def test_primer_Design():
''' test_primer_design'''
a=Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
b=Dseqrecord("ccaaacccaccaggtaccttatgtaagtacttcaagtcgccagaagacttcttggtcaagttgcc")
c=Dseqrecord("tgtactggtgctgaaccttgtatcaagttgggtgttgacgccattgccccaggtggtcgtttcgtt")
primer_pairs = assembly_primers([a,b,c])
frags=[]
for (f,r),t in zip(primer_pairs,[a,b,c]):
frags.append(pcr(f,r,t))
asm=Assembly(frags)
assert asm.linear_products[0].seguid() == "1eNv3d_1PqDPP8qJZIVoA45Www8"
frags=[]
primer_pairs = assembly_primers([a,b,c], circular=True)
for (f,r),t in zip(primer_pairs,[a,b,c]):
frags.append(pcr(f,r,t))
#print frags
asm=Assembly(frags)
assert asm.circular_products[0].cseguid() == "V3Mi8zilejgyoH833UbjJOtDMbc"
def test_primer_Design_with_linker(self):
''' test_primer_design'''
from pydna import Dseqrecord, Assembly, pcr, assembly_primers
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c))
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm1 = Assembly((nb,nc))
self.assertEqual(asm1.linear_products[0].seguid(),(b+l+c).seguid(),'l95igKB8iKAKrvvqE9CYksyNx40')
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c), circular = True)
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm = Assembly((nb,nc))
self.assertEqual((b+l+c).looped().cseguid(), asm.circular_products[0].cseguid(), 'qMEHxKkTsWIXkbqGA5O35631eMU')
def test_primer_Design_with_linker():
''' test_primer_design'''
from pydna import Dseqrecord, Assembly, pcr, assembly_primers
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c))
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm1 = Assembly((nb,nc))
assert asm1.linear_products[0].seguid(),(b+l+c).seguid() == 'l95igKB8iKAKrvvqE9CYksyNx40'
b = Dseqrecord("agctactgactattaggggttattctgatcatctgatctactatctgactgtactgatcta")
l = Dseqrecord("AAATTTCCCGGG")
c = Dseqrecord("tctgatctactatctgactgtactgatctattgacactgtgatcattctagtgtattactc")
((bf,br),(cf,cr)) = assembly_primers((b,l,c), circular = True)
nb = pcr((bf,br),b)
nc = pcr((cf,cr),c)
asm = Assembly((nb,nc))
#print (b+l+c).looped().seq
assert (b+l+c).looped().cseguid() == asm.circular_products[0].cseguid()
#print (b+l+c).looped().cseguid() == 'jdHXfQI5k4Sk2ESiZYfKv4oP2FI'
assert (b+l+c).looped().cseguid() == 'jdHXfQI5k4Sk2ESiZYfKv4oP2FI'
# import pydna
# template = pydna.read(">t\ntacactcaccgtctatcattatctactatcgactgtatcatctgatagcac")
# p1 = pydna.read(">p1\ntacactcaccgtctatcattatc", ds = False)
# p2 = pydna.read(">p2\ngtgctatcagatgatacagtcg", ds = False)
# ann = pydna.Anneal((p1, p2), template)
import pydna
a = pydna.Dseqrecord("atgactgctaacccttccttggtgttgaacaagatcgacgacatttcgttcgaaacttacgatg")
b = pydna.Dseqrecord(
"ccaaacccaccaggtaccttatgtaagtacttcaagtcgccagaagacttcttggtcaagttgcc"
)
c = pydna.Dseqrecord(
"tgtactggtgctgaaccttgtatcaagttgggtgttgacgccattgccccaggtggtcgtttcgtt"
)
primer_pairs = pydna.assembly_primers([a, b, c], circular=True)
p = []
for t, (f, r) in zip([a, b, c], primer_pairs):
p.append(pydna.pcr(f, r, t))
obj = pydna.Assembly(p)
# print(assemblyobj)
# @memorize("function")
# def times_two(n):
# return n*2
#
# @memorize("method")
# class Doubler(object):
# def __init__(self, n):
# self.n=n
# self.key=str(n)