Mercurial > repos > iuc > data_manager_fetch_busco_options

annotate data_manager/extract.py @ 0:4e3bbaa0b70f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
author iuc
date Tue, 22 Apr 2025 13:12:07 +0000
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4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
1 import json
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
2 import os
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
3 import re
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
4 import sys
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
5
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
6 busco_db = os.path.join(sys.argv[1], "lineages")
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
7 busco_db_value = sys.argv[2]
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
8 dmjson = sys.argv[3]
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
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9
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
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10 content = []
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
11 for d in os.scandir(busco_db):
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
12 if not d.is_dir():
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
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13 continue
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
14 if not os.path.exists(os.path.join(d, "dataset.cfg")):
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
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15 continue
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
16 name = re.sub(r"_odb\d+", "", d.name)
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
17 name = name.replace("_", " ").capitalize()
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
diff changeset
18 content.append({'value': d.name, 'name': name, 'db_value': busco_db_value})
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
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4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
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20 with open(dmjson, "w") as fh:
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
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21 json.dump({"data_tables": {"busco_database_options": content}}, fh)
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
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22
4e3bbaa0b70f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
parents:
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23 print(f'{len(content)} x busco_db\n')