[Bioperl-l] arabidopsis + load_seqdatabase.pl

Angshu Kar angshu96 at gmail.com
Mon Dec 19 17:39:37 EST 2005


I've tried .faa, .fna and .gbk files in the link mentioned below. After
running the script when I saw the loaded database, I saw that in the
bioentry table the 3 fields accession, identifier and name containing the
same data.Also, the version column was not populated. I want them to be
correctly parsed. So I want an arabidopsis data file that "goes well" with
the load_seqdatabase.pl script.


On 12/19/05, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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.
> Sean

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