', '', '',
'', '', '', '', '', '', '', '', ''])
self.assertEqual(len(res), 2)
def test_create_all_init(self):
var = Variant('NM_015120.4:c.34=',
quibble='NM_015120.4:c.34=',
warnings=['Got a warning'],
write=False,
primary_assembly='GRCh37',
order=1)
self.assertEqual(var.quibble, 'NM_015120.4:c.34=')
self.assertEqual(var.warnings, ['Got a warning'])
self.assertFalse(var.write)
self.assertEqual(var.primary_assembly, 'GRCh37')
self.assertEqual(var.order, 1)
def test_dict_one_intergenic_and_one_gene_reversed(self):
var1 = Variant('var1')
var1.output_type_flag = 'intergenic'
var2 = Variant('var2')
var2.output_type_flag = 'gene'
obj = ValOutput([var2, var1], self.vv)
res = obj.format_as_dict(with_meta=False)
print(res)
self.assertIsInstance(res, dict)
self.assertEqual(list(res), ['flag', 'None', 'intergenic_variant_1'])
self.assertEqual(res['flag'], 'intergenic')
self.assertEqual(res['intergenic_variant_1']['submitted_variant'], 'var1')
self.assertEqual(res['None']['submitted_variant'], 'var2')
def test_all_defaults(self):
var = Variant('NM_015120.4:c.34=')
self.assertEqual(var.hgvs_formatted, None)
self.assertEqual(var.hgvs_genomic, None)
self.assertEqual(var.hgvs_coding, None)
self.assertEqual(var.post_format_conversion, None)
self.assertEqual(var.pre_RNA_conversion, None)
self.assertEqual(var.input_parses, None)
self.assertEqual(var.description, '')
self.assertEqual(var.coding, '')
self.assertEqual(var.coding_g, '')
self.assertEqual(var.genomic_r, '')
self.assertEqual(var.genomic_g, '')
self.assertEqual(var.protein, '')
self.assertEqual(var.output_type_flag, 'warning')
self.assertEqual(var.gene_symbol, '')
self.assertEqual(var.timing, {})
self.assertEqual(var.refsource, None)
self.assertEqual(var.reftype, None)
# Normalizers
self.assertEqual(var.hn, None)
self.assertEqual(var.reverse_normalizer, None)
self.assertEqual(var.evm, None)
self.assertEqual(var.no_norm_evm, None)
self.assertEqual(var.min_evm, None)
self.assertEqual(var.lose_vm, None)
# Required for output
self.assertEqual(var.hgvs_transcript_variant, None)
self.assertEqual(var.genome_context_intronic_sequence, None)
self.assertEqual(var.refseqgene_context_intronic_sequence, None)
self.assertEqual(var.hgvs_refseqgene_variant, None)
self.assertEqual(var.hgvs_predicted_protein_consequence, None)
self.assertEqual(var.hgvs_lrg_transcript_variant, None)
self.assertEqual(var.hgvs_lrg_variant, None)
self.assertEqual(var.alt_genomic_loci, None)
self.assertEqual(var.primary_assembly_loci, None)
self.assertEqual(var.reference_sequence_records, None)
self.assertEqual(var.validated, False)
def test_warnings_type_int(self):
var = Variant('NM_015120.4:c.34=', warnings=0)
self.assertEqual(var.warnings, [0])
def test_table_intergenic_warnings(self):
var1 = Variant('var1')
var1.output_type_flag = 'intergenic'
var1.warnings = ['Validation error']
var2 = Variant('var2')
var2.output_type_flag = 'intergenic'
var2.warnings = ['obsolete']
var3 = Variant('var3')
var3.output_type_flag = 'intergenic'
var3.warnings = ['obsolete']
var3.hgvs_transcript_variant = ''
obj = ValOutput([var1, var2, var3], self.vv)
res = obj.format_as_table(with_meta=False)
self.assertIsInstance(res, list)
self.assertEqual(res[1], [
'var1', 'Validation error', None, None, None, None, None, None, '',
'', '', '', '', '', '', '', '', '', '', '', '', '', '', '', ''
])
self.assertEqual(res[2], [
'var2', 'obsolete', None, None, None, None, None, None, '', '', '',
'', '', '', '', '', '', '', '', '', '', '', '', '', ''
])
self.assertEqual(res[3], [
'var3', 'obsolete', '', None, None, None, None, None, '', '', '',
