[Gmod-ajax] jbrowse/flatfile-to-json.pl not adding all tracks

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[Gmod-ajax] jbrowse/flatfile-to-json.pl not adding all tracks

Dana Price
I've got a gff generated via MAKER of a contig.  It's got 9 features of type "gene", but when I run flatfile-to-json.pl to create a track out of these, it only adds 5 of them.  I'm using the command:
/var/www/jbrowse/bin/flatfile-to-json.pl --tracklabel "Genes" --key "Genes" --getType --getLabel --autocomplete label --cssclass feature5 --type gene --gff ./ConsensusfromContig25517.gff


Is there any particular reason it wouldn't add all features present?

Thanks!


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Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu
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Re: jbrowse/flatfile-to-json.pl not adding all tracks

Mitch Skinner
I'm not aware of any reason why this would happen.  Could you send your GFF, so I can try to reproduce this?

Mitch

On 12/14/2010 08:15 PM, Dana Price wrote:
I've got a gff generated via MAKER of a contig.  It's got 9 features of type "gene", but when I run flatfile-to-json.pl to create a track out of these, it only adds 5 of them.  I'm using the command:
/var/www/jbrowse/bin/flatfile-to-json.pl --tracklabel "Genes" --key "Genes" --getType --getLabel --autocomplete label --cssclass feature5 --type gene --gff ./ConsensusfromContig25517.gff


Is there any particular reason it wouldn't add all features present?

Thanks!


--
Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu
[hidden email]
------------------------------------------------------------------------------ Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d
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