pCAPs_EcoRV = pCAPs.cut(EcoRV).pop()
pCAPs_ZraI_ScTEF1tp = (pCAPs_ZraI + ScTEF1tp).looped()
pCAPs_ZraI_ScTDH3tp = (pCAPs_ZraI + ScTDH3tp).looped()
pCAPs_EcoRV_ScTDH3tp = (pCAPs_EcoRV + ScTDH3tp).looped()
pCAPs_ZraI_ScPGI1tp = (pCAPs_ZraI + ScPGI1tp).looped()
pCAPs_EcoRV_ScPGI1tp = (pCAPs_EcoRV + ScPGI1tp).looped()
pCAPs_ZraI_ScFBA1tp = (pCAPs_ZraI + ScFBA1tp).looped()
pCAPs_EcoRV_ScFBA1tp = (pCAPs_EcoRV + ScFBA1tp).looped()
pCAPs_EcoRV_ScPDC1tp = (pCAPs_EcoRV + ScPDC1tp).looped()
XYL1 = pcr( primer[620], primer[619], gb("X59465") ) #xyl1 P. stipitis
pCAPs_AjiI_XR = (pCAPs_AjiI + XYL1).looped()
XYL2 = pcr( primer[618], primer[617], gb("A16166") ) #xyl2 P. stipitis
pCAPs_AjiI_XDH = (pCAPs_AjiI + XYL2).looped()
ScXK = pcr( primer[616], primer[615], sgd.cds("XKS1"))
pCAPs_AjiI_XK = (pCAPs_AjiI + ScXK).looped()
ScTAL1 = pcr( primer[614], primer[613], sgd.cds("TAL1"))
pCAPs_AjiI_TAL = (pCAPs_AjiI + ScTAL1).looped()
pCAPs_pSU0 = read("/home/bjorn/Dropbox/wikidata/pCAPs-pSU0.wiki")
pCAPs_pSU0_E_Z, stuffer = pCAPs_pSU0.cut((EcoRV,ZraI))
#ypk_primer = parse("/home/bjorn/Dropbox/wikidata/ypk_primers.wiki")
pCAPs_ZraI = pCAPs.cut(ZraI).pop()
pCAPs_EcoRV = pCAPs.cut(EcoRV).pop()
pCAPs_pSU0_E_Z, stuffer = pCAPs_pSU0.cut((EcoRV,ZraI))
pCAPs_ZraI_ScTEF1tp = (pCAPs_ZraI + ScTEF1tp).looped()
pCAPs_EcoRV_ScTPI1tp = (pCAPs_EcoRV + ScTPI1tp).looped()
pCAPs_ZraI_ScTPI1tp = (pCAPs_ZraI + ScTPI1tp).looped()
pCAPs_ZraI_ScPDC1tp = (pCAPs_ZraI + ScPDC1tp).looped()
pCAPs_EcoRV_ScPDC1tp = (pCAPs_EcoRV + ScPDC1tp).looped()
pCAPs_ZraI_ScFBA1tp = (pCAPs_ZraI + ScFBA1tp).looped()
pCAPs_EcoRV_ScFBA1tp = (pCAPs_EcoRV + ScFBA1tp).looped()
pCAPs_EcoRV_ScTDH3tp = (pCAPs_EcoRV + ScTDH3tp).looped()
ypk_primer = parse("/home/bjorn/Dropbox/wikidata/ypk_primers.wiki")
XYL1=gb("X59465")
XYL2=gb("A16166")
EcoliXK = read("/home/bjorn/Dropbox/wikidata/EcXK.wiki")
# ScTEF1tp-E.coliXK-ScTPI1tp
A_ScTEF1tp_b = pcr( primer[167],primer[567], pCAPs_ZraI_ScTEF1tp)
EcXK = pcr( ypk_primer[12], ypk_primer[13], EcoliXK)
C_ScTPI1tp_d = pcr( primer[568],primer[166], pCAPs_EcoRV_ScTPI1tp)
