def test_genbank_function_set_email(monkeypatch):
from pydna.genbank import Genbank
mock_Gb = mock.MagicMock()
monkeypatch.setenv("pydna_cached_funcs", "")
monkeypatch.setenv("pydna_email", "*****@*****.**")
monkeypatch.setattr("pydna.genbank.Genbank", mock_Gb)
from pydna.genbank import genbank
s=genbank("X60065")
mock_Gb.assert_called_with("*****@*****.**")
from pydna.genbank import genbank
from pydna.design import primer_design
from pydna.amplify import pcr
from pydna.readers import read
from pydna.parsers import parse_primers
from pydna.assembly import Assembly
from pydna.gel import Gel
###############################################################################
saat = genbank("AF193791 REGION: 78..1895")
saat_pcr_prod = primer_design(saat)
pYPKa=read("pYPKa.gb")
from Bio.Restriction import AjiI
pYPKa_AjiI = pYPKa.linearize(AjiI)
pYPKa_A_saat = ( pYPKa_AjiI + saat_pcr_prod ).looped()
pYPKa_Z_prom = read("pYPKa_Z_TEF1.gb")
pYPKa_E_term = read("pYPKa_E_TPI1.gb")
p567,p577,p468,p467,p568,p578 = parse_primers('''
>567_pCAPsAjiIF (23-mer)
GTcggctgcaggtcactagtgag
>577_crp585-557 (29-mer)
pYPKa = read("pYPKa.gb")
pYPKa_Z = pYPKa.linearize(ZraI)
pYPKa_A = pYPKa.linearize(AjiI)
pYPKa_E = pYPKa.linearize(EcoRV)
bbdict = {"Z": pYPKa_Z, "A": pYPKa_A, "E": pYPKa_E}
fdict = {"Z": "promoter", "A": "gene", "E": "terminator"}
csvfile = "promoter_list_003.csv"
with open(csvfile) as csvfile:
reader = csv.reader(csvfile)
for row in reader:
ins, letter, pf, pr, template, comment = row
temp = genbank(template)
insert = pcr(p[int(pf)], p[int(pr)], temp)
label = f"{ins}_promoter"
if letter == "Z":
insert.add_feature(type="promoter",
name=label,
ApEinfo_label=label,
ApEinfo_fwdcolor="#FC6600",
ApEinfo_revcolor="#7C4700",
fp=p[int(pf)].format("tab").strip(),
rp=p[int(pr)].format("tab").strip(),
reference=template)