finish_argument_non_unique_CDS_IDS

gff3tool/lib/gff3_ID_generator.py

@@ -180,6 +180,7 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
         'missing': []
     }
     ID_order = []
+    Copy_ID_dict=[]
     roots = list()
     logger.info('Generate new ID for features in (%s)', in_gff)
     for line in gff3.lines:
@@ -188,10 +189,14 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
                 if uuid_on:
                     newID = str(uuid.uuid1())
                     if 'ID' in line['attributes']:
+                        #print line['attributes']
                         if line['attributes']['ID'] in ID_dict:
+                            #print line['attributes']['ID']
                             ID_dict[line['attributes']['ID']].append(newID)
                             if alias:
                                 line['attributes']['Alias'] = line['attributes']['ID']
+                            if line['attributes']['ID'] not in Copy_ID_dict:
+                                Copy_ID_dict.append(line['attributes']['ID'])
                             line['attributes']['ID'] = newID
                         else:
                             ID_dict[line['attributes']['ID']] = [newID]
@@ -202,6 +207,7 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
                     else:
                         ID_dict['missing'].append(newID)
                         line['attributes']['ID'] = newID
+
                     if 'Parent' in line['attributes']:
                         for index, parent in enumerate(line['attributes']['Parent']):
                             if parent in ID_dict:
@@ -217,6 +223,8 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
         except KeyError:
             logger.warning('[Missing Attributes] Line (%s)', str(line['line_index'] + 1))
     IDnumber = 0
+    #print Copy_ID_dict
+    #gene parent
     for root in roots:
         newID = idgenerator(prefix, IDnumber, digitlen)
         IDnumber = newID['maxnum']
@@ -231,7 +239,6 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
             for index, parent in enumerate(child['attributes']['Parent']):
                 if parent in ID_dict:
                     child['attributes']['Parent'][index] = newID['ID']
-
             newcID = '%s-R%s' % (newID['ID'], alphabets.pop(0))
             ID_dict[child['attributes']['ID']] = [newcID]
             ID_order.append(child['attributes']['ID'])
@@ -271,6 +278,7 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
                                 descend['attributes']['ID'] = newdID['ID']
                                 flag = True
                             descend['attributes']['Parent'][index] = ID_dict[parent][0]
+
     if merge_report and out_merge_report:
         logger.info('Update report file generated by gff3_merge program with new IDs.')
         with open(out_merge_report, 'w') as out_f:
@@ -287,17 +295,48 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
             for log_line in log_lines:
                 out_f.write('\t'.join(log_line) + '\n')
     logger.info('Write out gff3 file: (%s)', out_gff)
+
+    #cds_share_id
+    cds_parent=[]
+    Copy_ID_dict_value=[]
+    listid=[]
+    if args.type:
+        for line in gff3.lines:
+            if line['type']=='CDS':
+                for i in line['attributes']['Parent']:
+                    if i not in cds_parent:
+                        cds_parent.append(i)
+
+                #parent_feature
+                for z in cds_parent:
+                    newID2 = str(uuid.uuid4())
+                    if z not in Copy_ID_dict_value:
+                        Copy_ID_dict_value.append(z)
+                        keyparent={'Parent':z,'ID':[newID2]}
+                        #listid will store all newid in order
+                        listid.append(keyparent['ID'])
+                    #overwrite gff3 file
+                    line['attributes'].update(keyparent)
+
+        cds_update_part = {}
+        for k,v in zip(Copy_ID_dict, listid):
+            cds_update_part.setdefault(k,v)
+            #cds_update_part.setdefault(k, []).append(v)
+
+        #overwrite report file
+        ID_dict.update(cds_update_part)
+
     write_gff3(gff3, out_gff)
     if report:
         ID_order.append('missing')
         logger.info('Generate a report of comparison between old and new IDs: (%s)', report)
         out_line = 'Old_ID\tNewID'
         out_report.write(out_line+'\n')
+
         for key in ID_order:
             for value in ID_dict[key]:
                 out_line = '%s\t%s' % (key, value)
                 out_report.write(out_line+'\n')
-
         out_report.close()
 
 if __name__ == '__main__':
@@ -318,6 +357,7 @@ def main(in_gff, merge_report, out_merge_report, out_gff, uuid_on, prefix, digit
     parser.add_argument('-r', '--report', type=str, help='Generate a table of comparison between old and new IDs.')
     parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + __version__)
     parser.add_argument('-a', '--alias', action='store_true', default=False, help='Specify this argument if you want old IDs to be retained in the gff3 file as an Alias attribute')
+    parser.add_argument('-t','--type', type=str)
 
     args = parser.parse_args()
     main(in_gff=args.gff, merge_report=args.merge_report, out_merge_report=args.out_merge_report, out_gff=args.output_gff, uuid_on=args.universally_unique_identifier, prefix=args.idprefix, digitlen=args.digitlen, report=args.report, alias=args.alias)