def test_primer_design_same_first_and_third_Dseqrecord():
from pydna.dseqrecord import Dseqrecord
x = [primer_design(f) for f in frags]
y = assembly_fragments([frags[0], x[1], frags[0]], 20)
z = Assembly(y, limit=20)
result = z.assemble_circular()[0]
assert result.cseguid() == (frags[0] + frags[1]).looped().cseguid()
a = Dseqrecord("ccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatcc",
name="a")
b = Dseqrecord(
"ctgtcgagaaacttgtatccctctaactagtatggatagccgtgtcttcactgtgctgcggctacccatcccaaggacacaatcgagctc",
name="b",
)
z = Assembly((a, b, a), limit=20)
result = z.assemble_linear()[0]
assert (
str(result.seq) ==
"ccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatccctctaactagtatggatagccgtgtcttcactgtgctgcggctacccatcccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatcc"
)
result = z.assemble_circular()[0]
assert result.cseguid() == (frags[0] + frags[1]).looped().cseguid()
def test_primer_Design_with_linker():
''' test_primer_design'''
b = Dseqrecord(
"agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord(
"tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
frags = assembly_fragments((primer_design(b), l, primer_design(c)))
asm1 = Assembly(frags)
assert asm1.assemble_linear()[0].seguid(), (
b + l + c).seguid() == 'l95igKB8iKAKrvvqE9CYksyNx40'
frags = assembly_fragments(
(primer_design(b), l, primer_design(c), primer_design(b)))
b2 = pcr(frags[-1].forward_primer, frags[0].reverse_primer, b)
asm2 = Assembly((b2, frags[1], frags[2]))
assert (b + l +
c).looped().cseguid() == asm2.assemble_circular()[0].cseguid()
assert (b + l + c).looped().cseguid() == 'jdHXfQI5k4Sk2ESiZYfKv4oP2FI'
def test_circular_assembly_fragments2():
x = [primer_design(f) for f in frags]
y = circular_assembly_fragments((frags[0], x[1], x[2]), 20)
z = Assembly(y, limit=20)
result = z.assemble_circular()[0]
assert str(
result.seq
) == "ccaaggacacaatcgagctccgatccgtactgtcgagaaacttgtatccctctaactagtatggatagccgtgtcttcactgtgctgcggctacccatcgtagtgaaacatacacgttgctcgggttcaccccggtccgttctgagtcga"
def test_primer_Design():
''' test_primer_design'''
a = Dseqrecord(
"atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
b = Dseqrecord(
"ccaaacccaccaggtaccttatgtaagtacttcaagtcgccagaagacttcttggtcaagttgcc")
c = Dseqrecord(
"tgtactggtgctgaaccttgtatcaagttgggtgttgacgccattgccccaggtggtcgtttcgtt")
frags = assembly_fragments([primer_design(r) for r in (a, b, c)])
asm = Assembly(frags)
assert asm.assemble_linear()[0].seguid() == "1eNv3d_1PqDPP8qJZIVoA45Www8"
frags = assembly_fragments([primer_design(r) for r in (a, b, c, a)])
a2 = pcr(frags[-1].forward_primer, frags[0].reverse_primer, a)
asm = Assembly((a2, frags[1], frags[2]))
assert asm.assemble_circular()[0].cseguid(
) == "V3Mi8zilejgyoH833UbjJOtDMbc"
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")
from Bio.Restriction import ZraI
pYPKpw_lin = pYPKpw.linearize(ZraI)
asm = Assembly((pYPKpw_lin, p, g, t))
candidate = asm.assemble_circular()[0]
pYPK0_TDH3_FaPDC_TEF1 = candidate.synced(pYPKa)
pYPK0_TDH3_FaPDC_TEF1.write("pYPK0_TDH3_FaPDC_TPI1.gb")
def test_reverse_complement(monkeypatch):
from pydna._pretty import pretty_str
from pydna.assembly import Assembly
from pydna.dseqrecord import Dseqrecord
a = Dseqrecord("acgatgctatactgtgCCNCCtgtgctgtgctcta")
#12345678901234
b = Dseqrecord("tgtgctgtgctctaTTTTTTTtattctggctgtatc")
#123456789012345
c = Dseqrecord("tattctggctgtatcGGGGGtacgatgctatactgtg")
a.name = "aaa" #1234567890123456
b.name = "bbb"
c.name = "ccc"
asm = Assembly((a, b, c), limit=14)
x = asm.assemble_circular()[0]
y = x.rc()
z = y.rc()
assert x.figure() == z.figure()
assert x.detailed_figure() == z.detailed_figure()
xfig = '''\
-|aaa|14
| \\/
| /\\
| 14|bbb|15
| \\/
| /\\
| 15|ccc|16
| \\/
| /\\
| 16-
| |
-----------------------
'''.rstrip()
xdfig = pretty_str('''\
||||||||||||||||
acgatgctatactgtgCCNCCtgtgctgtgctcta
TGTGCTGTGCTCTA
tgtgctgtgctctaTTTTTTTtattctggctgtatc
TATTCTGGCTGTATC
tattctggctgtatcGGGGGtacgatgctatactgtg
ACGATGCTATACTGTG
'''.rstrip() + "\n")
assert x.figure() == xfig
assert x.detailed_figure() == xdfig
yfig = '''\
-|ccc_rc|15
| \\/
| /\\
| 15|bbb_rc|14
| \\/
| /\\
| 14|aaa_rc|16
| \\/
| /\\
| 16-
| |
--------------------------------
'''.rstrip()
ydfig = '''\
||||||||||||||||
cacagtatagcatcgtaCCCCCgatacagccagaata
GATACAGCCAGAATA
gatacagccagaataAAAAAAAtagagcacagcaca
TAGAGCACAGCACA
tagagcacagcacaGGNGGcacagtatagcatcgt
CACAGTATAGCATCGT
'''.rstrip() + "\n"
assert y.figure() == yfig
assert y.detailed_figure() == ydfig
def test_contig(monkeypatch):
monkeypatch.setenv("pydna_cached_funcs", "")
from pydna import contig
from pydna.assembly import Assembly
from pydna.dseqrecord import Dseqrecord
a = Dseqrecord("acgatgctatactgCCCCCtgtgctgtgctcta", name="one")
b = Dseqrecord("tgtgctgtgctctaTTTTTtattctggctgtatc", name="two")
c = Dseqrecord("tattctggctgtatcGGGGGtacgatgctatactg", name="three")
asm = Assembly((a, b, c), limit=14)
cnt = asm.assemble_circular()[0]
assert repr(cnt) == "Contig(o59)"
assert cnt.detailed_figure() == str(
"||||||||||||||\n"
"acgatgctatactgCCCCCtgtgctgtgctcta\n"
" TGTGCTGTGCTCTA\n"
" tgtgctgtgctctaTTTTTtattctggctgtatc\n"
" TATTCTGGCTGTATC\n"
" tattctggctgtatcGGGGGtacgatgctatactg\n"
" ACGATGCTATACTG\n"
)
from textwrap import indent
fig = """ -|one|14
| \\/
| /\\
| 14|two|15
| \\/
| /\\
| 15|three|14
| \\/
| /\\
| 14-
| |
-------------------------"""
cnt2 = asm.assemble_linear()[0]
fig = ('one|14\n'
' \\/\n'
' /\\\n'
' 14|two|15\n'
' \\/\n'
' /\\\n'
' 15|three')
assert fig == cnt2.figure()
assert repr(cnt2) == 'Contig(-73)'
#print(repr(cnt2._repr_html_()))
assert cnt2._repr_html_(
) == '<pre>one|14\n \\/\n /\\\n 14|two|15\n \\/\n /\\\n 15|three</pre>'
from unittest.mock import MagicMock
pp = MagicMock()
cnt2._repr_pretty_(pp, None)
pp.text.assert_called_with('Contig(-73)')
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from pydna.seqrecord import SeqRecord
arg = SeqRecord(Seq("aaa", IUPACAmbiguousDNA()))
import networkx as nx
x = contig.Contig.from_SeqRecord(arg, graph=nx.MultiDiGraph())