Adding nested lists for relationships. These are imported when 'relat…

…ionship' is added to the optional_attrs. This way, they can be used more easily in analysis. Pretty printing has been updated also, to account for this.

goatools/obo_parser.py

@@ -7,6 +7,7 @@
 """Read and store Gene Ontology's obo file."""
 # -*- coding: UTF-8 -*-
 from __future__ import print_function
+from collections import defaultdict
 import sys
 import os
 import re
@@ -120,17 +121,36 @@ def update_rec(self, rec, name, value):
  # 'def' is a reserved word in python, do not use it as a Class attr.
  if name == "def":
  name = "defn"
+
+ # If we have a relationship, then we will split this into a further
+ # dictionary.
+
  if hasattr(rec, name):
  if name not in self.attrs_scalar:
- getattr(rec, name).add(value)
+ if name not in self.attrs_nested:
+ getattr(rec, name).add(value)
+ else:
+ self._add_nested(rec, name, value)
  else:
  raise Exception("ATTR({NAME}) ALREADY SET({VAL})".format(
  NAME=name, VAL=getattr(rec, name)))
  else: # Initialize new GOTerm attr
  if name in self.attrs_scalar:
  setattr(rec, name, value)
- else:
+ elif name not in self.attrs_nested:
  setattr(rec, name, set([value]))
+ else:
+ name = '_{:s}'.format(name)
+ setattr(rec, name, defaultdict(list))
+ self._add_nested(rec, name, value)
+
+ def _add_nested(self, rec, name, value):
+ """Adds a term's nested attributes."""
+ # Remove comments and split term into typedef / target term.
+ (typedef, target_term) = value.split('!')[0].rstrip().split(' ')
+
+ # Save the nested term.
+ getattr(rec, name)[typedef].append(target_term)
 
  def _init_optional_attrs(self, optional_attrs):
  """Prepare to store data from user-desired optional fields.
@@ -147,6 +167,7 @@ def _init_optional_attrs(self, optional_attrs):
  self.attrs_scalar = ['comment', 'defn',
  'is_class_level', 'is_metadata_tag',
  'is_transitive', 'transitive_over']
+ self.attrs_nested = frozenset(['relationship'])
  # Allow user to specify either: 'def' or 'defn'
  # 'def' is an obo field name, but 'defn' is legal Python attribute name
  fnc = lambda aopt: aopt if aopt != "defn" else "def"
@@ -206,8 +227,16 @@ def __repr__(self):
  else:
  ret.append("{K}: {V} items".format(K=key, V=len(val)))
  if len(val) < 10:
- for elem in val:
- ret.append(" {ELEM}".format(ELEM=elem))
+ if not isinstance(val, dict):
+ for elem in val:
+ ret.append(" {ELEM}".format(ELEM=elem))
+ else:
+ for (typedef, terms) in val.items():
+ ret.append(" {TYPEDEF}: {NTERMS} items"
+ .format(TYPEDEF=typedef,
+ NTERMS=len(terms)))
+ for t in terms:
+ ret.append(" {TERM}".format(TERM=t))
  return "\n ".join(ret)
 
  def has_parent(self, term):
@@ -327,10 +356,16 @@ def _init_depth(rec):
  rec.depth = max(_init_depth(rec) for rec in rec.parents) + 1
  return rec.depth
 
- # make the parents references to the GO terms
+ # Make parents and relationships references to the actual GO terms.
  for rec in self.values():
  rec.parents = [self[x] for x in rec._parents]
 
+ if hasattr(rec, '_relationship'):
+ rec.relationship = defaultdict(list)
+ for (typedef, terms) in rec._relationship.items():
+ rec.relationship[typedef] = [self[x] for x in terms]
+ delattr(rec, '_relationship')
+
  # populate children and levels
  for rec in self.values():
  for p in rec.parents: