def test_protein_subsequence_does_not_overlap_substitution():
# testing that we got the correct properties for case where "SIINFEKL" was
# mutated into "SIINFEQL" and then sliced to keep just "FEQL"
p = ProteinSequence(amino_acids="SIINFEQL",
contains_mutation=True,
mutation_start_idx=len("SIINFE"),
mutation_end_idx=len("SIINFEQ"),
ends_with_stop_codon=True,
frameshift=False,
translations=[])
p2 = p.subsequence(0, len("SIIN"))
eq_(p2.amino_acids, "SIIN")
eq_(p2.contains_mutation, False)
eq_(p2.contains_deletion, False)
eq_(p2.frameshift, False)
eq_(p2.ends_with_stop_codon, False)
eq_(p2.num_mutant_amino_acids, 0)
eq_(p2.mutant_amino_acids, "")
eq_(len(p2), 4)
def test_protein_subsequence_does_not_overlap_deletion():
# testing that we got correct properties for the case
# where "SIINFEKL" was mutated into "SIINFEL" (by a deletion of "K")
# and then we took the subsequence "SIINFE"
p = ProteinSequence(amino_acids="SIINFEL",
contains_mutation=True,
mutation_start_idx=len("SIINFE"),
mutation_end_idx=len("SIINFE"),
ends_with_stop_codon=True,
frameshift=False,
translations=[])
p2 = p.subsequence(None, len("SIINFE"))
eq_(len(p2), 6)
eq_(p2.amino_acids, "SIINFE")
eq_(p2.contains_deletion, False)
eq_(p2.contains_mutation, False)
eq_(p2.frameshift, False)
eq_(p2.ends_with_stop_codon, False)
eq_(p2.mutant_amino_acids, "")
eq_(p2.num_mutant_amino_acids, 0)