[Biopython-dev] [Bug 2639] SeqRecord.init doesn't check for arguments to 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|RESOLVED                    |REOPENED
         Resolution|FIXED                       |




------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-06 06:50 EST -------
(In reply to comment #3)
> Created an attachment (id=1041)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1041&action=view) [details]
> add a check for the seq argument in seqrecord, to be a Seq object and not None
>
> This patch adds a check for the seq argument in SeqRecord.
> If seq is None (by default), it raises a ValueError Exception.
> If it is a Seq objects, it saves it as self.seq.
> If it is another kind of object (string, list, integer), it is converted to a
> string, and then used to instantiate a seq object.

I was deliberately not checking the seq argument.  There are several reasonable
use cases:

* a Seq object (normal) or a subclass of it.
* a MutableSeq object (seems reasonable, note this is not a subclass of Seq)
* None (seems a good way to handle sequence records where we don't know the
sequence - for example some GenBank files).
* a user defined sequence object which implements the Seq API but does not
subclass Seq or MutableSeq (this is more difficult to check).

> I thought that someone could use an integer (e.g.: 010100010101101) as a
> sequence, and in this case, the integer is first converted to a string
> (otherwise Seq() would return an error).

Note that if someone did want to use some weird numerical sequence, then the
SeqRecord object should NOT be trying to do anything special (guessing what is
intended). The user should create a suitable Seq object themselves (ideally
with a numerical alphabet object).  Explicit rather than implicit (Zen of
python).

--

Note that I'm not 100% happy with the type checking we've just added.  See
"duck-typing" and interfaces versus types,
http://www.python.org/doc/2.5.2/tut/node18.html#l2h-46

The checks I've added shouldn't be too constraining - but maybe they should use
using interface checking instead (or just revert back to no checking).

Any comments from other people?  This should be being CC'd to the dev mailing
list.


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