Mercurial > repos > tduigou > cloning_simulation

comparison 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
comparison
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0:3a3b0f7cb5c2 1:2655e08cd61a
1 import argparse 1 import argparse
2 import os 2 import os
3 import json
3 import zipfile 4 import zipfile
4 import pandas 5 import pandas
5 import dnacauldron 6 import dnacauldron
6 7
7 8
141 help="List of GenBank files (Comma-separated)") 142 help="List of GenBank files (Comma-separated)")
142 parser.add_argument("--domesticated_seq", required=True, 143 parser.add_argument("--domesticated_seq", required=True,
143 help="output of domestication (ganbank list)") 144 help="output of domestication (ganbank list)")
144 parser.add_argument("--assembly_csv", required=True, 145 parser.add_argument("--assembly_csv", required=True,
145 help="csv assembly") 146 help="csv assembly")
146 parser.add_argument('--assembly_plan_name', type=str, 147 parser.add_argument('--assembly_plan_name', type=str, required=False,
147 help='type of assembly') 148 help='type of assembly')
148 parser.add_argument('--topology', type=str, 149 parser.add_argument('--topology', type=str, required=False,
149 help='"circular" or "linear"') 150 help='"circular" or "linear"')
150 parser.add_argument('--file_name_mapping', type=str, 151 parser.add_argument('--file_name_mapping', type=str,
151 help='Mapping of Galaxy filenames to original filenames') 152 help='Mapping of Galaxy filenames to original filenames')
152 parser.add_argument('--file_name_mapping_dom', type=str, 153 parser.add_argument('--file_name_mapping_dom', type=str,
153 help='Mapping of Galaxy filenames to original domestication filenames') 154 help='Mapping of Galaxy filenames to original domestication filenames')
155 help="Use file names as IDs (True/False)") 156 help="Use file names as IDs (True/False)")
156 parser.add_argument("--outdir_simulation", required=True, 157 parser.add_argument("--outdir_simulation", required=True,
157 help="dir output for cloning simulation results") 158 help="dir output for cloning simulation results")
158 parser.add_argument("--output_simulation", required=True, 159 parser.add_argument("--output_simulation", required=True,
159 help="zip output for cloning simulation results") 160 help="zip output for cloning simulation results")
160 parser.add_argument('--enzyme', type=str, 161 parser.add_argument('--enzyme', type=str,required=False,
161 help='enzyme to use') 162 help='enzyme to use')
162 parser.add_argument("--outdir_gb", required=True, 163 parser.add_argument("--outdir_gb", required=True,
163 help="dir output constructs gb files") 164 help="dir output constructs gb files")
165 parser.add_argument("--use_json_paramers", required=True,
166 help="Use parameters from JSON: true/false")
167 parser.add_argument("--json_conf", required=False,
168 help="JSON config file with DB parameters")
164 169
165 return parser.parse_args() 170 return parser.parse_args()
166 171
167 172
168 if __name__ == "__main__": 173 if __name__ == "__main__":
169 args = parse_command_line_args() 174 args = parse_command_line_args()
170 175
176 #json param checking
177 config_params = {}
178 use_json = args.use_json_paramers == 'true'
179 if use_json:
180 if not args.json_conf:
181 raise ValueError("You must provide --json_conf when --use_json_paramers is 'true'")
182 with open(args.json_conf, "r") as f:
183 config_params = json.load(f)
184 else:
185 config_params = {
186 "assembly_plan_name": args.assembly_plan_name,
187 "topology": args.topology,
188 "enzyme": args.enzyme
189 }
190 assembly_plan_name = config_params["assembly_plan_name"]
191 topology = config_params["topology"]
192 enzyme = config_params["enzyme"]
193
171 cloning_simulation( 194 cloning_simulation(
172 args.parts_files, args.domesticated_seq, 195 args.parts_files, args.domesticated_seq,
173 args.assembly_csv, args.assembly_plan_name, args.topology, 196 args.assembly_csv, assembly_plan_name, topology,
174 args.file_name_mapping, args.file_name_mapping_dom, 197 args.file_name_mapping, args.file_name_mapping_dom,
175 args.use_file_names_as_id, args.outdir_simulation, 198 args.use_file_names_as_id, args.outdir_simulation,
176 args.output_simulation, args.enzyme, args.outdir_gb 199 args.output_simulation, enzyme, args.outdir_gb
177 ) 200 )