Add files via upload

definition_main.py

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+import json
+import glob
+import os
+import csv
+import re
+
+#Load .json file
+with open("input_data.json","r") as f:
+    json_data = json.load(f)
+
+#Get every value from .json file
+front_elements = json_data["front_elements"]
+back_elements = json_data["back_elements"]
+spaces = json_data["spaces"]
+alignment_name = json_data["alignment_name"]
+input_file_path = json_data["input_file_path"]
+output_file_path = json_data["output_file_path"]
+
+def confirm_files():
+    #Confirm input file
+    print("-----------------")
+    txt_files=glob.glob(r'{}/*.txt'.format(input_file_path)) #LIST
+    fasta_files=glob.glob(r'{}/*.fasta'.format(input_file_path)) #LIST
+    search_data =txt_files+fasta_files #LIST
+    print(search_data)
+    print("-----------------")
+    return search_data
+
+def info_print(*args):
+    print("-----------------")
+    for i in args:
+        print(str(i))
+    print("-----------------")
+
+def logic_and_output(name,sequence,N_count):
+    #Initialize
+    cordence_rows = []
+    semi_cordence_rows = []
+    header = ["front_elements","spaces",
+        "back_elements","start_num","end_num","region"
+        ] #columns: 1~6
+    os.makedirs(output_file_path, exist_ok=True)
+
+    #The Length of back_elements, front_elements
+    b_len = len(back_elements)
+    f_len = len(front_elements)
+
+    #Find "front_elements" from "sequence"
+    iterator_front = re.finditer(front_elements,sequence) #ITERATOR
+    if any(iterator_front): #True/False
+        for i in iterator_front:
+            group = i.group()
+            s = i.start()+N_count
+            e = i.end()+N_count #end_num
+            region =str(s)+":"+str(e)
+            print("\t"+group+str(s)+str(e))
+            try:
+                expected_b = sequence[e+spaces:e+spaces+b_len]
+                if expected_b == back_elements: #cordence
+                    print("\t"+"  [cordence sequence EXISTS!]")
+                    cordence_rows.append([front_elements,spaces,back_elements,s,e,region])
+                else: #semi_cordence
+                    print("\t"+"  Only semi_cordence")
+                    semi_cordence_rows.append([front_elements,spaces,expected_b,s,e,region])
+            except IndexError as IE:
+                print(IE)
+            except PermissionError as PE:
+                print(PE)
+    else:
+        print("\t"+str(front_elements)+" is not found")
+
+    #Find "back_elements" from "sequence"
+    iterator_back = re.finditer(back_elements,sequence) #ITERATOR
+    if any(iterator_back):#True/False
+        for i in iterator_back:
+            group = i.group()
+            s = i.start()+N_count #start_num
+            e = i.end()+N_count
+            region =str(s)+":"+str(e)
+            print("\t"+group+str(s)+str(e))
+            try:
+                expected_f = sequence[s-spaces-f_len:s-spaces]
+                if expected_f == front_elements:#cordence
+                    print("\t"+"  [cordence sequence EXISTS!]")
+                    cordence_rows.append([front_elements,spaces,back_elements,s,e,region]) #columns: 1~6
+                else:#semi_cordence
+                    print("\t"+"  Only semi_cordence")
+                    semi_cordence_rows.append([expected_f,spaces,back_elements,s,e,region]) #columns: 1~6
+            except IndexError as IE:
+                print(IE)
+            except PermissionError as PE:
+                print(PE)
+    else:
+        print("\t"+str(back_elements)+" is not found")
+
+    #Write "cordence_rows" on .csv file
+    cordence_="./cordence_result_"+name+".csv"
+    cordence_csv=r"{}".format(output_file_path+cordence_)
+    with open(cordence_csv,"w",newline="") as f:
+        w = csv.writer(f)
+        w.writerow(header)
+        w.writerows(cordence_rows)
+
+    #Write "semi_cordence_rows" on .csv file
+    semi_cordence_="./semi_cordence_result_"+name+".csv"
+    semi_cordence_csv=r"{}".format(output_file_path+semi_cordence_)
+    with open(semi_cordence_csv,"w",newline="") as f:
+        w = csv.writer(f)
+        w.writerow(header)
+        w.writerows(semi_cordence_rows)
+
+
+def main():
+    search_data = confirm_files() #LIST
+    total = str(len(search_data))
+    print("=================START=================")
+    for idx,search_file in enumerate(search_data,start=1):
+        with open(search_file,"r") as f1:
+            #Initialize
+            name = f1.readline()
+            num = 5 if search_file.endswith(".txt") else 1
+            name = name[num:40] #info_print(arg), logic_and_output(arg)
+
+            #Initialize AND Pass args to info_print()
+            sequence=f1.read() #logic_and_output(arg)
+            N_count=sequence.count("N")
+            N_info = "N_counts: "+str(N_count) #info_print(arg)
+            base_pairs = str(len(sequence))+"bp" #info_print(arg)
+            sequence=sequence.replace("N", "").replace(" ", "").replace("\n", "") #info_print(arg)
+            info_print(name,N_info,base_pairs)
+
+            #Search
+            logic_and_output(name,sequence,N_count)
+        print("===============continue("+str(idx)+"/"+total+")==============") #Example: ==continue(8/24)==
+    print("[All completed]: "+total+" files!")
+    print("==================END==================")
+
+if __name__ == "__main__":
+    main()

input_data.json

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+{
+    "front_elements":"AAACTAT",
+    "back_elements":"TCCTCAGT",
+    "spaces":27,
+    "alignment_name":"PTENP1_POU5F1B_alignment",
+    "input_file_path":"./input_folder",
+    "output_file_path":"./output_folder"
+}

output_folder/example/cordence_result_NC_000021.9 Homo sapiens chromosome 21,.csv

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+front_elements,spaces,back_elements,start_num,end_num,region