'', '', '', '', '', '', '', '', '', '', '', '', '', ''
])
self.assertEqual(len(res), 4)
def test_dict_each_obsolete(self):
var1 = Variant('var1')
var1.warnings = ['obsolete']
var1.output_type_flag = 'gene'
var2 = Variant('var2')
var2.warnings = ['obsolete']
var2.output_type_flag = 'intergenic'
var3 = Variant('var3')
var3.warnings = ['obsolete']
var4 = Variant('var4')
var4.warnings = ['obsolete']
var4.output_type_flag = 'gene'
var4.hgvs_transcript_variant = ''
obj = ValOutput([var1, var2, var3, var4], self.vv)
res = obj.format_as_dict(with_meta=False)
print(res)
self.assertIsInstance(res, dict)
self.assertEqual(list(res), [
'flag', 'None', 'intergenic_variant_1', 'obsolete_record_1',
'obsolete_record_2'
])
self.assertEqual(res['flag'], 'gene_variant')
self.assertEqual(res['None']['submitted_variant'], 'var1')
self.assertEqual(res['intergenic_variant_1']['submitted_variant'],
'var2')
self.assertEqual(res['obsolete_record_1']['submitted_variant'], 'var3')
self.assertEqual(res['obsolete_record_2']['submitted_variant'], 'var4')
def test_dict_each_with_error_in_warnings(self):
var1 = Variant('var1')
var1.warnings = ['Validation error']
var1.output_type_flag = 'gene'
var2 = Variant('var2')
var2.warnings = ['Validation error']
var2.output_type_flag = 'intergenic'
var3 = Variant('var3')
var3.warnings = ['Validation error']
obj = ValOutput([var1, var2, var3], self.vv)
res = obj.format_as_dict(with_meta=False)
print(res)
self.assertIsInstance(res, dict)
self.assertEqual(list(res), [
'flag', 'validation_error_1', 'intergenic_variant_1',
'validation_error_2'
])
self.assertEqual(res['flag'], 'intergenic')
self.assertEqual(res['validation_error_1']['submitted_variant'],
'var1')
self.assertEqual(res['intergenic_variant_1']['submitted_variant'],
'var2')
self.assertEqual(res['validation_error_2']['submitted_variant'],
'var3')
def test_create(self):
var = Variant('NM_015120.4:c.34=')
self.assertIsInstance(var, Variant)
self.assertEqual(var.original, 'NM_015120.4:c.34=')
def test_order_not_set(self):
var = Variant('NM_015120.4:c.34=')
self.assertEqual(var.order, False)
def test_write_not_set(self):
var = Variant('NM_015120.4:c.34=')
self.assertEqual(var.write, True)
def test_primary_assembly_not_set(self):
var = Variant('NM_015120.4:c.34=')
self.assertEqual(var.primary_assembly, False)
def test_warnings_not_set(self):
var = Variant('NM_015120.4:c.34=')
self.assertEqual(var.warnings, [])
def test_write_type(self):
var = Variant('NM_015120.4:c.34=', write='banana')
self.assertEqual(var.write, 'banana')
class TestMethods(TestCase):
""" Test each method in the Variant Obj"""
def setUp(self):
self.var = Variant('NM_015120.4:c.34=')
def test_is_ascii(self):
self.assertTrue(self.var.is_ascii())
def test_is_ascii_false(self):
self.var.quibble = 'NM_015120.4:c.34=\u0086'
self.assertFalse(self.var.is_ascii())
def test_is_ascii_false2(self):
self.var.quibble = 'NM_015120.4:c.34='
self.assertFalse(self.var.is_ascii())
def test_get_non_ascii(self):
chars, pos = self.var.get_non_ascii()
self.assertEqual(chars, [])
self.assertEqual(pos, [])
def test_get_non_ascii_encoded(self):
self.var.quibble = 'NM_\u0086015120.4:c.34='
chars, pos = self.var.get_non_ascii()
self.assertEqual(chars, [''])
self.assertEqual(pos, [4])
def test_get_non_ascii_decoded(self):
self.var.quibble = 'NM_015120.4:c.34='
chars, pos = self.var.get_non_ascii()
self.assertEqual(chars, [''])
self.assertEqual(pos, [18])
def test_get_non_ascii_pair(self):
self.var.quibble = 'NM_\u0086015120.4:c.34='
chars, pos = self.var.get_non_ascii()
self.assertEqual(chars, ['', ''])
