[Bioperl-l] PullHSP bug
cjfields at illinois.edu
Wed Dec 3 10:06:06 EST 2008
On Dec 3, 2008, at 5:38 AM, Sendu Bala wrote:
> Chris Fields wrote:
>> The short and easy fix is either having get_nse() or blast_pull
>> fall back to '', but both are technically wrong as there isn't a
>> true ID. Ideas? Maybe a fallback 'unknown' ID (which seems to be
>> used as a ).
...fallback in some cases (Can tell I was getting tired).
> I'd say for now at least the fix would be to alter get_nse() to fall
> back to ''. You don't want the work-around code duplicated in
> multiple places. Indeed, the normal blast parser should be altered
> to return undef as well.
That solution requires get_nse to silently convert this; the exception
is raised b/c the N/S-E is used for indexing (so lack of any one of
those may result in indexing issues, such as replacing sequences with
same ID but no S-E, etc.).
> Then if a more desirable solution is thought of in the future,
> there's just one place to implement it: in get_nse().
We don't want the exception turned off unless it is explicitly known
the sequence instance lacks any or all of the N/S-E, such as in this
case. Setting an explicit LocatableSeq flag for such instances
(force_nse), then having get_nse() DTRT internally would be easy to
Odd, list mail hasn't been coming through (bioperl-gut either). I'll
post something to support.
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