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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2557


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

Thank you for reporting this oversight,

Peter


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.