Re: [Gmod-ajax] flatfile-to-json.pl error with GFF

[David B. <dav...@gm...>]

Thank you Scott and Mitch!

On Fri, Jul 23, 2010 at 6:25 PM, Mitch Skinner
<mit...@be...> wrote:
> This one is usually the result of a previous flatfile-to-json.pl or
> biodb-to-json.pl run that didn't specify a track label.
>
> Look in data/trackInfo.js for an entry that doesn't have a "label"
> attribute.  Entries are supposed to look something like this:
>
>   {
>      "url" : "data/tracks/{refseq}/gene/trackData.json",
>      "label" : "gene",
>      "type" : "FeatureTrack",
>      "key" : "Gene"
>   },
>
> but if "label" is missing then you'll see that error message.
>
> I thought I added a check that would give a nicer error if the user forgets
> to specify a label, but that might have been only on the development branch.
>  I'll check again.
>
> Mitch
>
> On 07/23/2010 07:54 AM, David Breimann wrote:
>>
>> I am trying to set up my first genome, after successfully playing with
>> the tutorial examples. and I run into some problems.
>>
>> I use a fasta and a gff file from NCBI:
>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.fna
>> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Frankia_CcI3/NC_007777.gff
>>
>> Setting up the sequence file seems to pass OK, but when I run
>> flatfile-to-json.pl with the GFF I get an error:
>>
>>
>> ../../../jbrowse/bin/flatfile-to-json.pl --gff NC_007777.gff
>> --tracklabel test -key test
>>
>> working on seq gi|86738724|ref|NC_007777.1|
>> Use of uninitialized value in string eq at
>> ../../../jbrowse/bin/flatfile-to-json.pl line 179,<GEN2>  line 24.
>>
>> What's wrong?
>>
>> Thank you,
>> David
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Sprint
>> What will you do first with EVO, the first 4G phone?
>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>