def toDSEQ(self, graph, edges, nodes):
complements = self.generateComplements(nodes)
dna = []
offset = -10
for edge in edges:
seq = Dseq(edges[edge], complements[edge[1]], ovhg=offset)
x = Dseqrecord(seq)
x.name = edge[0] + "_" + edge[1]
x.seq = seq
dna.append(x)
return dna
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
