def test_mutation_space():
loc1, seqs1 = (0, 2), ["AT", "TG"]
loc2, seqs2 = (2, 5), ["TTC", "TTA", "TTT"]
c1 = MutationChoice(loc1, seqs1)
c2 = MutationChoice(loc2, seqs2)
space = MutationSpace([c1, c1, c2, c2, c2])
loc, seq = space.pick_random_mutations(n_mutations=1, sequence="ATTTC")[0]
assert loc in [loc1, loc2]
assert seq in (seqs1 + seqs2)
def test_mutation_space():
loc1, seqs1 = (0, 2), ['AT', 'TG']
loc2, seqs2 = (2, 5), ['TTC', 'TTA', 'TTT']
c1 = MutationChoice(loc1, seqs1)
c2 = MutationChoice(loc2, seqs2)
space = MutationSpace([c1, c1, c2, c2, c2])
loc, seq = space.pick_random_mutations(n_mutations=1, sequence='ATTTC')[0]
assert loc in [loc1, loc2]
assert seq in (seqs1 + seqs2)
def test_mutation_choice_extract_varying_region():
choice = MutationChoice((5, 12), [
'ATGCGTG',
'AAAAATG',
'AAATGTG',
'ATGAATG',
])
choices = choice.extract_varying_region()
assert [c.segment for c in choices] == [(5, 6), (6, 10), (10, 12)]
choice = MutationChoice((5, 12), [
'TAGCGTG',
'AAAAATG',
'AAATGTG',
'ATGAATG',
])
choices = choice.extract_varying_region()
assert [c.segment for c in choices] == [(5, 10), (10, 12)]
choice = MutationChoice((5, 12), [
'ATGCGTG',
'AAAAACC',
'AAATGTG',
'ATGAATG',
])
choices = choice.extract_varying_region()
assert [c.segment for c in choices] == [(5, 6), (6, 12)]
def test_mutation_choice_io():
choice = MutationChoice((5, 12), [
'ATGCGTG',
'AAAAACC',
'AAATGTG',
'ATGAATG',
])
assert 'ATGCGTG-AAAAACC-AAATGTG-ATGAATG' in str(choice)
def test_mutation_choice_io():
choice = MutationChoice((5, 12),
["ATGCGTG", "AAAAACC", "AAATGTG", "ATGAATG"])
assert "ATGCGTG-AAAAACC-AAATGTG-ATGAATG" in str(choice)
import seqspace
from dnachisel.MutationSpace import MutationSpace, MutationChoice
loc1, seqs1 = (0, 2), ["AT", "TG"]
loc2, seqs2 = (2, 5), ["TTC", "TAA", "GGG"]
loc3, seqs3 = (5, 6), ["T"]
c1 = MutationChoice(loc1, seqs1)
c2 = MutationChoice(loc2, seqs2)
c3 = MutationChoice(loc3, seqs3)
space = MutationSpace([c1, c1, c2, c2, c2, c3])
# SeqSpace class tests:
def test_get_string():
seq_space = seqspace.SeqSpace(space, "test_seq")
assert seq_space.get_string() == "AT,TG|TTC,TAA,GGG|T|"
def test_make_filetext():
seq_space = seqspace.SeqSpace(space, "test_seq")
assert seq_space.make_filetext() == ">test_seq\nAT,TG|TTC,TAA,GGG|T|\n"
# SeqSpace functions:
def test_make_aa_to_codon_backtable():
codontable = {
"TTT": "F",
"TTC": "F",
"TTA": "L",
"TTG": "L",