[Biopython-dev] [Bug 2639] SeqRecord.init doesn't check for arguments for their types

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2639


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

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|REOPENED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2009-01-30 06:54 EST -------
(In reply to comment #5)
> Ok, understood. I didn't thought of these cases.
> However, having not a Seq causes errors that are difficult to
> understand in other functions that use SeqRecord.
> For example, if you do:
> 
> >>> a = SeqRecord(id = '1')
> >>> a.format('fasta')
> 
> you get the error: 
> <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute
> 'tostring'
> 
> This could scary an eventual biopython newbie, an exception like to
> 'error - current SeqRecord object doesn't have a Seq' could be better.

Well, if you want to create a SeqRecord where the sequence is None, you'd have
to do SeqRecord(None, id="1") - your suggestion of SeqRecord(id="1") doesn't
work as the sequence is a mandatory argument.

However, I see your point that the current AttributeError isn't helpful in this
special case.  I've updated the Bio/SeqIO/FastaIO.py file in CVS (revision
1.15) to give a TypeError in this situation which will try to explain the
problem.

> What do you think about creating a 'NullSeq' object, which represent a
> Seq with no value, and using it as a default for SeqRecord?
> Later we could modify the other functions like .format e Seq.translate to
> intercept these objects and return the right error message.

Hmm.  It seems rather complicated for a rare case.  Using None to mean
"missing" or "null" is done in other python libraries/code (e.g. database
access), which is why I suggested someone might want to do this.

Marking this bug as fixed.


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