Mercurial > repos > iuc > data_manager_fetch_busco
comparison data_manager/extract.py @ 5:6ab91825be22 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
| author | iuc |
|---|---|
| date | Fri, 04 Apr 2025 10:12:43 +0000 |
| parents | |
| children |
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| 4:828d961faea7 | 5:6ab91825be22 |
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| 1 import json | |
| 2 import os | |
| 3 import re | |
| 4 import sys | |
| 5 | |
| 6 busco_db = os.path.join(sys.argv[1], "lineages") | |
| 7 busco_db_value = sys.argv[2] | |
| 8 dmjson = sys.argv[3] | |
| 9 | |
| 10 content = [] | |
| 11 for d in os.scandir(busco_db): | |
| 12 if not d.is_dir(): | |
| 13 continue | |
| 14 if not os.path.exists(os.path.join(d, "dataset.cfg")): | |
| 15 continue | |
| 16 name = re.sub(r"_odb\d+", "", d.name) | |
| 17 name = name.replace("_", " ").capitalize() | |
| 18 content.append({'value': d.name, 'name': name, 'db_value': busco_db_value}) | |
| 19 | |
| 20 with open(dmjson, "w") as fh: | |
| 21 json.dump({"data_tables": {"busco_database_options": content}}, fh) | |
| 22 | |
| 23 print(f'{len(content)} x busco_db\n') |