def test_primer_Design_given_both_primers():
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
with pytest.raises(ValueError):
primer_design(b,
fp=Primer("agctactgactattag"),
rp=Primer("tagatcagtacagtca"))
def test_amplicon_dbd_low_gc():
from pydna.amplify import Anneal
from pydna.dseqrecord import Dseqrecord
from pydna.primer import Primer
from textwrap import dedent
template = Dseqrecord("AAAATATTTTTATACATAATACAATTGTATATTCTTAAATAAAAAATACGTCATC")
p1 = Primer("AAAATATTTTTATACAT")
p2 = Primer("GATGACGTATTTTTTAT")
ann = Anneal((p1,p2),template)
prod = ann.products[0]
assert repr(prod) == 'Amplicon(55)'
fig =( r'''
Pfu-Sso7d (rate 15s/kb) |55bp
Three-step| 30 cycles | |Tm formula: Pydna tmbresluc
98.0°C |98.0°C | |SaltC 50mM
__________|_____ 72.0°C |72.0°C|Primer1C 1.0µM
00min30s |10s \ 39.0°C ________|______|Primer2C 1.0µM
| \______/ 0min 0s|10min |GC 14%
| 10s | |4-12°C
'''[1:])
fig = dedent(fig)
assert str(prod.pfu_sso7d_program()) == fig
def test_amplicon_dbd():
from pydna.amplify import Anneal
from pydna.dseqrecord import Dseqrecord
from pydna.primer import Primer
from textwrap import dedent
template = Dseqrecord("GCGTCCAGCGGCTGCCCGAGGCGCCAAGTGCCCGGGCCGAGCCCGCATCTGAGGCCGCCGCGGGC")
p1 = Primer("GCGTCCAGCGGCTGCCCGAGG")
p2 = Primer("GCCCGCGGCGGCCTCAGATGCGG")
ann = Anneal((p1,p2),template)
prod = ann.products[0]
assert repr(prod) == 'Amplicon(65)'
fig =( r'''
Pfu-Sso7d (rate 15s/kb)
Two-step| 30 cycles | |65bp
98.0°C |98.0C | |Tm formula: Pydna tmbresluc
_____ __|_____ | |SaltC 50mM
00min30s|10s \ | |Primer1C 1.0µM
| \ 72.0°C|72.0°C|Primer2C 1.0µM
| \______|______|GC 81%
| 0min 0s|10min |4-12°C
'''[1:])
fig = dedent(fig)
assert str(prod.pfu_sso7d_program()) == fig
def test_amplicon():
from pydna.amplify import Anneal
from pydna.dseqrecord import Dseqrecord
from pydna.primer import Primer
template = Dseqrecord("AAAtacactcaccgtctatcattatctactatcgactgtatcatctgatagcacTTT")
p1 = Primer("CCCtacactcaccgtctatcattatc")
p2 = Primer("GGGgtgctatcagatgatacagtcg")
ann = Anneal((p1,p2),template)
prod = ann.products[0]
assert repr(prod) == 'Amplicon(57)'
assert prod._repr_html_() == 'Amplicon(57)'
from unittest.mock import MagicMock
pp = MagicMock()
prod._repr_pretty_(pp, None)
#assert pp.text.assert_called_with('Amplicon(57)')
fig=''' 5tacactcaccgtctatcattatc...cgactgtatcatctgatagcac3
|||||||||||||||||||||| tm 55.9 (dbd) 60.5
3gctgacatagtagactatcgtgGGG5
5CCCtacactcaccgtctatcattatc3
||||||||||||||||||||||| tm 54.6 (dbd) 58.8
3atgtgagtggcagatagtaatag...gctgacatagtagactatcgtg5'''
import textwrap
assert prod.figure() == textwrap.dedent(fig)
assert prod.program() == prod.taq_program()
assert prod.pfu_sso7d_program() == prod.dbd_program()
from pydna.amplicon import Amplicon
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from pydna.seqrecord import SeqRecord
arg = SeqRecord(Seq("aaa", IUPACAmbiguousDNA()))
x = Amplicon.from_SeqRecord(arg)
from pydna.design import primer_design
from pydna.dseqrecord import Dseqrecord
t = Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
from pydna.primer import Primer
pf = Primer("atgactgctaacccttccttggtg")
print(pf.name)
ampl = primer_design(t, fp=pf)
print(ampl.forward_primer.name)
def test_primer_Design_given_rv_primer():
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
a = primer_design(b, rp=Primer("tagatcagtacagtca"))
assert str(a.forward_primer.seq) == 'agctactgactattag' #g
def test_primer_Design_given_fw_primer():
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
a = primer_design(b, fp=Primer("agctactgactattag"))
assert str(a.reverse_primer.seq) == 'tagatcagtacagtca'