[Biopython-dev] EMBL flatfile parsing

Peter biopython-dev at maubp.freeserve.co.uk
Tue Feb 20 10:48:45 UTC 2007

Michiel de Hoon wrote:
> 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.

Embarrassingly, it also does this on Linux.  I should have caught that...

This was caused by the fasta writer checking that the record ID and 
description do not contain new lines, which should normally be the case.

When I tried just "python test_SeqIO" I found that the SwissProt parser 
had created a record from SwissProt/sp003 whose description contained a 
new line.  Arguably we should update Bio.SwissProt to clean up new line 
characters in the description...

I have updated FastaIO.py to cope with newlines in the ID or description 
(by replacing them with spaces) and the SeqIO unit test now passes on 
Linux.  It should be fine on MacOS too.


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