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

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

On 15 Sep 2009, at 14:49, Giles Velarde wrote:

>
> On 15 Sep 2009, at 09:41, Giles Velarde wrote:
>
>>
>> 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.
>>
>
>
> Using the config file does indeed seem to be the best option for me.  
> I ended up writing a little bash script :
>
> rm -rf data
> for file in /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/*.gff
> do
>    echo "processing GFF file? $file"
>    ./bin/prepare-refseqs.pl -gff $file --conf conf.json
> done
> ./bin/biodb-to-json.pl --conf conf.json
> ./bin/generate-names.pl -v
>
>
>
> and used it with the following conf file :
>
>
>
>
> {
>  "description": "GFF Database",
>  "db_adaptor": "Bio::DB::SeqFeature::Store",
>  "db_args": { "-adaptor": "memory",
>               "-dir": "/data/gv1/gff3-ftp/export_2009-09-14/ 
> Lmajor/" },
>
>  "TRACK DEFAULTS": {
>    "class": "feature",
>    "autocomplete": "all",
>     "urlTemplate": "http://beta.genedb.org/NamedFeature? 
> name={load_id}",
>      "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
>  },
>
>  "tracks": [
>    {
>        "track" : "Gene",
>        "feature": ["gene"],
>        "key" : "Gene Span",
>        "class": "dblhelix",
>        "category": "Gene Model features"
>    }
>  ]
> }
>
>
> Thanks again, Mitch!
> Giles
>
>


Hi All,

Just wanted to report that I am getting a lot of

print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 597, <GEN4> line 1423.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1423.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1456.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1489.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1523.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1556.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1589.
.........
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN38> line 11008.

on the console when running

	./bin/biodb-to-json.pl --conf conf.json

Other than that, everything seems to be working with the GFF building...

Best,
Giles





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