diff editDB.py @ 1:6e3a843b6304 draft

planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/editDB.py	Mon Jun 05 02:53:18 2023 +0000
@@ -0,0 +1,63 @@
+# Remove duplicate terms. As well as add any that is needed.
+
+import explodeJSON as ej
+from explodeJSON import save_dict_to_json
+
+
+### create new key
+def add_new_key(db, add_key=[]):
+    """Set of keys to add to the database"""
+    for new_key in add_key:
+        db[new_key] = []
+
+    return db
+
+
+### Add values to dbase:
+def add_value_to_term(index_val, db, add_value=[]):
+    """index value, put in value"""
+    for val in add_value:
+        db[index_val].append(val)
+
+    return db
+
+
+### Remove values from dbase:
+def remove_value_from_term(index_val, db, remove_value=[]):
+    """remove values from list"""
+    for val in remove_value:
+        db[index_val].remove(val)
+
+    return db
+
+
+### Terms to add from a file
+def add_from_file(input_file, index_val, db, sep="\n"):
+    """input file, new line separated currently, and append files to correct key, return is altered dictionary"""
+    terms = open(input_file).read().splitlines()
+    db = add_value_to_term(index_val, db, terms)
+    return db
+
+
+if __name__ == "__main__":
+
+    lysis_json = "data/lysis-family-v1.0.2.json"  # insert json of choice
+    db = ej.explodeJSON(lysis_json)
+    db = db.readJSON()
+    # revise_db = add_new_key(db=db,add_key=["spanins"])
+    # files = ["data/term_additions/200505_holin_domains.txt","data/term_additions/200505_Spanin_Domains.txt"]
+    terms = [
+        "DUF2570",
+        "PF10828",
+        "IPR022538",
+        "DUF2514",
+        "PF10721",
+        "IPR019659",
+        "DUF2681",
+        "PF10883",
+        "IPR020274",
+    ]
+    # revise_db = add_from_file(files[0],"holin_domains",revise_db)
+    # revise_db = add_from_file(files[1],"spanin_domains",revise_db)
+    revise_db = add_value_to_term("spanin_domains", db, add_value=terms)
+    save_dict_to_json(obj=revise_db, filename="data/lysis-family-v1.0.3.json")