Construction of pYPK3_RPS19b_HIS3_RPS19a

In [1]:

    

from pydna.all import *


    

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, NotI


    

In [4]:

    

pYPK3 =read("pYPK3.gb")


    

In [5]:

    

promoter_clone = pYPKa_Z_RPS19btp =read("pYPKa_Z_RPS19b.gb")


    

In [6]:

    

gene_clone =read("pYPKa_A_ScHIS3.gb")


    

In [7]:

    

terminator_clone = pYPKa_E_RPS19atp =read("pYPKa_E_RPS19a.gb")


    

In [8]:

    

p  =pcr( p167, p567, promoter_clone)
g  =pcr( p468, p467, gene_clone)
t  =pcr( p568, p166, terminator_clone)


    

In [9]:

    

pYPK3_E_N, stuffer = pYPK3.cut((EcoRV, NotI))


    

In [10]:

    

(pYPK3_E_N, p, g, t)


    

    
Out[10]:





(Dseqrecord(-5201), Amplicon(787), Amplicon(761), Amplicon(649))

In [11]:

    

asm =Assembly((pYPK3_E_N, p, g, t), limit=31)


    

In [12]:

    

asm


    

    
Out[12]:





Assembly
fragments..: 5201bp 787bp 761bp 649bp
limit(bp)..: 31
G.nodes....: 8
algorithm..: common_sub_strings

In [13]:

    

candidate = asm.assemble_circular()[0]
candidate.figure()


    

    
Out[13]:





 -|name|92
|       \/
|       /\
|       92|787bp_PCR_prod|50
|                         \/
|                         /\
|                         50|761bp_PCR_prod|37
|                                           \/
|                                           /\
|                                           37|649bp_PCR_prod|61
|                                                             \/
|                                                             /\
|                                                             61-
|                                                                |
 ----------------------------------------------------------------

In [14]:

    

result = candidate.synced(pYPK3)


    

In [15]:

    

result.write("pYPK3_RPS19b_HIS3_RPS19a.gb")


    

    





pYPK3_RPS19b_HIS3_RPS19a.gb

In [16]:

    

from pydna.all import *


    

In [17]:

    

reloaded =read("pYPK3_RPS19b_HIS3_RPS19a.gb")


    

In [18]:

    

reloaded.cseguid()


    

    
Out[18]:





eLY9Niw8HWC2cKKEnB-bZ8ofukQ