<jupyter_start><jupyter_text>Construction of pYPK0_TDH3_PsXYL2_PGI1 (pMEC1128)[pYPKa_Z_TDH3](pYPKa_Z_TDH3.ipynb)[pYPKa_E_PGI1](pYPKa_E_PGI1.ipynb)<jupyter_code>from pydna.all import *
p567,p577,p468,p467,p568,p578,p775,p778,p167,p166 = parse("yeast_pahtway_kit_standard_primers.txt")<jupyter_output><empty_output><jupyter_text>[Yeast Pathway Kit Standard Primers](ypk_std_primers.ipynb)<jupyter_code>from Bio.Restriction import ZraI, AjiI, EcoRV
pYPK0 =read("pYPK0.gb")
promoter_clone = pYPKa_Z_TDH3 =read("pYPKa_Z_TDH3.gb")<jupyter_output><empty_output><jupyter_text>[Genbank](http://www.ncbi.nlm.nih.gov/nuccore/A16166.1) record<jupyter_code># NBVAL_IGNORE_OUTPUT
from IPython.display import IFrame
IFrame('http://google.com/patents/EP0450430A2?cl=es', width='100%', height=250)
gb =Genbank("<EMAIL>")
gene_template = gb.nucleotide("A16166.1")
gene_template.list_features()
orf = gene_template.extract_feature(1)
print(orf.seq)
orf.isorf()
print(len(orf))
orf.seguid()
print(str(orf.seq.translate()))
pf, pr =parse('''>XDH_YPK_rec_fwd 
                        gtcgaggaacgccaggttgcccactttctcactagtgaAAATGACTGCTAACCCTTCCTTGGTG
                        >XDH_YPK_rec_rev 
                        ATTTAAatcctgatgcgtttgtctgcacagatggcgcgTTACTCAGGGCCGTCAATGAGACA''')
g =pcr( pf, pr, orf)
g.figure()
terminator_clone = pYPKa_E_PGI1 =read("pYPKa_E_PGI1.gb")
p  =pcr( p167, p567, promoter_clone)
t  =pcr( p568, p166, terminator_clone)
pYPK0_E_Z, stuffer = pYPK0.cut((EcoRV, ZraI))
(pYPK0_E_Z, p, g, t)
asm =Assembly((pYPK0_E_Z, p, g, t), limit=31)
asm
candidate = asm.assemble_circular()[0]
candidate.figure()
pYPK0_TDH3_PsXYL2_PGI1 = candidate.synced(pYPK0)<jupyter_output><empty_output><jupyter_text>The pYPK0_TDH3_PsXYL2_PGI1 has cseguid ```ycHQ8EOwqQihZOUFmIbCiwHhMZ0``` and 8015 bp<jupyter_code>print(len(pYPK0_TDH3_PsXYL2_PGI1))
pYPK0_TDH3_PsXYL2_PGI1.cseguid()
pYPK0_TDH3_PsXYL2_PGI1.name="pMEC1128"
#pYPK0_TDH3_PsXYL2_PGI1.description = "pYPK0_TDH3_PsXYL2_PGI1tp"
pYPK0_TDH3_PsXYL2_PGI1.stamp()
pYPK0_TDH3_PsXYL2_PGI1.write("pYPK0_TDH3_PsXYL2_PGI1.gb")<jupyter_output><empty_output><jupyter_text>Download sequence[pYPK0_TDH3_PsXYL2_PGI1tpp](pYPK0_TDH3_PsXYL2_PGI1.gb)<jupyter_code>reloaded =read("pYPK0_TDH3_PsXYL2_PGI1.gb")
reloaded.cseguid()
reloaded.description<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.1256544502617801, 'fraction_numerical': 0.06849912739965096, 'mean_word_length': 8.594142259414227, 'pattern_counts': {'":': 0, '<': 22, '<?xml version=': 0, '>': 24, 'https://': 0, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 1, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '5', 'dir': 'jupyter-structured-clean-dedup', 'id': '371642', 'license': 'BSD-3-Clause', 'n_tokens_mistral': 1223, 'n_tokens_neox': 1126, 'n_words': 105, 'path': 'notebooks/pYPK0_TDH3_PsXYL2_PGI1.ipynb', 'repo_name': 'MetabolicEngineeringGroupCBMA/ypk-xylose-pathways', 'size': '2305'}