Mercurial > repos > tduigou > cloning_simulation

annotate cloning_simulation.py @ 1:2655e08cd61a draft default tip

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:46:59 +0000
parents 3a3b0f7cb5c2
children
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3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
1 import argparse
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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2 import os
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2655e08cd61a planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 0
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3 import json
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3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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4 import zipfile
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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5 import pandas
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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6 import dnacauldron
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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7
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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8
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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9 def cloning_simulation(files_to_assembly, domesticated_list,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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10 csv_file, assembly_type, topology,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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11 file_name_mapping, file_name_mapping_dom,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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12 use_file_names_as_id,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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13 outdir_simulation, output_simulation, enzyme, outdir_gb):
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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14
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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15 files_to_assembly = files_to_assembly.split(',')
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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16
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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17 repository = dnacauldron.SequenceRepository()
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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18 repository.import_records(files=files_to_assembly,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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19 use_file_names_as_ids=use_file_names_as_id,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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20 topology=topology)
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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21 if domesticated_list:
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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22 domesticated_files = domesticated_list.split(',')
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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23 repository.import_records(files=domesticated_files,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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24 use_file_names_as_ids=use_file_names_as_id,
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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25 topology=topology)
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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26
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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27 # refine the real record name dict
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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28 if isinstance(file_name_mapping, str):
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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29 file_name_mapping = dict(
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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30 item.split(":") for item in file_name_mapping.split(",")
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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31 )
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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32 real_names = {
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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33 os.path.splitext(os.path.basename(k))[0]: v.replace(".gb", "")
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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34 for k, v in file_name_mapping.items()
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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35 }
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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36
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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37 # refine the real record name dict_dom
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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38 if file_name_mapping_dom == "":
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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39 file_name_mapping_dom = {}
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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40 else:
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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41 if isinstance(file_name_mapping_dom, str):
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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42 file_name_mapping_dom = dict(
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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43 item.split(":") for item in file_name_mapping_dom.split(",")
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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44 )
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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45 dom_real_names = {
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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46 os.path.splitext(os.path.basename(k))[0]: v.replace(".gb", "")
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
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47 for k, v in file_name_mapping_dom.items()
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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48 }
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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49 real_names.update(dom_real_names)
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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50
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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51 # update the records
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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52
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53 for key, record in list(repository.collections["parts"].items()):
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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54 current_id = record.id
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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55 if current_id in real_names:
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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56 new_id = real_names[current_id]
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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57 record.id = new_id
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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58 record.name = new_id
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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59 record.description = new_id
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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60 repository.collections["parts"][new_id] = repository.collections["parts"].pop(key)
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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61 ########################################################
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62 # print (f"repo: {vars(repository)}")
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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63 # any(pandas.read_csv(csv_file, index_col=0, header=None).duplicated())
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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64 df = pandas.read_csv(csv_file, index_col=0, header=None)
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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65 if df.duplicated().any():
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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66 raise ValueError("Duplicate rows found in the data!")
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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67
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68 if assembly_type == "Type2sRestrictionAssembly":
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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69 assembly_class = dnacauldron.Type2sRestrictionAssembly
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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70 elif assembly_type == "GibsonAssembly":
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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71 assembly_class = dnacauldron.GibsonAssembly
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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72 elif assembly_type == "BASICAssembly":
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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73 assembly_class = dnacauldron.BASICAssembly
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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74 elif assembly_type == "BioBrickStandardAssembly":
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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75 assembly_class = dnacauldron.BioBrickStandardAssembly
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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76 elif assembly_type == "OligoPairAnnealin":
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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77 assembly_class = dnacauldron.OligoPairAnnealin
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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78 elif assembly_type == "LigaseCyclingReactionAssembly":
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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79 assembly_class = dnacauldron.LigaseCyclingReactionAssembly
