1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
|
"""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"]
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()
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)
|