self.assertEqual(pos, [4, 12])
def test_remove_whitespace(self):
self.var.remove_whitespace()
self.assertEqual(self.var.quibble, 'NM_015120.4:c.34=')
def test_remove_whitespace_space(self):
self.var.quibble = 'NM_015120 .4:c. 34='
self.var.remove_whitespace()
self.assertEqual(self.var.quibble, 'NM_015120.4:c.34=')
def test_remove_whitespace_tab(self):
self.var.quibble = 'NM_015120.\t4:c.34 ='
self.var.remove_whitespace()
self.assertEqual(self.var.quibble, 'NM_015120.4:c.34=')
def test_remove_whitespace_newline(self):
self.var.quibble = 'NM_015120.4:c\n.34='
self.var.remove_whitespace()
self.assertEqual(self.var.quibble, 'NM_015120.4:c.34=')
def test_format_quibble(self):
output = self.var.format_quibble()
self.assertEqual(self.var.quibble, 'NM_015120.4:c.34=')
self.assertFalse(output)
def test_format_quibble_brackets(self):
self.var.quibble = 'NM_0151(REMOVE)20.4:c.34='
output = self.var.format_quibble()
self.assertEqual(self.var.quibble, 'NM_015120.4:c.34=')
self.assertFalse(output)
def test_format_quibble_source_fail(self):
self.var.quibble = 'F_015120.4:c.34='
output = self.var.format_quibble()
self.assertTrue(output)
self.assertEqual(self.var.quibble, 'F_015120.4:c.34=')
def test_format_quibble_type_fail(self):
self.var.quibble = 'NM_015120.4:w.34='
output = self.var.format_quibble()
self.assertTrue(output)
self.assertEqual(self.var.quibble, 'NM_015120.4:w.34=')
def test_set_reftype(self):
self.var.set_reftype()
self.assertEqual(self.var.reftype, ':c.')
def test_set_reftype_rna(self):
self.var.quibble = 'NM_015120.4:r.34='
self.var.set_reftype()
self.assertEqual(self.var.reftype, ':r.')
def test_set_reftype_nucl(self):
self.var.quibble = 'NM_015120.4:n.34='
self.var.set_reftype()
self.assertEqual(self.var.reftype, ':n.')
def test_set_reftype_mito(self):
self.var.quibble = 'NM_015120.4:m.34='
self.var.set_reftype()
self.assertEqual(self.var.reftype, ':m.')
def test_set_reftype_genome(self):
self.var.quibble = 'NM_015120.4:g.34='
self.var.set_reftype()
self.assertEqual(self.var.reftype, ':g.')
def test_set_reftype_prot(self):
self.var.quibble = 'NM_015120.4:p.34='
self.var.set_reftype()
self.assertEqual(self.var.reftype, ':p.')
def test_set_reftype_est(self):
self.var.quibble = 'NM_015120.4:3.34='
self.var.set_reftype()
self.assertEqual(self.var.reftype, 'est')
def test_set_reftype_none(self):
self.var.quibble = 'NM_015120.4:.34='
with self.assertRaises(VariantValidatorError):
self.var.set_reftype()
def test_set_source(self):
self.var.set_refsource()
self.assertEqual(self.var.refsource, 'RefSeq')
def test_set_source_refseq_min(self):
self.var.quibble = 'N'
self.var.set_refsource()
self.assertEqual(self.var.refsource, 'RefSeq')
def test_set_source_lrg(self):
self.var.quibble = 'LRG_015120.4:c.34='
self.var.set_refsource()
self.assertEqual(self.var.refsource, 'LRG')
def test_set_source_lrg_min(self):
self.var.quibble = 'LRG'
self.var.set_refsource()
self.assertEqual(self.var.refsource, 'LRG')
def test_set_source_ens(self):
self.var.quibble = 'ENSG_015120.4:c.34='
self.var.set_refsource()
self.assertEqual(self.var.refsource, 'ENS')
def test_set_source_ens_min(self):
self.var.quibble = 'ENS'
self.var.set_refsource()
self.assertEqual(self.var.refsource, 'ENS')
def test_set_source_none(self):
self.var.quibble = 'SOMETHING ELSE'
with self.assertRaises(VariantValidatorError):
self.var.set_refsource()
def test_set_quibble(self):
self.var.set_quibble('New:c.var')
self.assertEqual(self.var.quibble, 'New:c.var')
self.assertEqual(self.var.refsource, 'RefSeq')
self.assertEqual(self.var.reftype, ':c.')
