def test_invalid_line_ordered_chr(self):
vep_input_format_validator.previous_line = "5 130500 130500 G/C +"
vep_input_format_validator.chrs_seen = { '5' : 1, '8' : 1 }
line = "8 500255 500255 C/T +"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_ordered_chr - Variants not ordered by chromosome block")
self.assertEqual(report, "Not ordered: this entry on chromosome '8' is not ordered in the chromosome '8' block")
def test_valid_line_ordered(self):
vep_input_format_validator.previous_line = "5 130500 130500 G/C +"
vep_input_format_validator.chrs_seen = { '5' : 1 }
line = "5 140532 140532 T/C +"
report = vep_input_format_validator.check_line(line)
print("\n> test_valid_line_ordered - Variants ordered by location")
self.assertEqual(report, '')
def test_invalid_line_ordered(self):
vep_input_format_validator.previous_line = "5 130500 130500 G/C +"
vep_input_format_validator.chrs_seen = { '5' : 1 }
line = "5 120500 120500 A/G +"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_ordered - Variants not ordered by location")
self.assertEqual(report, 'Not ordered: 5:120500 vs previous line 5:130500')
def test_invalid_line_allele_length(self):
line = "3 319781 319782 A/- +"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_allele_length - allele length don't match the given coordinates")
self.assertEqual(report, "Allele length don't match the given coordinates")
def test_valid_line(self):
line = "5 140532 140532 T/C +"
report = vep_input_format_validator.check_line(line)
print("\n> test_valid_line - test a valid line")
self.assertEqual(report, '')
def test_valid_line_insertion(self):
line = "1 881907 881906 -/C +"
report = vep_input_format_validator.check_line(line)
print("\n> test_valid_line_insertion - Test a valid line with variant insertion")
self.assertEqual(report, '')
def test_invalid_line_insertion(self):
line = "1 881906 881906 -/C +"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_insertion - for insertion, the start coordinate should be greater than the end coordinate")
self.assertEqual(report, "For insertion, the start coordinate should be greater than the end coordinate")
def test_invalid_line_allele_no_ref(self):
line = "5 140532 140532 /C +"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_allele_no_ref - missing reference allele")
self.assertEqual(report, "Allele '/C' is not in the supported format 'REF/ALT' (e.g. A/C), except for structural variants")
def test_invalid_line_allele_no_alt_2(self):
line = "5 140532 140532 T/ +"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_allele_no_alt_2 - missing alternative allele after '/'")
self.assertEqual(report, "Allele 'T/' is not in the supported format 'REF/ALT' (e.g. A/C), except for structural variants")
def test_invalid_line_allele_char(self):
line = "5 140532 140532 T/0 +"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_allele_char - for insertion, the start coordinate should be greater than the end coordinate")
self.assertEqual(report, "Non supported characters in the allele 'T/0'")
def test_valid_line_allele_sv_char(self):
line = "5 140532 140834 DEL +"
report = vep_input_format_validator.check_line(line)
print("\n> test_valid_line_allele_sv_char - test a valid SV entry")
self.assertEqual(report, '')
def test_invalid_line_strand(self):
line = "3 319781 319782 A/- f"
report = vep_input_format_validator.check_line(line)
print("\n> test_invalid_line_strand - strand value/character not supported")
self.assertEqual(report, "Strand is not in the expected format (+ or -)")