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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2007 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests the basic functionality of the KEGG parsers."""
from __future__ import print_function
import os
from Bio.KEGG import Enzyme
from Bio.KEGG import Compound
from Bio.KEGG import Map
from Bio.Pathway import System
# TODO - use unittest instead of print-and-compare testing
test_KEGG_Enzyme_files = ["enzyme.sample", "enzyme.irregular", "enzyme.new"]
test_KEGG_Compound_files = ["compound.sample", "compound.irregular"]
test_KEGG_Map_files = ["map00950.rea"]
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 i, record in enumerate(records):
print(record)
fh.seek(0)
if i == 0:
print(Enzyme.read(fh))
else:
try:
print(Enzyme.read(fh))
assert False
except ValueError as e:
assert str(e) == 'More than one record found in handle'
print("\n")
fh.close()
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()
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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