added project structure

Author: itaybroder

.gitignore

@@ -0,0 +1 @@
+__pycache__/

__pycache__/tools.cpython-310.pyc

@@ -4,9 +4,9 @@
 
 #getting a list of all mutations from the file
 voc_mutation_list = []
-mutation_list = pd.read_csv("all_mut.csv")["Mutation"]
+mutation_list = pd.read_csv("./data/all_mut.csv")["Mutation"]
 
-with open("voc_mutation.txt", "r") as f:
+with open("./data/voc_mutation.txt", "r") as f:
     lines = f.readlines()
 
 for line in lines:
@@ -25,20 +25,18 @@
     for mut in mutation_list:
         if("-" in mut):
             continue
-        mut_pos = int(mut[1:-1])
+        mut_pos = int(mut[1:-1]) 
         new_aa = mut[-1]
         start_pos = int(peptide[1])
         end_pos = int(peptide[2])
-        if(mut_pos >= start_pos and  end_pos >= mut_pos):
-            relative_index = mut_pos-start_pos-1
+        if(mut_pos >= start_pos and  end_pos > mut_pos):
+            relative_index = mut_pos-start_pos 
             new_peptide = peptide[0]
             new_peptide = list(new_peptide)
             new_peptide[relative_index] = new_aa 
             new_peptide = "".join(new_peptide)
             rows.append([mut_pos, new_aa, start_pos, end_pos, peptide[0], new_peptide, is_vocs(mut, voc_mutation_list)])
 
 df = pd.DataFrame(rows, columns=cols)
-df.to_csv("mutation_peptide_df.csv")
-#------------------------------------------------------------------------------------------------------------------
-
-
+df.to_csv("./data/mutation_peptide_df.csv")
+#------------------------------------------------------------------------------------------------------------------