def test_write(self) :
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
fout = StringIO()
null_io.write(fout,seqs)
fout.seek(0)
self.assertEqual(fout.read(), '')
def test_write(self):
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
fout = StringIO()
null_io.write(fout, seqs)
fout.seek(0)
self.assertEqual(fout.read(), '')
def test_write_seq(self):
f = StringIO(array_io.example)
seqs = array_io.read(f)
fout = StringIO()
array_io.write(fout, seqs)
fout.seek(0)
seqs2 = array_io.read(fout)
self.assertEqual(seqs, seqs2)
def test_write_seq(self):
f = StringIO(array_io.example)
seqs = array_io.read(f)
fout = StringIO()
array_io.write(fout, seqs)
fout.seek(0)
seqs2 = array_io.read(fout)
self.assertEqual(seqs, seqs2)
def test_write_comments(self):
f = StringIO(example_with_optional_comments)
seqs = fasta_io.read(f)
fout = StringIO()
fasta_io.write(fout, seqs)
fout.seek(0)
seqs2 = fasta_io.read(fout)
self.assertEqual(seqs, seqs2)
self.assertEqual(seqs[1].description, seqs2[1].description)
def test_write_comments(self) :
f = StringIO(example_with_optional_comments)
seqs = fasta_io.read(f)
fout = StringIO()
fasta_io.write(fout, seqs)
fout.seek(0)
seqs2 = fasta_io.read(fout)
self.assertEqual(seqs, seqs2)
self.assertEqual(seqs[1].description, seqs2[1].description)
def test_write(self):
f = StringIO(clustal_io.example)
seqs = clustal_io.read(f)
fout = StringIO()
clustal_io.write(fout, seqs)
fout.seek(0)
seqs2 = clustal_io.read(fout)
self.assertEqual(seqs, seqs2)
f.close()
def test_write(self):
f = StringIO(clustal_io.example)
seqs = clustal_io.read(f)
fout = StringIO()
clustal_io.write(fout, seqs)
fout.seek(0)
seqs2 = clustal_io.read(fout)
self.assertEqual(seqs, seqs2)
f.close()
def test_write_seq(self) :
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
fout = StringIO()
plain_io.write(fout,seqs)
fout.seek(0)
seqs2 = plain_io.read(fout)
#print seqs[0].alphabet !=seqs2[0].alphabet
self.assertEqual(seqs[0].alphabet, seqs2[0].alphabet)
self.assertEqual(seqs[0], seqs2[0])
self.assertEqual(seqs, seqs2)
def test_write_seq(self):
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
fout = StringIO()
plain_io.write(fout, seqs)
fout.seek(0)
seqs2 = plain_io.read(fout)
#print seqs[0].alphabet !=seqs2[0].alphabet
self.assertEqual(seqs[0].alphabet, seqs2[0].alphabet)
self.assertEqual(seqs[0], seqs2[0])
self.assertEqual(seqs, seqs2)
def read_seq_data(fin,
input_parser=seq_io.read,
alphabet=None,
ignore_lower_case=False,
max_file_size=0):
""" Read sequence data from the input stream and return a seqs object.
The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument.
Used to limit the load on the WebLogo webserver.
"""
max_file_size = int(os.environ.get("WEBLOGO_MAX_FILE_SIZE", max_file_size))
# If max_file_size is set, or if fin==stdin (which is non-seekable), we
# read the data and replace fin with a StringIO object.
if (max_file_size > 0):
data = fin.read(max_file_size)
more_data = fin.read(2)
if more_data != "":
raise IOError("File exceeds maximum allowed size: %d bytes" %
max_file_size)
fin = StringIO(data)
elif fin == sys.stdin:
fin = StringIO(fin.read())
fin.seek(0)
seqs = input_parser(fin)
if seqs is None or len(seqs) == 0:
raise ValueError("Please provide a multiple sequence alignment")
if ignore_lower_case:
# Case is significant. Do not count lower case letters.
for i, s in enumerate(seqs):
seqs[i] = s.mask()
# Add alphabet to seqs.
if alphabet:
seqs.alphabet = Alphabet(alphabet)
else:
seqs.alphabet = Alphabet.which(seqs)
return seqs
def read_seq_data(fin,
input_parser=seq_io.read,
alphabet=None,
ignore_lower_case=False,
max_file_size=0):
""" Read sequence data from the input stream and return a seqs object.
The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument.
Used to limit the load on the WebLogo webserver.
"""
max_file_size =int(os.environ.get("WEBLOGO_MAX_FILE_SIZE", max_file_size))
# If max_file_size is set, or if fin==stdin (which is non-seekable), we
# read the data and replace fin with a StringIO object.
if(max_file_size>0) :
data = fin.read(max_file_size)
more_data = fin.read(2)
if more_data != "" :
raise IOError("File exceeds maximum allowed size: %d bytes" % max_file_size)
fin = StringIO(data)
elif fin == sys.stdin:
fin = StringIO(fin.read())
fin.seek(0)
seqs = input_parser(fin)
if seqs is None or len(seqs) ==0 :
raise ValueError("Please provide a multiple sequence alignment")
if ignore_lower_case :
# Case is significant. Do not count lower case letters.
for i,s in enumerate(seqs) :
seqs[i] = s.mask()
# Add alphabet to seqs.
if alphabet :
seqs.alphabet = Alphabet(alphabet)
else :
seqs.alphabet = Alphabet.which(seqs)
return seqs
