[Biopython] About bioseqI0
Han Chen
han.chen1986 at gmail.com
Sat Nov 14 13:25:21 UTC 2009
Hi, List of helpful people,
could your please offer me some help about bioseqIo?
here is the error message when run "python setup.py test":
======================================================================
ERROR: test_SeqIO_online
----------------------------------------------------------------------
Traceback (most recent call last):
File "run_tests.py", line 248, in runTest
suite = unittest.TestLoader().loadTestsFromName(name)
File "/usr/local/lib/python2.6/unittest.py", line 576, in
loadTestsFromName
module = __import__('.'.join(parts_copy))
File "test_SeqIO_online.py", line 42, in <module>
records = list(SeqIO.parse(handle, "swiss"))
File
"/home/ch/biopython-1.51/build/lib.linux-x86_64-2.6/Bio/SeqIO/SwissIO.py",
line 39, in SwissIterator
for swiss_record in swiss_records:
File
"/home/ch/biopython-1.51/build/lib.linux-x86_64-2.6/Bio/SwissProt/__init__.py",
line 113, in parse
record = _read(handle)
File
"/home/ch/biopython-1.51/build/lib.linux-x86_64-2.6/Bio/SwissProt/__init__.py",
line 240, in _read
raise ValueError("Unknown keyword '%s' found" % key)
ValueError: Unknown keyword '>s' found
----------------------------------------------------------------------
Ran 124 tests in 60.180 seconds
FAILED (failures = 1)
Is there anything wrong with SeqIO? I meet the following error when using
other package:
DeprecationWarning: Bio.Fasta is deprecated. Please use the "fasta" support
in Bio.SeqIO (or Bio.AlignIO) instead
could you please help me about this? thank you very much!
sincerely yours,
Han
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