def test_prepend_primerlist(monkeypatch):
monkeypatch.setenv("pydna_primers", "primers_linux_line_endings.txt")
from pydna import myprimers
from pydna.parsers import parse_primers
from importlib import reload
# >3_primer
# aaaaaaaa
# >2_primer
# cccccccc
# >1_primer
# gggggggg
# >0_primer
# tttttttt
oldlist = myprimers.primerlist()
reload(myprimers)
newlist = parse_primers("""
>abc
aaa
>efg
ttt
""")
np = myprimers.prepend_primerlist(newlist, oldlist)
assert [s.name for s in parse_primers(np)] == ["5_abc", "4_efg"]
def test_too_short_primers():
f, r = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
ann = Anneal((f, r), t, limit=22)
assert ann.report() == (
"Template name 48 nt linear:\n"
"Primer ForwardPrimer anneals forward at position 22\n"
"\n"
"Primer ReversePrimer anneals reverse at position 26")
assert repr(ann) == "Reaction(products = 1)"
p = ann.products[0]
assert str(p.seq) == str(t.seq)
ann = Anneal((f, r), t, limit=23)
assert ann.products == []
assert ann.report() == ("Template name 48 nt linear:\n"
"No forward primers anneal...\n"
"\n"
"No reverse primers anneal...")
assert repr(ann) == "Reaction(products = 0)"
def test_myprimers(monkeypatch):
monkeypatch.setenv("pydna_primers", "primers_linux_line_endings.txt")
from pydna import myprimers
from pydna.parsers import parse_primers
from importlib import reload
reload(myprimers)
newlist = parse_primers("primers_linux_line_endings.txt")[::-1]
primerdict = myprimers.primerdict()
assert len(primerdict) == 4
primer_list = myprimers.primerlist()
assert primer_list == newlist
def test_myprimers(monkeypatch):
monkeypatch.setenv("pydna_primers", "primers_linux_line_endings.txt")
from pydna import myprimers
from pydna.parsers import parse_primers
from importlib import reload
reload(myprimers)
newlist = parse_primers("primers_linux_line_endings.txt")[::-1]
primerdict = myprimers.dict_primers
assert len(primerdict) == 4
primer_list = myprimers.list_primers
assert primer_list == newlist
with pytest.raises(NotImplementedError):
myprimers.append_primer_list("slask")
def test_no_fwdprimer_anneal():
f0, r0 = parse_primers('''>ForwardPrimer
gctact
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = f0
r = r0
t = t0
with pytest.raises(ValueError):
pcr(f, r, t)
def test_string_arguments():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = str(f0.seq)
r = str(r0.seq)
t = str(t0.seq)
assert str(pcr(
(f, r), t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_Primer_arguments():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = f0
r = r0
t = t0
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_Dseq_arguments():
from pydna.dseq import Dseq
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = Dseq(str(f0.seq))
r = Dseq(str(r0.seq))
t = Dseq(str(t0.seq))
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
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_Seq_arguments():
from Bio.Seq import Seq
f0, r0 = parse_primers(""">ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg""")
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = Seq(str(f0.seq))
r = Seq(str(r0.seq))
t = Seq(str(t0.seq))
assert str(pcr(
f, r, t).seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
def test_pcr_not_specific():
f0, r0 = parse_primers(""">ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg""")
t0 = Dseqrecord(
"gctactacacacgtactgactgtgctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
)
f = f0
r = r0
t = t0
with pytest.raises(ValueError):
pcr(f, r, t)
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"
def test_set_primer_footprint():
f, r = parse_primers(""">ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg""")
t = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
ampl = pcr((f, r), t)
assert len(ampl.forward_primer.footprint) == 22
assert len(ampl.reverse_primer.footprint) == 22
ampl.set_forward_primer_footprint(15)
ampl.set_reverse_primer_footprint(15)
assert len(ampl.forward_primer.footprint) == 15
assert len(ampl.reverse_primer.footprint) == 15
def test_Amplicon_argument():
f0, r0 = parse_primers('''>ForwardPrimer
gctactacacacgtactgactg
>ReversePrimer
tgtggttactgactctatcttg''')
t0 = Dseqrecord("gctactacacacgtactgactgcctccaagatagagtcagtaaccaca")
f = f0
r = r0
t = t0
ampl = pcr(f, r, t)
assert str(ampl.seq) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
amplicon_from_amplicon = pcr(ampl)
assert str(amplicon_from_amplicon.seq
) == "gctactacacacgtactgactgcctccaagatagagtcagtaaccaca"
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)
gttctgatcctcgagcatcttaagaattc
>468_pCAPs_release_fw (25-mer)
gtcgaggaacgccaggttgcccact
>467_pCAPs_release_re (31-mer)
ATTTAAatcctgatgcgtttgtctgcacaga
>568_pCAPsAjiIR (22-mer)
GTGCcatctgtgcagacaaacg
>578_crp42-70 (29-mer)
gttcttgtctcattgccacattcataagt''')
p = pcr(p577, p567, pYPKa_Z_prom)
g = pcr(p468, p467, pYPKa_A_saat)
t = pcr(p568, p578, pYPKa_E_term)
pYPKpw = read("pYPKpw.gb")
def test_parse_list():
from pydna.parsers import parse_primers
data = str(">1\n" "aaaa\n" ">2\n" "cccc\n")
parse_primers([data, data])
