def extract_sequences(file):
scanner = NCBIStandalone._Scanner()
consumer = SequencesExtractor()
file_to_parse = open(file, 'r')
scanner.feed(file_to_parse, consumer)
file_to_parse.close()
return consumer.sequences_list
handle = func("/somewhere/blast", "blastz", "nr",
"/tmp/example.fasta", \
nprocessors=4,
expectation="0.001",
filter= "F > /etc/passwd'")
assert False, "Attempted output redirection not caught!"
except ValueError, e:
assert str(e) == "Rejecting suspicious argument for filter"
#Good
### _Scanner
print "Running tests on _Scanner"
scanner = NCBIStandalone._Scanner()
for test in all_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("Blast", test)
scanner.feed(open(datafile), ParserSupport.AbstractConsumer())
for test in detailed_tests:
print "*" * 50, "TESTING %s" % test
datafile = os.path.join("Blast", test)
scanner.feed(open(datafile), ParserSupport.TaggingConsumer())
### BlastParser
print "Running tests on BlastParser"
parser = NCBIStandalone.BlastParser()
