--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactome_analysis.py	Sun Nov 26 19:29:17 2017 -0500
@@ -0,0 +1,99 @@
+import os
+import re
+import json
+import argparse
+
+CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+def id_valid(identifiers):
+    """
+    Validate IDs if they contain special characters
+    """
+    res = []
+    remove = []
+    for id in identifiers:
+        id = id.split(";")[0]
+        if re.match("^[A-Za-z0-9_-]*$", id):
+            res.append(id)
+        else:
+            remove.append(id)
+    return res, remove
+    
+def isnumber(format, n):
+    """
+    Check if an variable is numeric
+    """
+    float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$")
+    int_format = re.compile("^[\-]?[1-9][0-9]*$")
+    test = ""
+    if format == "int":
+        test = re.match(int_format, n)
+    elif format == "float":
+        test = re.match(float_format, n)
+    if test:
+        return True
+    else:
+        return False
+
+def data_json(identifiers):
+    """
+    Submit IDs list to Reactome and return results in json format
+    Return error in HTML format if web service is not available
+    """
+    trash = []
+    if identifiers[1] == "list":
+        ids = "\n".join(id_valid(identifiers[0].split())[0])
+        #print(ids)
+        #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
+        json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read()
+        if len(id_valid(identifiers[0].split())[1]) > 0:
+            trash = id_valid(identifiers[0].split())[1]
+    elif identifiers[1] == "file":
+        header = identifiers[2]
+        mq = open(identifiers[0]).readlines()
+        if isnumber("int", identifiers[3].replace("c", "")):
+            if header == "true":
+                idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq[1:]]
+            else:
+                idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq]
+            ids = "\n".join(id_valid(idens)[0])
+            #print(ids)
+            #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
+            json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read()
+            if len(id_valid(idens)[1]) > 0:
+                trash = id_valid(idens)[1]
+    print(json_string)
+    return json_string, trash
+
+def write_output(filename, json_string, 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: 
+        for line in template:
+            if "{token}" in line:
+                line = line.replace("{token}", json.loads(json_string)["summary"]["token"])
+            output.write(line)
+    except ValueError:
+        output.write("An error occurred due to unavailability of Reactome web service. Please return later.")
+    template.close()
+    output.close()
+    
+    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")
+    args = parser.parse_args()
+    filename = args.output
+    json_string, trash = data_json(args.json)
+    write_output(filename, json_string, args.trash, trash)
+
+if __name__ == "__main__":
+    options()