[Biopython-dev] [Bug 2557] AlignIO::write fails when delegating to SeqIO::write

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jul 30 08:55:42 UTC 2008


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED

------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-30 04:55 EST -------
That's embarrassing for me!  Bug confirmed and fixed in CVS.

I've used a very slightly simpler fix, taking advantage of the fact that you
can iterate for the SeqRecords within an alignment:

SeqIO.write(alignment, handle, format)

I've also updated the Bio.AlignIO unit test to cover writing a couple of the
formats supported via Bio.SeqIO ("fasta" and "tab"), although it might make
sense to try all of them...

Checking in Bio/AlignIO/__init__.py;
/home/repository/biopython/biopython/Bio/AlignIO/__init__.py,v  <-- 
new revision: 1.10; previous revision: 1.9
Checking in Tests/test_AlignIO.py;
/home/repository/biopython/biopython/Tests/test_AlignIO.py,v  <-- 
new revision: 1.12; previous revision: 1.11
Checking in Tests/output/test_AlignIO;
/home/repository/biopython/biopython/Tests/output/test_AlignIO,v  <-- 
new revision: 1.10; previous revision: 1.9

Thank you for reporting this oversight,


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