def test_editor_with_feature_label(monkeypatch):
import subprocess
from pydna import editor
Popen = mock.MagicMock(name="subprocess.Popen")
monkeypatch.setattr("subprocess.Popen", Popen)
monkeypatch.setenv("pydna_ape", "path/to/ape")
from pydna.dseqrecord import Dseqrecord
argument = Dseqrecord("ggatcc")
argument.add_feature(2, 4, label="lbl")
editor.ape(argument)
assert Popen.called
def test_editor_with_feature_wo_label_and_note(monkeypatch):
import subprocess
from pydna import editor
Popen = mock.MagicMock(name="subprocess.Popen")
monkeypatch.setattr("subprocess.Popen", Popen)
monkeypatch.setenv("pydna_ape", "path/to/ape")
from pydna.dseqrecord import Dseqrecord
argument = Dseqrecord("ggatcc")
argument.add_feature(2, 4)
del argument.features[0].qualifiers["label"]
editor.ape(argument)
assert Popen.called
def test_feature_label():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
t0.add_feature()
f = f0
r = r0
t = t0
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_feature_note():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
t0.add_feature()
del t0.features[0].qualifiers["label"]
t0.features[0].qualifiers["note"] = ["note"]
f = f0
r = r0
t = t0
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
assert pcr(f, r, t).name == "note"
from pydna.dseqrecord import Dseqrecord
from pydna import assembly
from pydna.parsers import parse
from pydna.utils import eq
a = Dseqrecord("ACTACGGCCTTCTCTCCCCCtgtgctgtgctcta", name="one34")
a.add_feature(1, 33, label="first")
b = Dseqrecord("tgtgctgtgctctaTTTTTtattctggctgtatct", name="two35")
b.add_feature(1, 34, label="scnd")
c = Dseqrecord("tattctggctgtatctGGGGGTacgatgctatactgg", name="three37")
c.add_feature(1, 36, label="third")
ln0 = assembly.Assembly((a, b, c), limit=14)
l = ln0.assemble_linear()[0]
assert str(
l.seq
) == 'ACTACGGCCTTCTCTCCCCCtgtgctgtgctctaTTTTTtattctggctgtatctGGGGGTacgatgctatactgg'
a = Dseqrecord("acgatgctatactggCCCCCtgtgctgtgctct", name="one")
b = Dseqrecord("tgtgctgtgctctTTTTTtattctggctgtat", name="two")
c = Dseqrecord("tattctggctgtatGGGGGtacgatgctatactgg", name="three")
c0 = assembly.Assembly((a, b, c), limit=13)
z = c0.assemble_circular()[0]
y = z.rc()
