[Bioperl-l] arabidopsis + load_seqdatabase.pl
angshu96 at gmail.com
Tue Dec 20 12:43:32 EST 2005
On 12/20/05, Brian Osborne <osborne1 at optonline.net> wrote:
> >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,
> genes, mRNAs, and proteins are called features. Read the
> 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
> > 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"
> > 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
> >> 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
> >> file isn't being loaded as you think it should be. For example, if
> >> 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,
> >> annotation associated with the foo tag is stored.
> >> Sean
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