[Gmod-ajax] auto-complete problem

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[Gmod-ajax] auto-complete problem

David Breimann
Hello,

I have a GFF3 file with lines like:
NC_007488       GenBank gene    109368  110333  .       -       1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942
NC_007488       GenBank gene    108526  109371  .       -       1       ID=RSP_3943;Dbxref=GeneID:3712060;Name=yurM;locus_tag=RSP_3943

I added it using --type=gene --autocomplete=all, then generated names.
However, I can only look for genes using their names (e.g. yurN) and not their IDs or locus_tags.

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Re: auto-complete problem

Mitch Skinner
Since some data sources (chado, SeqFeature::Store) have IDs which aren't meaningful to users, JBrowse currently doesn't do searches on the ID field.  In the future, we probably should, but for right now you can add an Alias tag to your GFF3, something like:

NC_007488       GenBank gene    109368  110333  .       -       1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942

And if you have more than one, you can make Alias be a comma-separated list:

NC_007488       GenBank gene    109368  110333  .       -       1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942,foo,bar

Regards,
Mitch


On 09/26/2010 01:53 AM, David Breimann wrote:
Hello,

I have a GFF3 file with lines like:
NC_007488       GenBank gene    109368  110333  .       -       1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942
NC_007488       GenBank gene    108526  109371  .       -       1       ID=RSP_3943;Dbxref=GeneID:3712060;Name=yurM;locus_tag=RSP_3943

I added it using --type=gene --autocomplete=all, then generated names.
However, I can only look for genes using their names (e.g. yurN) and not their IDs or locus_tags.
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Re: auto-complete problem

David Breimann
Thanks Mitch,

I indeed think you should add it in the future.
I would also like to remind of the problem with "wrapped" features in GFF of circular genomes, which are currently simply chopped off.

Keep up the good work,
Dave

On Tue, Sep 28, 2010 at 4:50 PM, Mitch Skinner <[hidden email]> wrote:
Since some data sources (chado, SeqFeature::Store) have IDs which aren't meaningful to users, JBrowse currently doesn't do searches on the ID field.  In the future, we probably should, but for right now you can add an Alias tag to your GFF3, something like:

NC_007488       GenBank gene    109368  110333  .       -       1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942

And if you have more than one, you can make Alias be a comma-separated list:

NC_007488       GenBank gene    109368  110333  .       -       1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942,foo,bar

Regards,
Mitch



On 09/26/2010 01:53 AM, David Breimann wrote:
Hello,

I have a GFF3 file with lines like:
NC_007488       GenBank gene    109368  110333  .       -       1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942
NC_007488       GenBank gene    108526  109371  .       -       1       ID=RSP_3943;Dbxref=GeneID:3712060;Name=yurM;locus_tag=RSP_3943

I added it using --type=gene --autocomplete=all, then generated names.
However, I can only look for genes using their names (e.g. yurN) and not their IDs or locus_tags.
------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev
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