Re: [Gmod-ajax] many tracks per GFF file

[Giles V. <gv...@sa...>]

On 11 Sep 2009, at 17:19, Mitch Skinner wrote:

> On 09/11/2009 07:23 AM, Giles Velarde wrote:
>> My apologies for sending this on a Friday afternoon. Since this is my
>> first mail to the list let me say that JBrowse looks fantastic.
>
> Thanks!
>
>>    bin/flatfile-to-json.pl -gff
>> /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/Lmjchr10.gff
>> --autocomplete all --getType --getLabel --getSubs --subfeatureClasses
>> '{"CDS": "transcript-CDS", "exon": "transcript-exon"}' --getPhase
>>
>>    bin/generate-names.pl -v
>>
>> This works fine (see screenshot below). However I don't see quite how
>> to split things up into several tracks using this approach.Should I  
>> be
>> using a config file to do that? If that's the case, does anyone have
>> an example config file for specifying loading from GFF files? The
>> provided example is for a DB.
>
> You have two options; one is to use flatfile-to-json.pl with the -- 
> type
> command line parameter.  That allows you to filter the GFF file for
> specific feature types (you can have more than one --type option on  
> the
> command line).  The other option is to use a config file.  The example
> in docs/tutorial/conf_files uses the Bio::DB::SeqFeature::Store  
> "memory"
> adaptor, which reads a flat file into memory and then acts as a DB.
> That allows you to use a config file with a GFF source of features.
>
> If you use flatfile-to-json.pl, you probably also want to specify the
> --cssclass, --tracklabel, and --key command line parameters.
>
> Hope this helps; I'm assuming you want to organize your tracks by
> feature type.
>
> Mitch
>


Thanks, Mitch! I'll have a go.





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