In [1]:

    

from pydna.amplify  import pcr
from pydna.parsers  import parse
from pydna.readers  import read
from pydna.genbank  import Genbank
from pydna.assembly import Assembly
from pydna.dseqrecord import Dseqrecord
import ipynb


    

In [2]:

    

p567,p577,p468,p467,p568,p578,p775,p778,p167,p166 = parse("yeast_pahtway_kit_standard_primers.txt")


    

In [3]:

    

from Bio.Restriction import ZraI, AjiI, EcoRV


    

In [4]:

    

pYPKpw = read("pYPKpw.gb")


    

In [5]:

    

pYPKpw_lin = pYPKpw.linearize(EcoRV)


    

In [6]:

    

from ipynb.fs.full.pYPKa_Z_PGI1 import pYPKa_Z_PGI1 as first


    

    





pYPKa_Z_PGI1.gb

In [7]:

    

middle = read("pYPKa_A_CiGXF1.gb")


    

In [8]:

    

from ipynb.fs.full.pYPKa_E_TDH3 import pYPKa_E_TDH3 as last


    

    




ATAAAAAACACGCTTTTTCAGTTCGAGTTTATCATTATCAATACTGCCATTTCAAAGAATACGTAAATAATTAATAGTAGTGATTTTCCTAACTTTATTTAGTCAAAAAATTAGCCTTTTAATTCTGCTGTAACCCGTACATGCCCAAAATAGGGGGCGGGTTACACAGAATATATAACATCGTAGGTGTCTGGGTGAACAGTTTATTCCTGGCATCCACTAAATATAATGGAGCCCGCTTTTTAAGCTGGCATCCAGAAAAAAAAAGAATCCCAGCACCAAAATATTGTTTTCTTCACCAACCATCAGTTCATAGGTCCATTCTCTTAGCGCAACTACAGAGAACAGGGGCACAAACAGGCAAAAAACGGGCACAACCTCAATGGAGTGATGCAACCTGCCTGGAGTAAATGATGACACAAGGCAATTGACCCACGCATGTATCTATCTCATTTTCTTACACCTTCTATTACCTTCTGCTCTCTCTGATTTGGAAAAAGCTGAAAAAAAAGGTTGAAACCAGTTCCCTGAAATTATTCCCCTACTTGACTAATAAGTATATAAAGACGGTAGGTATTGATTGTAATTCTGTAAATCTATTTCTTAAACTTCTTAAATTCTACTTTTATAGTTAGTCTTTTTTTTAGTTTTAAAACACCAAGAACTTAGTTTCGAATAAACACACATAAACAAACAAA






    





pYPKa_E_TDH3.gb

In [9]:

    

first  = pcr( p577, p567, first)
middle = pcr( p468, p467, middle)
last   = pcr( p568, p578, last)


    

In [10]:

    

asm = Assembly((pYPKpw_lin, first, middle, last), limit=31)


    

In [11]:

    

asm


    

    
Out[11]:





Assembly
fragments..: 5603bp 1231bp 1742bp 1038bp
limit(bp)..: 31
G.nodes....: 8
algorithm..: common_sub_strings

In [12]:

    

pYPK0_PGI1_CiGXF1_TDH3 = asm.assemble_circular()[0].synced("tcgcgcgtttcggtgatgacggtgaaaacctctg")


    

In [13]:

    

pYPK0_PGI1_CiGXF1_TDH3.write("pYPK0_PGI1_CiGXF1_TDH3.gb")


    

    





pYPK0_PGI1_CiGXF1_TDH3.gb