GO workflow. Does not work.

workflows/geneontology.py

@@ -0,0 +1,132 @@
+import networkx
+import re
+
+class GOTerm:
+    def __init__(self):
+        self.d = {}
+
+        ## Create empty lists for all list values
+        for l in GOTerm.lists:
+            self.d[l] = []
+        for s in GOTerm.scalars:
+            self.d[l] = None
+        
+    def __getitem__(self, key):
+        if self.d.has_key(key):
+            return self.d[key]
+        return None
+
+    def __setitem__(self, key, value):
+        self.d[key] = value
+
+GOTerm.lists = ['is_a', 'alt_id', 'exact_synonym', 'broad_synonym',
+                'narrow_synonym', 'related_synonym', 'relationship',
+                'subset', 'synonym', 'xref_analog', 'xref_unknown']
+GOTerm.scalars = ['name', 'id', 'namespace', 'def', 'is_transitive',
+                  'comment', 'is_obsolete']
+
+
+class GeneOntology(networkx.XDiGraph):
+    def __init__(self):
+        networkx.XDiGraph.__init__(self)
+        self.by_id = {}
+
+    def add_term(self, term):
+        self.add_node(term)
+        self.by_id[term['id']] = term
+        
+    def link_ontology(self, linkattr, obsolete=False):
+        for node in self.nodes():
+            for link in node[linkattr]:
+                self.add_edge(node, self.by_id[link], linkattr)
+
+    def get_bp(self):
+        return self.by_id['GO:0008150']
+
+    def get_cc(self):
+        return self.by_id['id: GO:0005575']
+
+    def get_mf(self):
+        return self.by_id['GO:0003674']
+
+
+def _split_obo_line(line):
+    """Splits a line from an obo file in its three constituent parts.
+    
+    @param line: A string containing a line from an obo file. The line must
+        either be a section definition field with a section name in brackets
+        or a line of the form: keyword: value ! comment
+    @returns: A tuple of four strings conaining the section, key, value and 
+        description defined in the string. If the section part is None, all
+        the other fields are strings and if section is a string, all the other
+        fields are None.
+    """
+    attrib_re = re.compile(r'^\s*([\w-]+)\s*:\s*([^!]*)!?(.*$)')
+    s = line.strip()    
+    if s == "":
+        return (None, None, None, None)
+    elif s.startswith('[') and s.endswith(']'):
+        return (s[1:-1], None, None, None)
+    else:
+        m = attrib_re.match(s)
+        if m:
+            key, value, comment = [x.strip() for x in m.groups()]        
+            return (None, key, value, comment)
+        else:
+            raise Exception('Unparsable line: %s' % line)
+
+
+def _add_term_attribute(term, key, value, comment):
+    if key in GOTerm.scalars:
+        term[key] = value
+    elif key in GOTerm.lists:
+        term[key].append(value)
+    else:
+        raise Exception('Unknown key %s: %s' % (key, value))
+   
+
+def read_gene_ontology(fd):
+    """Reads the Gene Ontology from an obo file.
+
+    @param fd: An open file object to the obo file.
+    """
+    go = GeneOntology()
+    term = None
+    section = None
+
+    line = fd.readline()
+    while line:
+        s, k, v, c = _split_obo_line(line)
+        if s == None and k == None:
+            pass
+        elif s:
+            if term:
+                go.add_term(term)
+
+            section = s
+            if s == 'Term':
+                term = GOTerm()
+                print "[Term]"
+            else:
+                term = None
+                print "ignoring: %s" %s
+        else:
+            if term:
+                _add_term_attribute(term, k, v, c)
+#                print "    %s: %s" % (k, v)
+            else:
+                print "no term: ignoring: %s" %line
+        print '.',
+        line = fd.readline()
+
+    if term:
+        go.add_term(term)
+
+    return go            
+
+def read_default_go():
+    f = open("/usr/share/gene-ontology/gene_ontology.obo")
+    go = read_gene_ontology(f)
+
+    f.close()
+    return go