Mercurial > repos > tduigou > cloning_simulation

comparison cloning_simulation.py @ 8:07e902da89ad draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 26 May 2025 09:23:51 +0000
parents 044d36066cb3
children eaff3028ba07
comparison
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7:296e5145a862 8:07e902da89ad
57 record.name = new_id 57 record.name = new_id
58 record.description = new_id 58 record.description = new_id
59 repository.collections["parts"][new_id] = repository.collections["parts"].pop(key) 59 repository.collections["parts"][new_id] = repository.collections["parts"].pop(key)
60 ######################################################## 60 ########################################################
61 #print (f"repo: {vars(repository)}") 61 #print (f"repo: {vars(repository)}")
62 any(pandas.read_csv(csv_file, index_col=0, header=None).duplicated()) 62 #any(pandas.read_csv(csv_file, index_col=0, header=None).duplicated())
63 df=pandas.read_csv(csv_file, index_col=0, header=None)
64 if df.duplicated().any():
65 raise ValueError("Duplicate rows found in the data!")
63 66
64 if assembly_type == "Type2sRestrictionAssembly": 67 if assembly_type == "Type2sRestrictionAssembly":
65 assembly_class = dnacauldron.Type2sRestrictionAssembly 68 assembly_class = dnacauldron.Type2sRestrictionAssembly
66 elif assembly_type == "GibsonAssembly": 69 elif assembly_type == "GibsonAssembly":
67 assembly_class = dnacauldron.GibsonAssembly 70 assembly_class = dnacauldron.GibsonAssembly
80 os.rename(csv_file, new_csvname) 83 os.rename(csv_file, new_csvname)
81 84
82 assembly_plan = dnacauldron.AssemblyPlan.from_spreadsheet( 85 assembly_plan = dnacauldron.AssemblyPlan.from_spreadsheet(
83 name="auto_from_filename", 86 name="auto_from_filename",
84 path=new_csvname, 87 path=new_csvname,
88 header=[0],
85 assembly_class=assembly_class 89 assembly_class=assembly_class
86 ) 90 )
87 if enzyme != 'auto': 91 if enzyme != 'auto':
88 for assembly in assembly_plan.assemblies: 92 for assembly in assembly_plan.assemblies:
89 assembly.enzyme = enzyme 93 assembly.enzyme = enzyme