Mercurial > repos > tduigou > cloning_simulation

comparison cloning_simulation.py @ 2:3171db614963 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Fri, 16 May 2025 11:32:06 +0000
parents dc450979fcd4
children 044d36066cb3
comparison
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1:32e44a646b68 2:3171db614963
7 7
8 def cloning_simulation(files_to_assembly, domesticated_list, 8 def cloning_simulation(files_to_assembly, domesticated_list,
9 csv_file, assembly_type, topology, 9 csv_file, assembly_type, topology,
10 file_name_mapping, file_name_mapping_dom, 10 file_name_mapping, file_name_mapping_dom,
11 use_file_names_as_id, 11 use_file_names_as_id,
12 outdir_simulation, output_simulation,enzyme): 12 outdir_simulation, output_simulation,enzyme,outdir_gb):
13 13
14 files_to_assembly = files_to_assembly.split(',') 14 files_to_assembly = files_to_assembly.split(',')
15 15
16 repository = dnacauldron.SequenceRepository() 16 repository = dnacauldron.SequenceRepository()
17 repository.import_records(files=files_to_assembly, 17 repository.import_records(files=files_to_assembly,
106 for root, dirs, files in os.walk(outdir_simulation): 106 for root, dirs, files in os.walk(outdir_simulation):
107 for file in files: 107 for file in files:
108 full_path = os.path.join(root, file) 108 full_path = os.path.join(root, file)
109 arcname = os.path.relpath(full_path, outdir_simulation) 109 arcname = os.path.relpath(full_path, outdir_simulation)
110 zipf.write(full_path, arcname) 110 zipf.write(full_path, arcname)
111 print("Files in the zip archive:") 111 #print("Files in the zip archive:")
112 for info in zipf.infolist(): 112 #for info in zipf.infolist():
113 print(info.filename) 113 #print(info.filename)
114 with zipfile.ZipFile(output_simulation, 'r') as zipf:
115 for member in zipf.namelist():
116 # Only extract actual files inside 'all_construct_records/' (not subfolders)
117 if member.startswith("all_construct_records/") and not member.endswith("/"):
118 # Get the file name only (strip folder path)
119 filename = os.path.basename(member)
120 if not filename:
121 continue # skip any edge cases
114 122
115 return output_simulation 123 # Destination path directly in outdir_dir
124 target_path = os.path.join(outdir_gb, filename)
125
126 # Write the file content
127 with zipf.open(member) as source, open(target_path, "wb") as target:
128 target.write(source.read())
129
130 return output_simulation, outdir_gb
116 131
117 132
118 def parse_command_line_args(): 133 def parse_command_line_args():
119 parser = argparse.ArgumentParser(description="Domestication") 134 parser = argparse.ArgumentParser(description="Domestication")
120 135
138 help="dir output for cloning simulation results") 153 help="dir output for cloning simulation results")
139 parser.add_argument("--output_simulation", required=True, 154 parser.add_argument("--output_simulation", required=True,
140 help="zip output for cloning simulation results") 155 help="zip output for cloning simulation results")
141 parser.add_argument('--enzyme', type=str, 156 parser.add_argument('--enzyme', type=str,
142 help='enzyme to use') 157 help='enzyme to use')
158 parser.add_argument("--outdir_gb", required=True,
159 help="dir output constructs gb files")
143 160
144 return parser.parse_args() 161 return parser.parse_args()
145 162
146 if __name__ == "__main__": 163 if __name__ == "__main__":
147 args = parse_command_line_args() 164 args = parse_command_line_args()
148 165
149 cloning_simulation( 166 cloning_simulation(
150 args.parts_files, args.domesticated_seq, 167 args.parts_files, args.domesticated_seq,
151 args.assembly_csv, args.assembly_plan_name, args.topology, 168 args.assembly_csv, args.assembly_plan_name, args.topology,
152 args.file_name_mapping, args.file_name_mapping_dom, 169 args.file_name_mapping, args.file_name_mapping_dom,
153 args.use_file_names_as_id, 170 args.use_file_names_as_id, args.outdir_simulation,
154 args.outdir_simulation,args.output_simulation, args.enzyme 171 args.output_simulation, args.enzyme, args.outdir_gb
155 ) 172 )