--- a/reactome_analysis.py	Fri Jan 24 10:45:56 2020 -0500
+++ b/reactome_analysis.py	Mon May 10 15:30:34 2021 +0000
@@ -1,7 +1,12 @@
-import os, re, json, argparse, csv
+import argparse
+import csv
+import json
+import os
+import re
 
 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
 
+
 def id_valid(identifiers):
     """
     Validate IDs if they contain special characters
@@ -15,7 +20,8 @@
         else:
             remove.append(id)
     return res, remove
-    
+
+
 def isnumber(format, n):
     """
     Check if an variable is numeric
@@ -32,6 +38,7 @@
     else:
         return False
 
+
 def data_json(identifiers):
     """
     Submit IDs list to Reactome and return results in json format
@@ -40,67 +47,70 @@
     trash = []
     if identifiers[1] == "list":
         ids = identifiers[0].split()
-        ids = [x.split(";") for x in ids]    
-        ids = [item.strip() for sublist in ids for item in sublist if item != '']
-        json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
+        ids = [x.split(";") for x in ids]
+        ids = [item.strip() for sublist in ids for item in sublist if item != '']  # noqa 501
+        json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()  # noqa 501
         if len(id_valid(identifiers[0].split())[1]) > 0:
             trash = id_valid(identifiers[0].split())[1]
     elif identifiers[1] == "file":
         header = identifiers[2]
-        with open(identifiers[0],"r") as mq :
-            file_content = csv.reader(mq,delimiter="\t")
-            file_content = list(file_content)   #csv object to list
+        with open(identifiers[0], "r") as mq:
+            file_content = csv.reader(mq, delimiter="\t")
+            file_content = list(file_content)   # csv object to list
             ncol = identifiers[3]
             if isnumber("int", ncol.replace("c", "")):
                 if header == "true":
-                    idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]]
+                    idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content[1:]]]  # noqa 501
                 else:
-                    idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]] 
-
-                idens = [item.strip() for sublist in idens for item in sublist if item != '']   #flat list of list of lists, remove empty items 
+                    idens = [x for x in [line[int(ncol.replace("c", ""))-1].split(";") for line in file_content]]  # noqa 501
+                # flat list of list of lists, remove empty items
+                idens = [item.strip() for sublist in idens for item in sublist if item != '']  # noqa 501
                 ids = "\n".join(id_valid(idens)[0])
-                json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> stderr" % ids).read()
+                json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> stderr" % ids).read()  # noqa 501
                 if len(id_valid(idens)[1]) > 0:
                     trash = id_valid(idens)[1]
-    #print(json_string)
+    # print(json_string)
     j = json.loads(json_string)
-    print ("Identifiers not found: " + str(j["identifiersNotFound"]))
-    print ("Pathways found: " + str(j["pathwaysFound"]))
+    print("Identifiers not found: " + str(j["identifiersNotFound"]))
+    print("Pathways found: " + str(j["pathwaysFound"]))
     return json_string, trash
 
+
 def write_output(filename, json_string, species, trash_file, trash):
     """
     Replace json result in template and print to output
     """
     template = open(os.path.join(CURRENT_DIR, "template.html"))
     output = open(filename, "w")
-    try: 
+    try:
         for line in template:
             if "{token}" in line:
                 line = line.replace("{species}", species)
-                line = line.replace("{token}", json.loads(json_string)["summary"]["token"])
+                line = line.replace("{token}", json.loads(json_string)["summary"]["token"])  # noqa 501
             output.write(line)
     except ValueError:
-        output.write("An error occurred due to unavailability of Reactome web service. Please return later.")
+        output.write("An error occurred due to unavailability of Reactome web service. Please return later.")  # noqa 501
     template.close()
     output.close()
-    
+
     if trash:
-        #print(trash)
+        # print(trash)
         trash_out = open(trash_file, "w")
         trash_out.write("\n".join(trash))
         trash_out.close()
 
+
 def options():
     parser = argparse.ArgumentParser()
     argument = parser.add_argument("--json", nargs="+", required=True)
     argument = parser.add_argument("--output", default="output.html")
     argument = parser.add_argument("--trash", default="trash.txt")
-    argument = parser.add_argument("--species", default="48887")
+    argument = parser.add_argument("--species", default="48887")  # noqa 841
     args = parser.parse_args()
     filename = args.output
     json_string, trash = data_json(args.json)
     write_output(filename, json_string, args.species, args.trash, trash)
 
+
 if __name__ == "__main__":
     options()