def test_concat_alignments(alb_resources, hf):
with pytest.raises(AttributeError) as e:
Alb.concat_alignments(alb_resources.get_one("p o g"), '.*')
assert "Please provide at least two alignments." in str(e)
tester = alb_resources.get_one("o p g")
tester.alignments.append(alb_resources.get_one("o p g").alignments[0])
with pytest.raises(ValueError) as e:
Alb.concat_alignments(tester, 'foo')
assert "No match found for record" in str(e)
with pytest.raises(ValueError) as e:
Alb.concat_alignments(tester, 'Panx')
assert "Replicate matches" in str(e)
tester = Sb.SeqBuddy("%sCnidaria_pep.nexus" % hf.resource_path)
Sb.pull_recs(tester, "Ccr|Cla|Hec")
tester = Alb.AlignBuddy(str(tester))
tester.alignments.append(tester.alignments[0])
assert hf.buddy2hash(Alb.concat_alignments(
Alb.make_copy(tester))) == '32a507107b7dcd044ea7760c8812441c'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)")
assert hf.buddy2hash(tester2) == '5ac908ebf7918a45664a31da480fda58'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)")
assert hf.buddy2hash(tester2) == '5ac908ebf7918a45664a31da480fda58'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...", "Panx.*")
assert hf.buddy2hash(tester2) == 'e754350b0397cf54f531421d1e85774f'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...",
"(P)an(x)(.)")
assert hf.buddy2hash(tester2) == '5c6653aec09489cadcbed68fbd2f7465'
shorten = Alb.delete_records(Alb.make_copy(tester), "Ccr")
tester.alignments[1] = shorten.alignments[1]
assert hf.buddy2hash(Alb.concat_alignments(
Alb.make_copy(tester))) == 'f3ed9139ab6f97042a244d3f791228b6'
def test_concat_alignments(alb_resources, hf):
with pytest.raises(AttributeError) as e:
Alb.concat_alignments(alb_resources.get_one("p o g"), '.*')
assert "Please provide at least two alignments." in str(e)
tester = alb_resources.get_one("o p g")
tester.alignments.append(alb_resources.get_one("o p g").alignments[0])
with pytest.raises(ValueError) as e:
Alb.concat_alignments(tester, 'foo')
assert "No match found for record" in str(e)
with pytest.raises(ValueError) as e:
Alb.concat_alignments(tester, 'Panx')
assert "Replicate matches" in str(e)
tester = Sb.SeqBuddy("%sCnidaria_pep.nexus" % hf.resource_path)
Sb.pull_recs(tester, "Ccr|Cla|Hec")
tester = Alb.AlignBuddy(str(tester))
tester.alignments.append(tester.alignments[0])
assert hf.buddy2hash(Alb.concat_alignments(
Alb.make_copy(tester))) == '32a507107b7dcd044ea7760c8812441c'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)")
assert hf.buddy2hash(tester2) == 'cd2b6594b22c431aea67fa45899f933a'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "(.).(.)-Panx(.)")
assert hf.buddy2hash(tester2) == 'cd2b6594b22c431aea67fa45899f933a'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...", "Panx.*")
assert hf.buddy2hash(tester2) == 'e49b26f695c910a93f93d70563fd9dd9'
tester.set_format("gb")
tester2 = Alb.concat_alignments(Alb.make_copy(tester), "...",
"(P)an(x)(.)")
assert hf.buddy2hash(tester2) == '3abfdf2217050ac2170c0de27352a8c6'
shorten = Alb.delete_records(Alb.make_copy(tester), "Ccr")
tester.alignments[1] = shorten.alignments[1]
assert hf.buddy2hash(Alb.concat_alignments(
Alb.make_copy(tester))) == '685f24ee1fc88860dd9465035040c91e'
def test_delete_records(alb_resources, hf, key, next_hash):
tester = Alb.delete_records(alb_resources.get_one(key), "α[1-5]|β[A-M]")
assert hf.buddy2hash(tester) == next_hash