sequences, circular = circular_assembly(( A_ScTEF1tp_b,
EcXK,
C_ScTPI1tp_d,
pCAPs_pSU0_E_Z), limit=28)
pYPK0_ScTEF1tp_EcXK_ScTPI1tp = circular[0]
pCAPs_ZraI_ScRPS19btp = (pYPKa_ZraI + ScRPS19btp).looped()
pCAPs_EcoRV_ScRPS19btp = (pYPKa_EcoRV + ScRPS19btp).looped()
pCAPs_ZraI_ScTPI1tp = (pYPKa_ZraI + ScTPI1tp).looped()
pCAPs_EcoRV_ScTPI1tp = (pYPKa_EcoRV + ScTPI1tp).looped()
pCAPs_EcoRV_ScENO2tp = (pYPKa_EcoRV + ScENO2tp).looped()
ScRPE1 = pcr( primer[556], primer[557], Dseqrecord(sgd.cds("RPE1")))
pCAPs_AjiI_ScRPE1 = (pYPKa_AjiI + ScRPE1).looped()
ScRKI1 = pcr( primer[555], primer[554], Dseqrecord(sgd.cds("RKI1")))
pCAPs_AjiI_ScRKI1 = (pYPKa_AjiI + ScRKI1).looped()
CiGXF1 = pcr( primer[553], primer[552], Dseqrecord(gb("AJ937350")))
pCAPs_AjiI_CiGXF1 = (pYPKa_AjiI + CiGXF1).looped()
from pYPK0 import pYPK0 as pCAPs_pSU0
pCAPs_pSU0_E_Z, stuffer = pCAPs_pSU0.cut((EcoRV,ZraI))
ypk_primer = parse("/home/bjorn/Dropbox/wikidata/ypk_primers.wiki")
#ScPDC1_PacI-ScTKL1-ScRPS19b_PacI
A_ScPDC1tp_b = pcr( primer[167], primer[567], pCAPs_ZraI_ScPDC1tp)
ScTKL1 = pcr( ypk_primer[8], ypk_primer[9], Dseqrecord(sgd.cds("TKL1")))
pCAPs_ZraI_ScRPS19btp = (pCAPs_ZraI + ScRPS19btp).looped()
pCAPs_EcoRV_ScRPS19btp = (pCAPs_EcoRV + ScRPS19btp).looped()
pCAPs_ZraI_ScTPI1tp = (pCAPs_ZraI + ScTPI1tp).looped()
pCAPs_EcoRV_ScTPI1tp = (pCAPs_EcoRV + ScTPI1tp).looped()
pCAPs_EcoRV_ScENO2tp = (pCAPs_EcoRV + ScENO2tp).looped()
ScRPE1 = pcr( primer[556], primer[557], sgd.cds("RPE1"))
pCAPs_AjiI_ScRPE1 = (pCAPs_AjiI + ScRPE1).looped()
ScRKI1 = pcr( primer[555], primer[554], sgd.cds("RKI1"))
pCAPs_AjiI_ScRKI1 = (pCAPs_AjiI + ScRKI1).looped()
CiGXF1 = pcr( primer[553], primer[552], gb("AJ937350"))
pCAPs_AjiI_CiGXF1 = (pCAPs_AjiI + CiGXF1).looped()
pCAPs_pSU0 = read("/home/bjorn/Dropbox/wikidata/pCAPs-pSU0.wiki")
pCAPs_pSU0_E_Z, stuffer = pCAPs_pSU0.cut((EcoRV,ZraI))
ypk_primer = parse("/home/bjorn/Dropbox/wikidata/ypk_primers.wiki")
#ScPDC1_PacI-ScTKL1-ScRPS19b_PacI
A_ScPDC1tp_b = pcr( primer[167], primer[567], pCAPs_ZraI_ScPDC1tp)
ScTKL1 = pcr( ypk_primer[8], ypk_primer[9], sgd.cds("TKL1"))