def test_basic_conversion(self):
old = Prepeptide(FeatureLocation(5, 95),
peptide_class="test_class",
core="coreseq...",
locus_tag="loc",
tool="test tool",
peptide_subclass="test_subclass",
score=20.4,
monoisotopic_mass=6.7,
molecular_weight=0.5,
alternative_weights=[5.2, 6.7, 20.5],
leader="leaderseq.",
tail="tailseq...")
leader, core, tail = old.to_biopython()
assert leader.location.start == 5
assert leader.location.end == 35
assert leader.qualifiers["prepeptide"] == ["leader"]
assert core.location.start == 35
assert core.location.end == 65
assert core.qualifiers["prepeptide"] == ["core"]
assert tail.location.start == 65
assert tail.location.end == 95
assert tail.qualifiers["prepeptide"] == ["tail"]
with self.assertRaisesRegex(
ValueError, "can only be reconstructed from core feature"):
Prepeptide.from_biopython(leader)
with self.assertRaisesRegex(
ValueError, "can only be reconstructed from core feature"):
Prepeptide.from_biopython(tail)
new = Prepeptide.from_biopython(core)
assert isinstance(new, Prepeptide)
assert str(new.location) == str(old.location)
assert new.peptide_class == old.peptide_class
assert new.core == old.core
assert new.locus_tag == old.locus_tag
assert new.peptide_subclass == old.peptide_subclass
assert new.score == old.score
assert new.monoisotopic_mass == old.monoisotopic_mass
assert new.molecular_weight == old.molecular_weight
assert new.alternative_weights == old.alternative_weights
assert new.leader == old.leader
assert new.tail == old.tail
def test_compound_location(self):
old = Prepeptide(CompoundLocation(
[FeatureLocation(10, 50, 1),
FeatureLocation(130, 180, 1)],
operator="join"),
peptide_class="test_class",
core="coreseq...",
locus_tag="loc",
tool="test tool",
leader="10chleader",
tail="10chartail")
leader, core, tail = old.to_biopython()
assert leader.location.start == 10
assert leader.location.end == 40
assert isinstance(core.location, CompoundLocation)
assert core.location.start == 40
assert core.location.end == 150
assert tail.location.start == 150
assert tail.location.end == 180
new = Prepeptide.from_biopython(core)
assert str(new.location) == str(old.location)