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# Copyright 2004 by Jason A. Hackney. 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.
import os
import string
#Bio.MEME is deprecated now, but I want to keep testing it until
#it is removed (without showing the deprecation warning)
import warnings
warnings.filterwarnings("ignore", category=DeprecationWarning)
from Bio.MEME import Parser
warnings.resetwarnings()
from Bio import ParserSupport
from Bio.File import UndoHandle
meme_tests = [
"meme.dna.oops.txt",
"meme.protein.oops.txt",
"meme.protein.tcm.txt"
]
mast_tests = [
"mast.dna.oops.txt",
"mast.protein.oops.txt",
"mast.protein.tcm.txt"
]
print "Testing MEME Scanner"
datafile = os.path.join("MEME", meme_tests[0])
uhandle = UndoHandle(open(datafile))
scanner = Parser._MEMEScanner()
consumer = ParserSupport.TaggingConsumer()
scanner.feed(uhandle, consumer)
print "Running tests on MEME parser"
meme_parser = Parser.MEMEParser()
for test in meme_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("MEME", test)
rec = meme_parser.parse(open(datafile))
print "Testing MEME Scanner"
datafile = os.path.join("MEME", mast_tests[0])
uhandle = UndoHandle(open(datafile))
scanner = Parser._MASTScanner()
consumer = ParserSupport.TaggingConsumer()
scanner.feed(uhandle, consumer)
print "Running tests on MAST parser"
mast_parser = Parser.MASTParser()
for test in mast_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("MEME", test)
rec = mast_parser.parse(open(datafile))
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