[Bioperl-l] arabidopsis + load_seqdatabase.pl

[Angshu Kar]

Thanks Brian.


On 12/20/05, Brian Osborne <osborne1 at optonline.net> wrote:
>
> Angshu,
>
> >I want them to be correctly parsed.
>
> They have been correctly parsed but you're looking in the wrong place. The
> names and identifiers associated with things like "CDS" or "gene" will not
> be found in the Bioentry table. The Bioentry is the entire NC_* record,
> the
> genes, mRNAs, and proteins are called features. Read the
> Feature-Annotation
> HOWTO and doc/schema-overview.txt in the biosql package.
>
> Brian O.
>
>
> On 12/19/05 5:39 PM, "Angshu Kar" <angshu96 at gmail.com> wrote:
>
> > Sean,
> >
> > 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.
> >
> > Thanks,
> > Angshu
> >
> >
> > 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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>
>
>