Construction of pYPK0_RPS19a_ScRKI1_TPI1 (pMEC1133)

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


    

In [4]:

    

pYPK0 =read("pYPK0.gb")


    

In [5]:

    

promoter_clone = pYPKa_Z_RPS19a =read("pYPKa_Z_RPS19a.gb")


    

In [6]:

    

gene_clone = pYPKa_A_ScRKI1 =read("pYPKa_A_ScRKI1.gb")


    

In [7]:

    

terminator_clone = pYPKa_E_TPI1 =read("pYPKa_E_TPI1.gb")


    

In [8]:

    

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


    

In [9]:

    

pYPK0_E_Z, stuffer = pYPK0.cut((EcoRV, ZraI))


    

In [10]:

    

(pYPK0_E_Z, p, g, t)


    

    
Out[10]:





(Dseqrecord(-5681), Amplicon(705), Amplicon(875), Amplicon(688))

In [11]:

    

asm =Assembly((pYPK0_E_Z, p, g, t), limit=31)


    

In [12]:

    

asm


    

    
Out[12]:





Assembly
fragments..: 5681bp 705bp 875bp 688bp
limit(bp)..: 31
G.nodes....: 8
algorithm..: common_sub_strings

In [13]:

    

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


    

    
Out[13]:





 -|name|98
|       \/
|       /\
|       98|705bp_PCR_prod|50
|                         \/
|                         /\
|                         50|875bp_PCR_prod|37
|                                           \/
|                                           /\
|                                           37|688bp_PCR_prod|61
|                                                             \/
|                                                             /\
|                                                             61-
|                                                                |
 ----------------------------------------------------------------

In [14]:

    

result = candidate.synced(pYPK0)


    

In [15]:

    

print(len(result))
result.cseguid()


    

    




7703






    
Out[15]:





79JiqIENZc7fgGgYo9WS44MLsBA

In [16]:

    

result.name = "pMEC1132"
result.description = "pYPK0_RPS19a_ScRKI1_TPI1tp"
result.stamp()


    

    
Out[16]:





cSEGUID_79JiqIENZc7fgGgYo9WS44MLsBA

In [17]:

    

result.write("pYPK0_RPS19a_ScRKI1_TPI1.gb")


    

    





pYPK0_RPS19a_ScRKI1_TPI1.gb

In [18]:

    

from pydna.all import *


    

In [19]:

    

reloaded =read("pYPK0_RPS19a_ScRKI1_TPI1.gb")


    

In [20]:

    

reloaded.cseguid()


    

    
Out[20]:





79JiqIENZc7fgGgYo9WS44MLsBA

In [21]:

    

reloaded.description


    

    
Out[21]:





'pYPK0_RPS19a_ScRKI1_TPI1tp cSEGUID_79JiqIENZc7fgGgYo9WS44MLsBA_2018-05-15T07:37:17.197151'