--- a/mature_mir_gff_translation.py	Tue Jul 25 11:04:28 2017 -0400
+++ b/mature_mir_gff_translation.py	Wed Jul 26 19:15:08 2017 -0400
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-import sys
 import argparse
 
 
@@ -9,24 +8,27 @@
     the_parser.add_argument(
         '--input', action="store", type=str, help="input miRBase GFF3 file")
     the_parser.add_argument(
-        '--output', action="store", type=str, help="output GFF3 file with converted mature mir coordinates")
+        '--output', action="store", type=str,
+        help="output GFF3 file with converted mature mir coordinates")
     args = the_parser.parse_args()
     return args
 
-GFF3_header= '''##gff-version 3
+
+GFF3_header = '''##gff-version 3
 ##generated by mature_mir_gff_translation.py
 #
 # Chromosomal coordinates of microRNAs ** relative to the hairpin precursors **
 # microRNAs:               miRBase current_version
 # genome-build-id:         check http://mirbase.org/
 #
-# Hairpin precursor sequences have type "miRNA_primary_transcript". 
-# Note, these sequences do not represent the full primary transcript, 
-# rather a predicted stem-loop portion that includes the precursor 
+# Hairpin precursor sequences have type "miRNA_primary_transcript".
+# Note, these sequences do not represent the full primary transcript,
+# rather a predicted stem-loop portion that includes the precursor
 # miRNA. Mature sequences have type "miRNA".
 #
 '''
 
+
 def load_gff_in_dict(gff_input_file):
     '''
     Reads the gff3 file and return a dictionary of dictionaries
@@ -35,26 +37,29 @@
     '''
     gff_dict = {}
     for line in open(gff_input_file, "r"):
-        if line[0]=="#":
+        if line[0] == "#":
             continue
-        gff_fields=line[:-1].split("\t")
-        ID=gff_fields[8].split("ID=")[1].split(";")[0]
+        gff_fields = line[:-1].split("\t")
+        ID = gff_fields[8].split("ID=")[1].split(";")[0]
         gff_dict[ID] = {}
-        gff_dict[ID]["seqid"]=gff_fields[0]
-        gff_dict[ID]["source"]=gff_fields[1]
-        gff_dict[ID]["type"]=gff_fields[2]
-        gff_dict[ID]["start"]=gff_fields[3]
-        gff_dict[ID]["end"]=gff_fields[4]
-        gff_dict[ID]["score"]=gff_fields[5]
-        gff_dict[ID]["strand"]=gff_fields[6]
-        gff_dict[ID]["phase"]=gff_fields[7]
-        gff_dict[ID]["attributes"]=gff_fields[8]
+        gff_dict[ID]["seqid"] = gff_fields[0]
+        gff_dict[ID]["source"] = gff_fields[1]
+        gff_dict[ID]["type"] = gff_fields[2]
+        gff_dict[ID]["start"] = gff_fields[3]
+        gff_dict[ID]["end"] = gff_fields[4]
+        gff_dict[ID]["score"] = gff_fields[5]
+        gff_dict[ID]["strand"] = gff_fields[6]
+        gff_dict[ID]["phase"] = gff_fields[7]
+        gff_dict[ID]["attributes"] = gff_fields[8]
         if "Derives_from" in gff_dict[ID]["attributes"]:
-            parent_primary_transcript=gff_dict[ID]["attributes"].split("Derives_from=")[1]
-            parent_primary_transcript=gff_dict[parent_primary_transcript]["attributes"].split("Name=")[1]
-            gff_dict[ID]["attributes"]="%s;Parent_mir_Name=%s" % (gff_dict[ID]["attributes"], parent_primary_transcript)
+            parent_primary_transcript = gff_dict[ID]["attributes"].split(
+                "Derives_from=")[1]
+            parent_primary_transcript = gff_dict[parent_primary_transcript][
+                                            "attributes"].split("Name=")[1]
+            gff_dict[ID]["attributes"] = "%s;Parent_mir_Name=%s" % (
+                gff_dict[ID]["attributes"], parent_primary_transcript)
     return gff_dict
-    
+
 
