[Bioperl-l] postgres 8.3 - load_seqdatabase.pl / swissprot

[Erik]

On Sun, March 23, 2008 20:22, Hilmar Lapp wrote:
>
> On Mar 23, 2008, at 2:16 PM, Erik wrote:
>> Sprot loaded in 20 hours. Only 170 were rejected - not
>> too bad.
>
> That's great. Would be nice if you can provide some rough
> summary as  to why they were rejected (if that's
obvious), such as taxon errors,
> or other errors.

see

   http://bugzilla.open-bio.org/show_bug.cgi?id=2474

So I think one easy improvement will be to enlarge that 
varchar(40) column, dbxref.accession. See the following:

select
	dbname
,	accession
,	length(accession)
from 	dbxref
where accession ~ 'Cyc'
order by length(accession) desc
limit 100

patch attached. (which will probably get bug 2389 resolved)

It seems to me bioentry.accession (maybe identifier too?)
needs a similar enlargement.


thanks,

Erikjan
-------------- next part --------------
A non-text attachment was scrubbed...
Name: biosqldb-pl.sql.diff
Type: application/octet-stream
Size: 535 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20080324/a564d7ee/attachment-0004.obj>