comparison cloning_simulation.py @ 2:3171db614963 draft

planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/tree/master commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae

1:32e44a646b68

def cloning_simulation(files_to_assembly, domesticated_list,
                       csv_file, assembly_type, topology,
                       file_name_mapping, file_name_mapping_dom,
                       use_file_names_as_id,
                       outdir_simulation, output_simulation,enzyme):

    files_to_assembly = files_to_assembly.split(',')

    repository = dnacauldron.SequenceRepository()
    repository.import_records(files=files_to_assembly, 

        for root, dirs, files in os.walk(outdir_simulation):
            for file in files:
                full_path = os.path.join(root, file)
                arcname = os.path.relpath(full_path, outdir_simulation)
                zipf.write(full_path, arcname)
        print("Files in the zip archive:")
        for info in zipf.infolist():
            print(info.filename)

    return output_simulation


def parse_command_line_args():
    parser = argparse.ArgumentParser(description="Domestication")

                        help="dir output for cloning simulation results")
    parser.add_argument("--output_simulation", required=True, 
                        help="zip output for cloning simulation results")
    parser.add_argument('--enzyme', type=str, 
                        help='enzyme to use')
 
    return parser.parse_args()

if __name__ == "__main__":
    args = parse_command_line_args()

    cloning_simulation(
        args.parts_files, args.domesticated_seq,
        args.assembly_csv, args.assembly_plan_name, args.topology,
        args.file_name_mapping, args.file_name_mapping_dom, 
        args.use_file_names_as_id,
        args.outdir_simulation,args.output_simulation, args.enzyme
    )

2:3171db614963

def cloning_simulation(files_to_assembly, domesticated_list,
                       csv_file, assembly_type, topology,
                       file_name_mapping, file_name_mapping_dom,
                       use_file_names_as_id,
                       outdir_simulation, output_simulation,enzyme,outdir_gb):

    files_to_assembly = files_to_assembly.split(',')

    repository = dnacauldron.SequenceRepository()
    repository.import_records(files=files_to_assembly, 

        for root, dirs, files in os.walk(outdir_simulation):
            for file in files:
                full_path = os.path.join(root, file)
                arcname = os.path.relpath(full_path, outdir_simulation)
                zipf.write(full_path, arcname)
        #print("Files in the zip archive:")
        #for info in zipf.infolist():
            #print(info.filename)
    with zipfile.ZipFile(output_simulation, 'r') as zipf:
        for member in zipf.namelist():
            # Only extract actual files inside 'all_construct_records/' (not subfolders)
            if member.startswith("all_construct_records/") and not member.endswith("/"):
                # Get the file name only (strip folder path)
                filename = os.path.basename(member)
                if not filename:
                    continue  # skip any edge cases

                # Destination path directly in outdir_dir
                target_path = os.path.join(outdir_gb, filename)

                # Write the file content
                with zipf.open(member) as source, open(target_path, "wb") as target:
                    target.write(source.read())

    return output_simulation, outdir_gb


def parse_command_line_args():
    parser = argparse.ArgumentParser(description="Domestication")

                        help="dir output for cloning simulation results")
    parser.add_argument("--output_simulation", required=True, 
                        help="zip output for cloning simulation results")
    parser.add_argument('--enzyme', type=str, 
                        help='enzyme to use')
    parser.add_argument("--outdir_gb", required=True, 
                        help="dir output constructs gb files")
 
    return parser.parse_args()

if __name__ == "__main__":
    args = parse_command_line_args()

    cloning_simulation(
        args.parts_files, args.domesticated_seq,
        args.assembly_csv, args.assembly_plan_name, args.topology,
        args.file_name_mapping, args.file_name_mapping_dom, 
        args.use_file_names_as_id, args.outdir_simulation,
        args.output_simulation, args.enzyme, args.outdir_gb
    )