diff data_manager/extract.py @ 5:5459ec34767a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/extract.py	Fri Mar 07 22:33:29 2025 +0000
@@ -0,0 +1,49 @@
+import json
+import os
+import sys
+
+fun_db = sys.argv[1]
+fun_db_value = sys.argv[2]
+dmjson = sys.argv[3]
+
+content = []
+# get options for parameter --busco_db
+# which are just the subfolders of the db dir (minus outgroups/ and trained_species/)
+# https://github.com/nextgenusfs/funannotate/blob/8cc40728fee61566fdf736c1f2292e14cc117660/funannotate/predict.py#L319
+for d in os.scandir(fun_db):
+    if not d.is_dir():
+        continue
+    if d.name in ['outgroups', 'trained_species']:
+        continue
+    if not os.path.exists(os.path.join(d, "dataset.cfg")):
+        continue
+    name = d.name.replace("_", " ").capitalize()
+    content.append({'value': d.name, 'name': name, 'select': 'busco_db', 'db_value': fun_db_value})
+
+# --busco_seed_species
+# trained_species
+for d in os.scandir(os.path.join(fun_db, "trained_species")):
+    if not d.is_dir():
+        continue
+    if not os.path.exists(os.path.join(d, "info.json")):
+        continue
+    name = d.name.replace("_", " ").capitalize()
+    content.append({'value': d.name, 'name': name, 'select': 'trained_species', 'db_value': fun_db_value})
+
+# --busco_seed_species
+# outgroups
+for f in os.scandir(os.path.join(fun_db, "outgroups")):
+    if f.is_dir():
+        continue
+    if not f.name.endswith("_buscos.fa"):
+        continue
+    value = f.name[:-10]
+    name = ' - '.join([x.replace("_", " ").capitalize() for x in value.split('.')])
+    content.append({'value': value, 'name': name, 'select': 'outgroup', 'db_value': fun_db_value})
+
+with open(dmjson, "w") as fh:
+    json.dump({"data_tables": {"funannotate_options": content}}, fh)
+
+print(f'{len([c for c in content if c["select"]=="busco_db"])} x busco_db\n')
+print(f'{len([c for c in content if c["select"]=="trained_species"])} x trained_species\n')
+print(f'{len([c for c in content if c["select"]=="outgroup"])} x outgroup\n')