[Gmod-ajax] working with a config file

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-ajax] working with a config file

David Breimann
Hi,

I use flat files (fasta, gff and wig) to build my JBrowse genomes. I wnat to start using configure files, but I'm not sure how to do that. Which db_adaptor should I use? Can I load the sequence file using the config also or only the tracks? What about the wig? How should I specify dir/file names?

I has a look at http://jbrowse.org/code/jbrowse-master/docs/config.html but didn't get it.

Thanks,
Dave

------------------------------------------------------------------------------
The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://ad.doubleclick.net/clk;226879339;13503038;l?
http://clk.atdmt.com/CRS/go/247765532/direct/01/
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: working with a config file

Mitch Skinner
Have you looked at docs/tutorial/conf_files/volvox.json?

It uses the "memory" adaptor, which loads the files in the specified directory into memory and makes those available to the JBrowse code.  That works fine if you have relatively small gff and fasta files.  Look at the "db_args" setting for an example of how to specify the directory, and at the bioperl documentation for Bio::DB::SeqFeature::Store::memory for more details.

If you have larger files, and if you're only using them with JBrowse and/or GBrowse, then the Bio::DB::SeqFeature::Store adaptor with a database is useful; that's how I've been setting up the Dmel demo.  Setting up the database is more complex, though; I wrote down the steps I take to set up the Dmel demo here:

http://sourceforge.net/mailarchive/forum.php?thread_name=4AC20FFC.7010605%40berkeley.edu&forum_name=gmod-ajax

If you're using the database with other GMOD tools then you can also use the Bio::DB::Das::Chado adaptor; if you google for it, you'll find the documentation for setting it up.  If you run into specific problems with it then we can probably help.

You can indeed load the sequence using a config file; prepare-refseqs.pl can take a config file as an argument.  When you do that, you also have to specify a list of reference sequence names or IDs.  The prepare-refseqs.pl usage message has some details.

Even if you use a config file for the sequence and feature data, that doesn't change how you process the wig data; you still use wig-to-json.pl.

Mitch

On 07/26/2010 06:17 AM, David Breimann wrote:
Hi,

I use flat files (fasta, gff and wig) to build my JBrowse genomes. I wnat to start using configure files, but I'm not sure how to do that. Which db_adaptor should I use? Can I load the sequence file using the config also or only the tracks? What about the wig? How should I specify dir/file names?

I has a look at http://jbrowse.org/code/jbrowse-master/docs/config.html but didn't get it.

Thanks,
Dave
------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://ad.doubleclick.net/clk;226879339;13503038;l? http://clk.atdmt.com/CRS/go/247765532/direct/01/
_______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://ad.doubleclick.net/clk;226879339;13503038;l?
http://clk.atdmt.com/CRS/go/247765532/direct/01/
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax