def assemble(self, assemblies):
primer_builder = ExtractionPrimerBuilder()
for assembly in assemblies:
part_records = []
part_amplicons = []
for part_node in assembly.parts:
part = part_node.part
part_amplicon, part_seq_record = primer_builder.design_primer_for_part(part)
part_records.append(part_seq_record)
part_amplicons.append(part_amplicon)
fragments = assembly_fragments(part_amplicons)
for idx in range(len(fragments)):
fragments[idx].locus = part_records[idx].name
#print(fragments)
assemblyobj = Assembly(
fragments,
limit=20)
linear_contigs = assemblyobj.assemble_linear()
if len(linear_contigs) != 1:
raise Exception(
'%s resulted in %d contigs. We were hoping for just one.' % (
len(linear_contigs)
))
assembly.contig = linear_contigs[0]
#print(assembly.contig.figure())
return assemblies
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_primer_design_four_fragments():
x = [primer_design(f) for f in frags]
fourth = Dseqrecord("TAAAAATAAAATTGTTGACAGCAGAAGTGATATAGAAATTTGTTAATTATTA")
y = assembly_fragments(x + [fourth], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + frags[2] + fourth).seq
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():
''' 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"
def test_primer_design_linker_first():
x = [primer_design(f) for f in frags]
y = assembly_fragments([bam, x[0], x[1], x[2]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (bam + frags[0] + frags[1] + frags[2]).seq
def test_primer_design_first_and_third_Dseqrecord():
x = [primer_design(f) for f in frags]
y = assembly_fragments([frags[0], x[1], frags[2]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + frags[2]).seq
def test_primer_design_all_pcr_products():
x = [primer_design(f) for f in frags]
y = assembly_fragments(x, 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + frags[2]).seq
def test_primer_design_two_fragments_flanking_linkers():
x = [primer_design(f) for f in frags]
y = assembly_fragments([bam, x[0], x[1], bam], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (bam + frags[0] + frags[1] + bam).seq
def test_primer_design_two_fragments_linker_in_between(): #
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], bam, x[1]], 20, 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + bam + frags[1]).seq
def test_primer_design_two_fragments():
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], x[1]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1]).seq
def test_primer_design_linker_second_before_Dseqrecord():
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], bam, frags[1], x[2]], 20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + bam + frags[1] + frags[2]).seq
def test_primer_design_linker_third(): #
x = [primer_design(f) for f in frags]
y = assembly_fragments([x[0], x[1], bam, x[2]], maxlink=6, overlap=20)
z = Assembly(y, limit=20)
result = z.assemble_linear()[0]
assert result.seq == (frags[0] + frags[1] + bam + frags[2]).seq
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())