Python gb Examples

Example #1

File: pYPK0_Df.py Project: BjornFJohansson/pYPKa_ZE

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")

Example #2

File: pYPK01.py Project: BjornFJohansson/pYPKa_ZE

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]

Example #3

File: pYPK0_T_new.py Project: BjornFJohansson/pYPKa_ZE

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")))

Example #4

File: pYPK0-T.py Project: BjornFJohansson/pYPKa_ZE

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"))