Re: [Gmod-ajax] sequences via database

[Robert B. <rb...@gm...>]

Hi Steffi,

I've done some work to explore this today, and basically, the way 
prepare-refseqs.pl is implemented right now, if you read sequences out 
of a database you need to have loaded some gff3 that defines the 
features those sequences belong to (if only with sequence-region 
pragmas) first.

If you really only want to do sequence right now, the easiest thing 
would be to convert your fasta to a gff3 file (with an embedded fasta 
section), using either gmod_fasta2gff3.pl (which comes with Chado), or 
by hand by just adding three lines to the top of a fasta file:

##gff3-version 3
chrI	.	chromosome	1	12345	.	.	.	Name=chrI
##FASTA
(and have the rest of your fasta here)

If you then load that with bp_seqfeature_load, then prepare-refseqs.pl 
should pick the sequences up correctly.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 09/13/2012 09:11 AM, Steffi Geisen wrote:
> Hi,
> how is the prepare-sequences.pl <http://prepare-sequences.pl> supposed
> to work with a configuration script?
> I loaded the sequences of the human chromosome 1 into the database
> (bio::db::seqfeature::store) via bp_seqfeature_load.pl
> <http://bp_seqfeature_load.pl>
> but cannot get them via prepare-sequences.pl
> <http://prepare-sequences.pl> and a configuration script.
> What do I have to add into the configuration script besides the adapter
> settings?
>
> I don't want to add this at the moment because I don't have features
> yet, I only want to see the DNA..
> "TRACK DEFAULTS": {
> "class": "feature",
> "autocomplete": "all"
>    },
>
> "tracks": [
>      {
> "track": "repeat_region",
> "key": "Repeat Region",
> "feature": ["repeat_region"],
> "class": "feature"
>      },
>
> without all these track settings (and also with these track settings)
> the error messages range from
>
>   bin/prepare-refseqs.pl <http://prepare-refseqs.pl> --conf
> customScripts/confTracks.conf --out hg19 --refids 1
> Can't call method "name" on an undefined value at
> /var/www/jbrowse/bin/../src/
> perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 254.
>
> to
>   bin/prepare-refseqs.pl <http://prepare-refseqs.pl> --conf
> customScripts/confTracks.conf --out hg19 --refs chr1
> WARNING: Reference sequence 'chr1' not found in input.
> No reference sequences found, exiting.
>
>
> Anyone knows how this has to work?
> with flatfile-to-json it works fine, but I don't want to load the data
> from flatfiles because I have to work with a database!
>
> Thanks in advance
>
>
>
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