[Biopython-dev] Almost there...

[Iddo Friedberg]

OK, we have a Nexus parser now. And Biopython is now compatible with 
Python versions >= 2.3

Thanks to Frank Kauff and Cymon Cox.

Thanks to James Casbon and Michiel for getting rid of that pesky 
Fasta.Dictionary bug.

I fixed the silly AlignInfo Information Content bug.

CAPS module on its way.


Still have these left:

1) test_PDB: Thomas?


test_PDB ... WARNING: disordered atom found with blanc altloc before 
line 31.
WARNING: Residue (' ', 4, ' ') redefined at line 41.
WARNING: Residue (' ', 10, ' ') redefined at line 73.
WARNING: Residue (' ', 14, ' ') redefined at line 104.
WARNING: Residue (' ', 16, ' ') redefined at line 133.
WARNING: Residue (' ', 80, ' ') redefined at line 631.
WARNING: Residue (' ', 81, ' ') redefined at line 644.

2)  Warnings in the GFF: Michael?

test_GFF ... 
/home/idoerg/biopy_cvs/biopython/build/lib.linux-i686-2.3/Bio/GFF/easy.py:595: 
DeprecationWarning: forward_complement in Bio.GFF is deprecated; please 
use complement in Bio.Seq instead
  category=DeprecationWarning)
/home/idoerg/biopy_cvs/biopython/build/lib.linux-i686-2.3/Bio/GFF/easy.py:640: 
DeprecationWarning: reverse_complement in Bio.GFF is deprecated; please 
use reverse_complement in Bio.Seq instead
  category=DeprecationWarning)


3) And failures in test_Registry and test_Restriction... Frederic and Jeff?


======================================================================
FAIL: test_Registry
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 148, in runTest
    self.runSafeTest()
  File "run_tests.py", line 185, in runSafeTest
    expected_handle)
  File "run_tests.py", line 285, in compare_output
    assert expected_line == output_line, \
AssertionError:
Output  : 'Retrieval of PDB data from various locations. ... ERROR\n'
Expected: 'Retrieval of PDB data from various locations. ... ok\n'

======================================================================
FAIL: test_Restriction
----------------------------------------------------------------------
Traceback (most recent call last):
  File "run_tests.py", line 148, in runTest
    self.runSafeTest()
  File "run_tests.py", line 185, in runSafeTest
    expected_handle)
  File "run_tests.py", line 285, in compare_output
    assert expected_line == output_line, \
AssertionError:
Output  : 'Test basic cutting with EcoRI. ... FAIL\n'
Expected: 'Test basic cutting with EcoRI. ... ok\n'

----------------------------------------------------------------------
Ran 91 tests in 182.965s





-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930
http://ffas.ljcrf.edu/~iddo
==========================
The First Automated Protein Function Prediction SIG
Detroit, MI June 24, 2005
http://ffas.burnham.org/AFP