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from pydna.all import *
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p567,p577,p468,p467,p568,p578,p775,p778,p167,p166 = parse("yeast_pahtway_kit_standard_primers.txt")
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from Bio.Restriction import ZraI, AjiI, EcoRV
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pYPK0 = read("pYPK0.gb")
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promoter_clone = pYPKa_Z_TEF1 = read("pYPKa_Z_TEF1.gb")
Genbank record
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# NBVAL_IGNORE_OUTPUT
from IPython.display import IFrame
IFrame('http://www.ncbi.nlm.nih.gov/pubmed/1756986', width='100%', height=250)
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gb =Genbank("bjornjobbb@gmail.com")
gene_template = gb.nucleotide("X59465.1")
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gene_template.list_features()
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orf = gene_template.extract_feature(7)
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orf.isorf()
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print(orf.seq)
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print(len(orf))
orf.seguid()
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print(str(orf.seq.translate()))
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pf, pr =parse('''
>XR_YPK_rec_fwd
gtcgaggaacgccaggttgcccactttctcactagtgaAAATGCCTTCTATTAAGTTGAACTCTGG
>XR_YPK_rec_rev
ATTTAAatcctgatgcgtttgtctgcacagatggcgcgTTAGACGAAGATAGGAATCTTGTCCC
''')
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g =pcr( pf, pr, orf)
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g.figure()
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terminator_clone = pYPKa_E_TDH3 =read("pYPKa_E_TDH3.gb")
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p = pcr( p167, p567, promoter_clone)
t = pcr( p568, p166, terminator_clone)
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pYPK0_E_Z, stuffer = pYPK0.cut((EcoRV, ZraI))
pYPK0_E_Z, stuffer
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(pYPK0_E_Z, p, g, t)
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asm =Assembly((pYPK0_E_Z, p, g, t), limit=29)
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asm
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candidate = asm.assemble_circular()[0]
candidate.figure()
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pYPK0_TEF1_PsXYL1_TDH3 = candidate.synced(pYPK0)
The pYPK0_TEF1_PsXYL1_TDH3 has cseguid ak608NPPLpMmn_YIHGwQPcQzee0
and 8015 bp
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print(len(pYPK0_TEF1_PsXYL1_TDH3))
pYPK0_TEF1_PsXYL1_TDH3.cseguid()
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pYPK0_TEF1_PsXYL1_TDH3.name="pMEC1126"
#pYPK0_TEF1_PsXYL1_TDH3.description = "pYPK0_TEF1_PsXYL1_TDH3tp"
pYPK0_TEF1_PsXYL1_TDH3.stamp()
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pYPK0_TEF1_PsXYL1_TDH3.write("pYPK0_TEF1_PsXYL1_TDH3.gb")
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reloaded =read("pYPK0_TEF1_PsXYL1_TDH3.gb")
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reloaded.cseguid()
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