def test_is_obsolete(self):
self.assertFalse(self.var.is_obsolete())
def test_is_obsolete_false(self):
self.var.warnings = ['Nearly obso', 'lete']
self.assertFalse(self.var.is_obsolete())
def test_is_obsolete_true(self):
self.var.warnings = ['obsoleteANDother']
self.assertTrue(self.var.is_obsolete())
def test_process_warnings(self):
output = self.var.process_warnings()
self.assertIsInstance(output, list)
self.assertEqual(output, [])
def test_process_warnings_sub(self):
self.var.warnings = ['variantdelATGCTAGCTA']
output = self.var.process_warnings()
self.assertEqual(output, ['variantdel'])
def test_process_warnings_sub_not(self):
self.var.warnings = ['variantdelATG']
output = self.var.process_warnings()
self.assertEqual(output, ['variantdelATG'])
def test_process_warnings_strip(self):
self.var.warnings = [' warning ']
output = self.var.process_warnings()
self.assertEqual(output, ['warning'])
def test_process_warnings_replace(self):
self.var.warnings = ['\'warning\'']
output = self.var.process_warnings()
self.assertEqual(output, ['warning'])
def test_process_warnings_unique(self):
self.var.warnings = ['one', 'two', 'one']
output = self.var.process_warnings()
self.assertEqual(output, ['one', 'two'])
def test_output_dict_empty(self):
output = self.var.output_dict()
self.assertIsInstance(output, dict)
self.assertEqual(
output, {
'submitted_variant': 'NM_015120.4:c.34=',
'gene_ids': None,
'gene_symbol': '',
'transcript_description': '',
'hgvs_transcript_variant': None,
'genome_context_intronic_sequence': None,
'refseqgene_context_intronic_sequence': None,
'hgvs_refseqgene_variant': None,
'hgvs_predicted_protein_consequence': None,
'validation_warnings': [],
'hgvs_lrg_transcript_variant': None,
'hgvs_lrg_variant': None,
'alt_genomic_loci': None,
'primary_assembly_loci': None,
'reference_sequence_records': None,
})
def test_output_dict_set(self):
self.var.gene_symbol = 'Symbol'
self.var.description = 'Desc'
self.var.stable_gene_ids = 'My_id'
self.var.hgvs_transcript_variant = 'hgvsvar'
self.var.genome_context_intronic_sequence = 'gintronic'
self.var.refseqgene_context_intronic_sequence = 'rintronic'
self.var.hgvs_refseqgene_variant = 'refseq'
self.var.hgvs_predicted_protein_consequence = 'prot'
self.var.warnings = ['warning']
self.var.hgvs_lrg_transcript_variant = 'lrgT'
self.var.hgvs_lrg_variant = 'lrg'
self.var.alt_genomic_loci = 'alt'
self.var.primary_assembly_loci = 'primary'
self.var.reference_sequence_records = 'records'
output = self.var.output_dict()
self.assertIsInstance(output, dict)
self.assertEqual(
output, {
'submitted_variant': 'NM_015120.4:c.34=',
'gene_symbol': 'Symbol',
'gene_ids': 'My_id',
'transcript_description': 'Desc',
'hgvs_transcript_variant': 'hgvsvar',
'genome_context_intronic_sequence': 'gintronic',
'refseqgene_context_intronic_sequence': 'rintronic',
'hgvs_refseqgene_variant': 'refseq',
'hgvs_predicted_protein_consequence': 'prot',
'validation_warnings': ['warning'],
'hgvs_lrg_transcript_variant': 'lrgT',
'hgvs_lrg_variant': 'lrg',
'alt_genomic_loci': 'alt',
'primary_assembly_loci': 'primary',
'reference_sequence_records': 'records',
})
def test_warnings_type(self):
var = Variant('NM_015120.4:c.34=', warnings='string')
self.assertEqual(var.warnings, ['string'])
def test_quibble_not_set(self):
var = Variant('NM_015120.4:c.34=')
self.assertEqual(var.quibble, 'NM_015120.4:c.34=')
def test_quibble_type(self):
var = Variant('NM_015120.4:c.34=', quibble=0)
self.assertEqual(var.quibble, 0)
def setUp(self):
self.var = Variant('NM_015120.4:c.34=')
