[Biopython-dev] swissprot not working ?

[Michal Kurowski]

Hi,
I've installed biopython-1.00a2 revently and I'm having some
unexpected problems:
1) swissprot module has some serious problems. Running "swissprot.py"
   from the "examples" directory gives traceback i am attaching.
2) installation won't go smoothly. ( I'm sure I've got TextTools
   installed ;-). The log is in a attachment.

My python is:

Python 2.0 (#1, Dec 20 2000, 15:28:16) 
[GCC 2.96 20000731 (Red Hat Linux 7.0)] on linux2
Type "copyright", "credits" or "license" for more information.
>>> 

from the redhat rpm package.

Cheers,

-- 
Michal Kurowski
<mkur at bio.iimcb.gov.pl>
-------------- next part --------------
Script started on Wed Aug 22 19:53:20 2001
]0;michal at a7: /home/michal[michal at a7 michal]$ python2 /home/seals/michal/bin/swiss_kinase.py
Traceback (most recent call last):
  File "/home/seals/michal/bin/swiss_kinase.py", line 23, in ?
    cur_record = s_iterator.next()
  File "/usr/lib/python2.0/site-packages/Bio/SwissProt/SProt.py", line 168, in next
    return self._parser.parse(File.StringHandle(data))
  File "/usr/lib/python2.0/site-packages/Bio/SwissProt/SProt.py", line 289, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.0/site-packages/Bio/SwissProt/SProt.py", line 332, in feed
    self._scan_record(uhandle, consumer)
  File "/usr/lib/python2.0/site-packages/Bio/SwissProt/SProt.py", line 337, in _scan_record
    fn(self, uhandle, consumer)
  File "/usr/lib/python2.0/site-packages/Bio/SwissProt/SProt.py", line 369, in _scan_id
    self._scan_line('ID', uhandle, consumer.identification, exactly_one=1)
  File "/usr/lib/python2.0/site-packages/Bio/SwissProt/SProt.py", line 359, in _scan_line
    read_and_call(uhandle, event_fn, start=line_type)
  File "/usr/lib/python2.0/site-packages/Bio/ParserSupport.py", line 326, in read_and_call
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'ID':
AC   P54646;

]0;michal at a7: /home/michal[michal at a7 michal]$ exit
exit

Script done on Wed Aug 22 19:53:25 2001
-------------- next part --------------
Script started on Wed Aug 22 19:50:29 2001
]0;michal at a7: /usr/local/src/biopython-1.00a2[root at a7 biopython-1.00a2]# python2 setup.py test
running test
test_Enzyme ... ok
test_FSSP ... ok
test_Fasta ... ok
test_Fasta2 ... ok
test_File ... ok
test_GenBank ... ok
test_GenBankFormat ... ok
test_KeyWList ... ok
test_Location ... ok
test_LocationParser ... ok
test_NCBIStandalone ... ok
test_NCBIWWW ... ok
test_ParserSupport ... ok
test_SProt ... ok
test_SubsMat ... ok
test_align ... ok
test_gobase ... ERROR
test_kabat ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite ... ok
test_prosite2 ... ok
test_rebase ... ERROR
test_seq ... ok
test_translate ... ok
test_unigene ... FAIL

======================================================================
ERROR: test_gobase
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 136, in runTest
    __import__(self.test_name)
  File "test_gobase.py", line 12, in ?
    from Bio import Gobase
  File "/usr/lib/python2.0/site-packages/Bio/Gobase/__init__.py", line 33, in ?
    from Bio import Sequence
ImportError: cannot import name Sequence
======================================================================
ERROR: test_rebase
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 136, in runTest
    __import__(self.test_name)
  File "test_rebase.py", line 12, in ?
    from Bio.Rebase import Rebase
  File "/usr/lib/python2.0/site-packages/Bio/Rebase/__init__.py", line 32, in ?
    from Bio import Sequence
ImportError: cannot import name Sequence
======================================================================
FAIL: test_unigene
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 153, in runTest
    expected_handle)
  File "run_tests.py", line 247, in compare_output
    assert expected_line == output_line, \
AssertionError: 
Output  : '        key is D61454\012'
Expected: '        key is F10922\012'
----------------------------------------------------------------------
Ran 26 tests in 49.226s

FAILED (failures=1, errors=2)
]0;michal at a7: /usr/local/src/biopython-1.00a2[root at a7 biopython-1.00a2]# exit
exit

Script done on Wed Aug 22 19:51:36 2001