Mercurial > repos > tduigou > cloning_simulation
comparison cloning_simulation.py @ 8:07e902da89ad draft
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 |
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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 |