[Biopython-dev] EMBL flatfile parsing

[Michiel de Hoon]

Hi Peter,

Currently, the SeqIO test fails on Mac OS X (see below). It looks like 
this is due to a different line separator being used on Macintosh.

--Michiel.


mdehoon:~/biopython/Tests $ python run_tests.py test_SeqIO
test_SeqIO ... FAIL

======================================================================
FAIL: test_SeqIO
----------------------------------------------------------------------
Traceback (most recent call last):
   File "run_tests.py", line 148, in runTest
     self.runSafeTest()
   File "run_tests.py", line 161, in runSafeTest
     cur_test = __import__(self.test_name)
   File "/Users/mdehoon/biopython/Tests/test_SeqIO.py", line 261, in 
<module>
     check_simple_write_read(records, test_write_read_non_alignment_formats)
   File "/Users/mdehoon/biopython/Tests/test_SeqIO.py", line 140, in 
check_simple_write_read
     WriteSequences(sequences=records, handle=handle, format=format)
   File 
"/Users/mdehoon/biopython/build/lib.macosx-10.3-i386-2.5/Bio/SeqIO/__init__.py", 
line 229, in WriteSequences
     writer_class(handle).write_file(sequences)
   File 
"/Users/mdehoon/biopython/build/lib.macosx-10.3-i386-2.5/Bio/SeqIO/Interfaces.py", 
line 235, in write_file
     self.write_records(records)
   File 
"/Users/mdehoon/biopython/build/lib.macosx-10.3-i386-2.5/Bio/SeqIO/Interfaces.py", 
line 225, in write_records
     self.write_record(record)
   File 
"/Users/mdehoon/biopython/build/lib.macosx-10.3-i386-2.5/Bio/SeqIO/FastaIO.py", 
line 108, in write_record
     assert os.linesep not in description
AssertionError

----------------------------------------------------------------------
Ran 1 test in 0.429s

FAILED (failures=1)
mdehoon:~/biopython/Tests $