Merge pull request #30 from dvklopfenstein/master

New GOTerm, id_num.  Help with install for those with pygraphviz dll issues.

README.rst

@@ -64,14 +64,21 @@ Dependencies
 
     easy_install fisher
 
-If you need to plot the ontology lineage, you need the following tools to be
-installed.
+- To plot the ontology lineage, install one of these two options:
 
-- `Graphviz <http://www.graphviz.org/>`_, for graph visualization.
-- `pygraphviz <http://networkx.lanl.gov/pygraphviz/>`_, Python binding for
-  communicating with Graphviz::
+  1. Graphviz
 
-    easy_install pygraphviz
+     - `Graphviz <http://www.graphviz.org/>`_, for graph visualization.
+     - `pygraphviz <http://networkx.lanl.gov/pygraphviz/>`_, Python binding for
+       communicating with Graphviz::
+     
+         easy_install pygraphviz
+
+  2. `pydot <https://code.google.com/p/pydot/>`_, a Python interface to Graphviz's Dot language.    
+     - `pyparsing <http://pyparsing.wikispaces.com/>`_ is a requirement for pydot    
+     - Images can be viewed using either:    
+       - `ImageMagick <http://www.imagemagick.org/>`_'s *display*
+       - `Graphviz <http://www.graphviz.org/>`_
 
 
 Cookbook

goatools/obo_parser.py

@@ -80,6 +80,9 @@ def __next__(self):
         for line in lines:
             if line.startswith("id:"):
                 rec.id = after_colon(line)
+                num = rec.id.replace("GO:", "", 1)
+                if num.isdigit():
+                  rec.id_num = int(num)
             if line.startswith("alt_id:"):
                 rec.alt_ids.append(after_colon(line))
             elif line.startswith("name:"):
@@ -102,6 +105,7 @@ class GOTerm:
 
     def __init__(self):
         self.id = ""                # GO:xxxxxx
+        self.id_num = None          # GO term integer
         self.name = ""              # description
         self.namespace = ""         # BP, CC, MF
         self._parents = []          # is_a basestring of parents

setup.py

@@ -26,5 +26,5 @@
     url='http://github.com/tanghaibao/goatools',
     description="Python scripts to find enrichment of GO terms",
     long_description=open("README.rst").read(),
-    install_requires=['fisher', 'pygraphviz']
+    install_requires=['fisher']
     )