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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80 else:
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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81 raise ValueError(f"Unsupported assembly type: {assembly_type}")
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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82
3a3b0f7cb5c2 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
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83 new_csvname = "assambly.csv"
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84 os.rename(csv_file, new_csvname)
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85
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86 assembly_plan = dnacauldron.AssemblyPlan.from_spreadsheet(
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87 name="auto_from_filename",
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88 path=new_csvname,
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89 dataframe=None,
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90 header=None,
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91 assembly_class=assembly_class
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92 )
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93 if enzyme != 'auto':
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94 for assembly in assembly_plan.assemblies:
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95 assembly.enzyme = enzyme
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96
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97 simulation = assembly_plan.simulate(sequence_repository=repository)
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98 stats = simulation.compute_stats()
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99 print(stats)
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100
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101 report_writer = dnacauldron.AssemblyReportWriter(
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102 include_mix_graphs=True,
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103 include_assembly_plots=True,
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104 show_overhangs_in_graph=True,
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105 annotate_parts_homologies=True,
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106 include_pdf_report=True,
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107 )
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108 simulation.write_report(outdir_simulation, assembly_report_writer=report_writer)
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109
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110 # Append report files to .dat (ZIP)
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111 with zipfile.ZipFile(output_simulation, mode='a', compression=zipfile.ZIP_DEFLATED) as zipf:
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112 for root, dirs, files in os.walk(outdir_simulation):
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113 for file in files:
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114 full_path = os.path.join(root, file)
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115 arcname = os.path.relpath(full_path, outdir_simulation)
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116 zipf.write(full_path, arcname)
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117 # print("Files in the zip archive:")
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118 # for info in zipf.infolist():
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119 # print(info.filename)
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120 for member in zipf.namelist():
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121 # Only extract actual files inside 'all_construct_records/' (not subfolders)
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122 if member.startswith("assambly_simulation/all_construct_records/") and not member.endswith("/"):
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123 # Get the file name only (strip folder path)
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124 filename = os.path.basename(member)
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125 if not filename:
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126 continue # skip any edge cases
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127
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128 # Destination path directly in outdir_dir
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129 target_path = os.path.join(outdir_gb, filename)
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130
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131 # Write the file content
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132 with zipf.open(member) as source, open(target_path, "wb") as target:
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133 target.write(source.read())
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134
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135 return output_simulation, outdir_gb
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136
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137
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138 def parse_command_line_args():
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139 parser = argparse.ArgumentParser(description="Domestication")
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140
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141 parser.add_argument("--parts_files", required=True,
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142 help="List of GenBank files (Comma-separated)")
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143 parser.add_argument("--domesticated_seq", required=True,
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144 help="output of domestication (ganbank list)")
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145 parser.add_argument("--assembly_csv", required=True,
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146 help="csv assembly")
1
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147 parser.add_argument('--assembly_plan_name', type=str, required=False,
0
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148 help='type of assembly')
1
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149 parser.add_argument('--topology', type=str, required=False,
0
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150 help='"circular" or "linear"')
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151 parser.add_argument('--file_name_mapping', type=str,
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152 help='Mapping of Galaxy filenames to original filenames')
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153 parser.add_argument('--file_name_mapping_dom', type=str,
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154 help='Mapping of Galaxy filenames to original domestication filenames')
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155 parser.add_argument("--use_file_names_as_id", type=lambda x: x.lower() == 'true', default=True,
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156 help="Use file names as IDs (True/False)")
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157 parser.add_argument("--outdir_simulation", required=True,
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158 help="dir output for cloning simulation results")
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159 parser.add_argument("--output_simulation", required=True,
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160 help="zip output for cloning simulation results")
1
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161 parser.add_argument('--enzyme', type=str,required=False,
0
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162 help='enzyme to use')
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163 parser.add_argument("--outdir_gb", required=True,
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164 help="dir output constructs gb files")
1
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165 parser.add_argument("--use_json_paramers", required=True,
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166 help="Use parameters from JSON: true/false")
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167 parser.add_argument("--json_conf", required=False,
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168 help="JSON config file with DB parameters")
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169
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170 return parser.parse_args()
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171
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172
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173 if __name__ == "__main__":
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174 args = parse_command_line_args()
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175
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176 #json param checking
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177 config_params = {}
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178 use_json = args.use_json_paramers == 'true'
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179 if use_json:
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180 if not args.json_conf:
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181 raise ValueError("You must provide --json_conf when --use_json_paramers is 'true'")
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182 with open(args.json_conf, "r") as f:
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183 config_params = json.load(f)
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184 else:
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185 config_params = {
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186 "assembly_plan_name": args.assembly_plan_name,
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187 "topology": args.topology,
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188 "enzyme": args.enzyme
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189 }
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190 assembly_plan_name = config_params["assembly_plan_name"]
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191 topology = config_params["topology"]
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192 enzyme = config_params["enzyme"]
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193
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194 cloning_simulation(
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195 args.parts_files, args.domesticated_seq,
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196 args.assembly_csv, assembly_plan_name, topology,
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197 args.file_name_mapping, args.file_name_mapping_dom,
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198 args.use_file_names_as_id, args.outdir_simulation,
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199 args.output_simulation, enzyme, args.outdir_gb
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200 )