Python cds Examples

Example #1

File: pYPK0_Df_new.py Project: BjornFJohansson/pYPKa_ZE

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: pYPK0_T_new.py Project: BjornFJohansson/pYPKa_ZE

pCAPs_ZraI_ScPDC1tp  = (pYPKa_ZraI  + ScPDC1tp).looped()

pCAPs_ZraI_ScRPS19atp  = (pYPKa_ZraI  + ScRPS19atp).looped()
pCAPs_EcoRV_ScRPS19atp = (pYPKa_EcoRV + ScRPS19atp).looped()

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")

Example #3

File: pYPK0_Df_new.py Project: BjornFJohansson/pYPKa_ZE

pCAPs_ZraI_ScPGI1tp    = (pYPKa_ZraI  + ScPGI1tp).looped()
pCAPs_EcoRV_ScPGI1tp   = (pYPKa_EcoRV + ScPGI1tp).looped()

pCAPs_ZraI_ScFBA1tp  = (pYPKa_ZraI  + ScFBA1tp).looped()
pCAPs_EcoRV_ScFBA1tp = (pYPKa_EcoRV + ScFBA1tp).looped()

pCAPs_EcoRV_ScPDC1tp = (pYPKa_EcoRV + ScPDC1tp).looped()

XYL1 = pcr( primer[620], primer[619], Dseqrecord(gb("X59465"))) #xyl1 P. stipitis
pCAPs_AjiI_XR  = (pYPKa_AjiI + XYL1).looped()

XYL2 = pcr( primer[618], primer[617], Dseqrecord(gb("A16166"))) #xyl2 P. stipitis
pCAPs_AjiI_XDH = (pYPKa_AjiI + XYL2).looped()

ScXK = pcr( primer[616], primer[615], Dseqrecord(sgd.cds("XKS1")))
pCAPs_AjiI_XK = (pYPKa_AjiI + ScXK).looped()

ScTAL1 = pcr( primer[614], primer[613], Dseqrecord(sgd.cds("TAL1")))
pCAPs_AjiI_TAL = (pYPKa_AjiI + ScTAL1).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")