From 1f0b688cde55432cfc009a35ef7a5e10e0b4f2f0 Mon Sep 17 00:00:00 2001
From: ParsaGhadermazi <54489047+ParsaGhadermazi@users.noreply.github.com>
Date: Thu, 17 Oct 2024 16:37:54 -0600
Subject: [PATCH] Update core.py

---
 adtoolbox/core.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/adtoolbox/core.py b/adtoolbox/core.py
index b22260b..26d2591 100644
--- a/adtoolbox/core.py
+++ b/adtoolbox/core.py
@@ -2293,7 +2293,28 @@ def run_qiime2_from_sra(self,
         if save_manifest:
             manifest.to_csv(os.path.join(manifest_dir,"manifest.tsv"),sep="\t",index=False)
         return qiime2_bash_str,manifest
+
+
+class Annotation:
     
+    def __init__(self,config:configs.Annotation):
+        self.config=config
+        
+    def annotate_with_metacyc_(
+                                alignment_file:str,
+                                )->dict[str,dict[str,str]]:
+        """"
+        This function annotates the genomes with the metabolic pathways using the metabolic pathways database.
+        Required Configs:
+            None
+        Args:
+            alignment_file (str): The path to the alignment file.
+        Returns:
+            dict: A dictionary containing the metabolic pathways  and their coverage in based on
+            the input alignment file.
+        """
+        pass
+        
 
 
 if __name__ == "__main__":