if failed[0]:
sys.stderr.write("FAILED\n")
sys.exit(30)
else: sys.stderr.write("PASSED\n")
RESOURCE_PATH = os.path.dirname(__file__)+"/test_data"
_ = "Test 2. Parse correct sequences"
sys.stderr.write(_+"... ")
test_items = os.listdir(RESOURCE_PATH+"/test01/in/")
f = open(RESOURCE_PATH+"/test01/references/reference.json", "r")
reference = json.load(f)
f.close()
for item in test_items:
try:
sqs = bioformats.read_sequences_from_file(RESOURCE_PATH+"/test01/in/"+item)
seqs = dict()
for name, value in sqs:
seqs[name.lower()] = value
assert len(seqs.keys())==len(reference.keys())
for key, value in reference.items():
assert key in seqs
assert seqs[key]==value
except:
failed[1] = True
if failed[1]: sys.stderr.write("FAILED\n")
else: sys.stderr.write("PASSED\n")
_ = "Test 3. Try to parse incorrect sequences"
sys.stderr.write(_+"... ")
test_items = os.listdir(RESOURCE_PATH+"/test01/in/")
elif arg.startswith("-"):
_print_usage_and_exit(0)
else:
if file1name is None:
file1name = arg
else:
file2name = arg
if run_selftest:
_run_selftest_and_exit()
if file1name is None:
_print_usage_and_exit(0)
seqs = []
try:
seqs += bioformats.read_sequences_from_file(file1name)
except BioFormatException as e:
sys.stderr.write("Error: "+e.text+"\n")
sys.exit(5)
if not file2name is None:
try:
seqs += bioformats.read_sequences_from_file(file1name)
except BioFormatException as e:
sys.stderr.write("Error: "+e.text+"\n")
sys.exit(5)
if len(seqs)<2:
sys.stderr.write("Error: requires at least two sequences\n")
sys.exit(6)
name1, seq1 = seqs[0]
if args.dist:
dist=args.dist;
if args.wlen:
wlen=args.wlen;
if args.wshift:
wshift=args.wshift;
if args.minscore:
minscore=args.minscore;
try:
sequences = bioformats.read_sequences_from_file(args.FILE)
except bioformats.BioFormatException as e:
sys.stderr.write("Error: "+e.text+"\n")
sys.exit(1)
if not sequences:
sys.stderr.write("Error: file does not contain any sequence\n")
sys.exit(2)
name, seq = sequences[0]
res = _rna.doAll(seq.encode('ascii'),wlen,wshift,minscore,sfrom,10000,seed)
import csv
writer = csv.writer(sys.stdout, dialect="excel")
writer.writerow(["start", "end", "score"])
