Added fix for Networkx v1.11 write_dot changes

README.md

@@ -42,6 +42,7 @@ Downloading the executable files from `ftp://ftp.ncbi.nih.gov/blast/executables/
 4. [Prettytable](https://code.google.com/p/prettytable/)
 5. [Levenshtein](https://pypi.python.org/pypi/python-Levenshtein/)
 6. [Networkx](https://networkx.github.io)
+7. It seems that v1.11 of Networkx behaves differently when writing dot files for use with Graphviz. If you have this (or later versions) you also need to install [PyDotPlus](http://pydotplus.readthedocs.org).
 
 
 ##Setup##

tracer_func.py

@@ -1055,13 +1055,21 @@ def draw_network_from_cells(cells, output_dir, output_format, dot, neato):
     colours = {'A' : '1', 'B' : '2', 'G' : '3', 'D' : '5', 'mean_both' : '#a8a8a8bf'}
     network, draw_tool = make_cell_network_from_dna(cells, colorscheme, colours, False, "box", dot, neato)
     network_file = "{}/clonotype_network_with_identifiers.dot".format(output_dir)
-    nx.write_dot(network, network_file)
+    try:
+        nx.write_dot(network, network_file)
+    except AttributeError:
+        import pydotplus
+        nx.drawing.nx_pydot.write_dot(network, network_file)
     command = draw_tool + ['-o', "{output_dir}/clonotype_network_with_identifiers.{output_format}".format(output_dir=output_dir, output_format=output_format), "-T", output_format, network_file]
     subprocess.check_call(command)
 
     network, draw_tool = make_cell_network_from_dna(cells, colorscheme, colours,  False, "circle", dot, neato)
     network_file = "{}/clonotype_network_without_identifiers.dot".format(output_dir)
-    nx.write_dot(network, network_file)
+    try:
+        nx.write_dot(network, network_file)
+    except AttributeError:
+        import pydotplus
+        nx.drawing.nx_pydot.write_dot(network, network_file)   
     command = draw_tool + ['-o', "{output_dir}/clonotype_network_without_identifiers.{output_format}".format(output_dir=output_dir, output_format=output_format), "-T", output_format, network_file]
     subprocess.check_call(command)