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test_KEGG.py

00001 """Tests the basic functionality of the KEGG parsers.
"""

import os

from Bio.KEGG import Enzyme
from Bio.KEGG import Compound
from Bio.KEGG import Map
from Bio.Pathway import System

test_KEGG_Enzyme_files   = ["enzyme.sample", "enzyme.irregular"]
test_KEGG_Compound_files = ["compound.sample", "compound.irregular"] 
test_KEGG_Map_files      = ["map00950.rea"]

00015 def t_KEGG_Enzyme(testfiles):
    """Tests Bio.KEGG.Enzyme functionality."""
    for file in testfiles:
        fh = open(os.path.join("KEGG", file))
        print "Testing Bio.KEGG.Enzyme on " + file + "\n\n"
        records = Enzyme.parse(fh)
        for record in records:
            print record
        print "\n"
        fh.close()

00026 def t_KEGG_Compound(testfiles):
    """Tests Bio.KEGG.Compound functionality."""
    for file in testfiles:
        fh = open(os.path.join("KEGG", file))
        print "Testing Bio.KEGG.Compound on " + file + "\n\n"
        records = Compound.parse(fh)
        for record in records:
            print record
        print "\n"
        fh.close()

00037 def t_KEGG_Map(testfiles):
    """Tests Bio.KEGG.Map functionality."""
    for file in testfiles:
        fh = open(os.path.join("KEGG", file))
        print "Testing Bio.KEGG.Map on " + file + "\n\n"
        reactions = Map.parse(fh)
        system = System()
        for reaction in reactions:
            system.add_reaction(reaction)
        # sort the reaction output by the string names, so that the
        # output will be consistent between python versions
        #def str_cmp(first, second):
        #    return cmp(str(first), str(second))
        rxs = system.reactions()
        #sort: key instead of compare function (for py3 support)
        #  The function str_cmp above can be removed if the
        #  solution below proves resilient
        rxs.sort(key=lambda x:str(x))
        for x in rxs:
            print str(x)
        fh.close()


t_KEGG_Enzyme(test_KEGG_Enzyme_files)
t_KEGG_Compound(test_KEGG_Compound_files)
t_KEGG_Map(test_KEGG_Map_files)



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