 def genome_to_mir_gff(gff_dict, output):
     '''
@@ -63,36 +68,50 @@
     Note that GFF files are 1-based coordinates
     '''
     for key in gff_dict:
-        name=gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
-        gff_dict[key]["seqid"]=name
+        name = gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
+        gff_dict[key]["seqid"] = name
         if "Derives_from=" in gff_dict[key]["attributes"]:
-            parent_ID=gff_dict[key]["attributes"].split("Derives_from=")[1].split(";")[0]
-            gff_dict[key]["start"]=str(int(gff_dict[key]["start"]) - int(gff_dict[parent_ID]["start"]) + 1)
-            gff_dict[key]["end"]=str(int(gff_dict[key]["end"]) - int(gff_dict[parent_ID]["start"]) + 1)
-    hairpins={}
-    matures={}
-    for key in gff_dict:  ## treats miRNA_primary_transcript coordinates in a second loop to avoid errors in conversion
-        if gff_dict[key]["type"]=="miRNA_primary_transcript":
-            gff_dict[key]["end"]=str(int(gff_dict[key]["end"]) - int(gff_dict[key]["start"]) + 1)
-            gff_dict[key]["start"]="1"
+            parent_ID = gff_dict[key]["attributes"].split(
+                                        "Derives_from=")[1].split(";")[0]
+            gff_dict[key]["start"] = str(int(gff_dict[key]["start"])-int(
+                                       gff_dict[parent_ID]["start"])+1)
+            gff_dict[key]["end"] = str(int(gff_dict[key]["end"])-int(
+                                     gff_dict[parent_ID]["start"])+1)
+    hairpins = {}
+    matures = {}
+    # treats miRNA_primary_transcript coordinates
+    # in a second loop to avoid errors in conversion
+    for key in gff_dict:
+        if gff_dict[key]["type"] == "miRNA_primary_transcript":
+            gff_dict[key]["end"] = str(int(gff_dict[key]["end"])-int(
+                                       gff_dict[key]["start"]) + 1)
+            gff_dict[key]["start"] = '1'
             # now, do a dict[ID]=Name but only for miRNA_primary_transcript
-            hairpins[key]=gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
+            hairpins[key] = gff_dict[key]["attributes"].split(
+                                                        "Name=")[1].split(
+                                                        ";")[0]
         else:
-            matures[key]=gff_dict[key]["attributes"].split("Name=")[1].split(";")[0]
+            matures[key] = gff_dict[key]["attributes"].split(
+                                                        "Name=")[1].split(
+                                                         ";")[0]
     with open(output, "w") as output:
         output.write(GFF3_header)
         for ID in sorted(hairpins, key=hairpins.get):
-            output.write("\t".join([gff_dict[ID]["seqid"], gff_dict[ID]["source"],
-                gff_dict[ID]["type"], gff_dict[ID]["start"], gff_dict[ID]["end"],
-                gff_dict[ID]["score"], gff_dict[ID]["strand"], gff_dict[ID]["phase"],
-                gff_dict[ID]["attributes"]]))
+            output.write("\t".join([gff_dict[ID]["seqid"],
+                         gff_dict[ID]["source"], gff_dict[ID]["type"],
+                         gff_dict[ID]["start"], gff_dict[ID]["end"],
+                         gff_dict[ID]["score"], gff_dict[ID]["strand"],
+                         gff_dict[ID]["phase"], gff_dict[ID]["attributes"]]))
             output.write("\n")
             for id in sorted(matures, key=matures.get, reverse=True):
                 if ID in gff_dict[id]["attributes"]:
-                    output.write("\t".join([gff_dict[id]["seqid"], gff_dict[id]["source"],
-                        gff_dict[id]["type"], gff_dict[id]["start"], gff_dict[id]["end"],
-                        gff_dict[id]["score"], gff_dict[id]["strand"],
-                        gff_dict[id]["phase"], gff_dict[id]["attributes"]]))
+                    output.write("\t".join([gff_dict[id]["seqid"],
+                                 gff_dict[id]["source"], gff_dict[id]["type"],
+                                 gff_dict[id]["start"], gff_dict[id]["end"],
+                                 gff_dict[id]["score"],
+                                 gff_dict[id]["strand"],
+                                 gff_dict[id]["phase"],
+                                 gff_dict[id]["attributes"]]))
                     output.write("\n")
 
 
@@ -103,4 +122,4 @@
 
 if __name__ == "__main__":
     args = Parser()
-    main(args.input, args.output)
\ No newline at end of file
+    main(args.input, args.output)