Create bio.py

plugins/bio.py

@@ -0,0 +1,55 @@
+#!/usr/bin/python3
+#
+# bio.py
+# Biopython plugin for Caterpillar Proxy
+#
+# Euiseo Cha (Wonkwang University) <zeroday0619_dev@outlook.com>
+# https://github.com/gnh1201/caterpillar
+# Created at: 2024-07-02
+# Updated at: 2024-07-02
+#
+
+import json
+from Bio.Seq import Seq
+from Bio.SeqUtils import gc_fraction
+
+from server import Extension
+
+
+def _analyze_sequence(sequence) -> dict[str, str]:
+    sequence_object = Seq(sequence)
+    return dict(
+        complement=str(sequence_object.complement()),
+        complement_rna=str(sequence_object.complement_rna()),
+        reverse_complement=str(sequence_object.reverse_complement()),
+        reverse_complement_rna=str(sequence_object.reverse_complement_rna()),
+        transcription=str(sequence_object.transcribe()),
+        translation=str(sequence_object.translate()),
+        back_transcribe=str(sequence_object.back_transcribe()),
+    )
+
+
+def _gc_content_calculation(sequence) -> dict[str, str]:
+    gc_content = gc_fraction(sequence)
+    return dict(
+        gc_content=gc_content,
+    )
+
+
+class PyBio(Extension):
+    def __init__(self):
+        self.type = "rpcmethod"
+        self.method = "analyze_sequence_init"
+        self.exported_methods = ["analyze_sequence", "gc_content_calculation"]
+
+    def dispatch(self, type, id, params, conn):
+        print("[*] Greeting! dispatch")
+        conn.send(b'Greeting! dispatch')
+
+    def analyze_sequence(self, type, id, params, conn):
+        result = _analyze_sequence(params['sequence'])
+        return result
+
+    def gc_content_calculation(self, type, id, params, conn):
+        result = _gc_content_calculation(params['sequence'])
+        return result