fix bug #15 even for python2.7

ppanggolin/ppanggolin.py

@@ -456,8 +456,7 @@ def __neighborhood_computation(self, directed = False):#,light = False, untangle
                 if contig in self.circular_contig_size:#circularization
                     self.__add_link(gene_info_start[FAMILY],family_id_nei,organism, (self.circular_contig_size[contig] - end_family_nei) + gene_info_start[START])
 
-                contig_annot[gene_start]=gene_info_start
-                contig_annot.move_to_end(gene_start, last=False)#move to the beginning
+                ordered_dict_prepend(contig_annot,gene_start,gene_info_start)#insert at the top
             # if light:
             #    del self.annotations[organism]
 

ppanggolin/utils.py

@@ -4,7 +4,7 @@
 import sys
 import gzip
 from decimal import Decimal
-from collections import defaultdict
+from collections import defaultdict, OrderedDict
 import math
 from random import sample
 from io import TextIOWrapper
@@ -79,4 +79,23 @@ def median(numbers):
         return numbers[n//2]
     else:
         i = n//2
-        return (numbers[i - 1] + numbers[i])/2
+        return (numbers[i - 1] + numbers[i])/2
+
+"""insertion of element at the top of an OrderedDict (for compatibility with python 2.7)
+from : https://stackoverflow.com/questions/16664874/how-can-i-add-an-element-at-the-top-of-an-ordereddict-in-python/18326914
+"""
+def ordered_dict_prepend(dct, key, value, dict_setitem=dict.__setitem__):
+    root = dct._OrderedDict__root
+    first = root[1]
+
+    if key in dct:
+        link = dct._OrderedDict__map[key]
+        link_prev, link_next, _ = link
+        link_prev[1] = link_next
+        link_next[0] = link_prev
+        link[0] = root
+        link[1] = first
+        root[1] = first[0] = link
+    else:
+        root[1] = first[0] = dct._OrderedDict__map[key] = [root, first, key]
+        dict_setitem(dct, key, value)