[Bioperl-l] arabidopsis + load_seqdatabase.pl

Sean Davis sdavis2 at mail.nih.gov
Mon Dec 19 16:50:20 EST 2005

On 12/19/05 3:20 PM, "Angshu Kar" <angshu96 at gmail.com> wrote:

> Sean,
> I've used files from
> ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_V  . But the script
> cannot parse them according to biosql-schema.
> So, I want some files that the script can parse correctly.
> Else, I've to load each and every file onto the biodb and then check whether
> it has been parsed correctly!

Which file are you trying to load?  What format is it in?  What values are
you expecting to be loaded that aren't?  For the answer to the last
question, it will likely help folks to see exactly what line of the input
file isn't being loaded as you think it should be.  For example, if there is
a line in a file that contains

     foo         /note="bar"

Then you can point out that you would like to know where, if at all, the
annotation associated with the foo tag is stored.


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