We tracked down the error to the fact that the Hilmar Oracle version (no
assertion is made about the complexity) uses CLOBs to store sequence while
the Len Oracle (no assertion about simplicity etc) version uses LONGs to
store sequence. The biojava support code seems to assume LONGs and
strange
I looked into this in a bit more detail earlier today and found that,
since some version of Oracle around the 9i point in time, the official
Oracle JDBC driver API for accessing LOBs in changed. This means that
whereas before the same code could be used in BioJava to access both
Hilmar's and Len's
CLOB is IMHO actually easier to handle. Also, LONG is really odd to
deal with in SQL whereas the Oracle server will nicely on-the-fly
convert strings to CLOB and vice versa so long as they are shorter than
4000 chars. Some of the type-generic functions that come with Oracle
will not accept LONG
Mark Schreiber wrote:
> store sequence. The biojava support code seems to assume LONGs and
> strangely until very recently the JDBC oracle dirver seems to let you
> write LONGs to CLOBs although the data that comes out again is completely
> munged.
>
> It would be possible to modify the biojav
Don't worry, I do know how to do it, it's just that in the existing
BioJava-live code it hasn't been done, and I'll need to be careful to
add the usual checks to see if we're using Oracle or not before choosing
the appropriate SQL to update biosequence with.
CLOBs under 4000 chars are certainly ea
You can use NCBI's eutils to get GenBank in XML format. BioJava has a
GenBankXML parser.
Robin XML <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
04/16/2005 07:23 PM
To: [email protected]
cc: [EMAIL PROTECTED], (bcc: Mark Schreiber/GP/Novartis)
Subject:
Use eutils
Here's an example:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&i
d=NM_003234&report=docsum&rettype=xml
Russell
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Robin XML
Sent: Saturday, 16 April 2005 11:23 p.m.
To
Sorry, here's the XML version:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&i
d=NM_003234&rettype=gb&retmode=text
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Robin XML
Sent: Saturday, 16 April 2005 11:23 p.m.
To: biojava-l@b
