goOboParser.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A constant-space parser for the GeneOntology OBO v1.2 format

Version 1.0
"""

from collections import defaultdict

__author__    = "Uli Koehler"
__copyright__ = "Copyright 2013 Uli Koehler"
__license__   = "Apache v2.0"

def processGOTerm(goTerm):
    """
    In an object representing a GO term, replace single-element lists with
    their only member.
    Returns the modified object as a dictionary.
    """
    ret = dict(goTerm) #Input is a defaultdict, might express unexpected behaviour
    for key, value in ret.items():
        if len(value) == 1:
            ret[key] = value[0]
    return ret

def parseGOOBO(filename):
    """
    Parses a Gene Ontology dump in OBO v1.2 format.
    Yields each 
    Keyword arguments:
        filename: The filename to read
    """
    with open(filename, "r") as infile:
        return _parseGOOBO(infile)

def _parseGOOBO(infile):
    currentGOTerm = None
    for line in infile:
        line = line.strip()
        if not line: continue #Skip empty
        if line == "[Term]":
            if currentGOTerm: yield processGOTerm(currentGOTerm)
            currentGOTerm = defaultdict(list)
        elif line == "[Typedef]":
            #Skip [Typedef sections]
            currentGOTerm = None
        else: #Not [Term]
            #Only process if we're inside a [Term] environment
            if currentGOTerm is None: continue
            key, sep, val = line.partition(":")
            currentGOTerm[key].append(val.strip())
    #Add last term
    if currentGOTerm is not None:
        yield processGOTerm(currentGOTerm)

if __name__ == "__main__":
    """Print out the number of GO objects in the given GO OBO file"""
    import argparse
    parser = argparse.ArgumentParser()
    parser.add_argument('infile', help='The input file in GO OBO v1.2 format.')
    args = parser.parse_args()
    #Iterate over GO terms
    termCounter = 0
    for goTerm in parseGOOBO(args.infile):
        termCounter += 1
    print("Found %d GO terms" % termCounter)