(no subject)

[Zhiliang Hu-2]

I have a hard time to make GBrowse to display a new set of gff3/fa data
set (search of any keyword gave "not found").  So I tried to load a set
of gff3 and fasta file into a new gbrowse database, and tried to take a
look what are loaded into the MySQL tables, in two ways:

> bp_bulk_load_gff.pl -d gb_bt --create Chr1.gff3 Chr1.fa

-- result in following mysql tables:

fattribute ( 3848 records )
fattribute_to_feature ( 8077 records )
fdata ( 16883 records )
fdna ( 78796 records )
fgroup ( 2723 records )
fmeta ( 4 records )
ftype ( 4 records )


> bp_seqfeature_load.pl -d gb_bt -c -f Chr1.gff3 Chr1.fa

-- result in following mysql tables (note different from above):

attribute ( 2218 records )
attributelist ( 5 records )
feature ( 16883 records )
locationlist ( 1 records )
meta ( 4 records )
name ( 893 records )
parent2child ( 15990 records )
sequence ( 78796 records )
typelist ( 4 records )

I wonder why? Should they both work? .. I see there are a number of
gbrowse data load tools (bp_load_gff.pl, bp_bulk_load_gff.pl,
bp_seqfeature_load.pl, bp_fast_load_gff.pl) in various GBrowse
documentations but am kind confused to clearly distinguish them (they have
good man pages though).  Is there a web page listing their differences
and/or best fit situations?

Thank you,
Zhiliang

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[Scott Cain-4]

Hi Zhiliang,

This page:

  http://gmod.org/wiki/GBrowse_adaptors

is a start at answering your questions, but is probably not enough.
The two loaders are for two different database adaptors that can be
used under different circumstances, thus the different in table names
and contents.

The Bio::DB::GFF adaptor has been around longer and works well with
GFF2 data; the bioperl scripts that works with it are bp_load_gff.pl,
bp_bulk_load_gff.pl, bp_fast_load_gff.pl.  Bio::DB::SeqFeature::Store
works best with GFF3 data, and the bp_seqfeature_load.pl script works
with it.

Scott


On Mon, Jun 8, 2009 at 9:23 AM, Zhiliang Hu<hu@...> wrote:

> I have a hard time to make GBrowse to display a new set of gff3/fa data
> set (search of any keyword gave "not found").  So I tried to load a set
> of gff3 and fasta file into a new gbrowse database, and tried to take a
> look what are loaded into the MySQL tables, in two ways:
>
>> bp_bulk_load_gff.pl -d gb_bt --create Chr1.gff3 Chr1.fa
>
> -- result in following mysql tables:
>
> fattribute ( 3848 records )
> fattribute_to_feature ( 8077 records )
> fdata ( 16883 records )
> fdna ( 78796 records )
> fgroup ( 2723 records )
> fmeta ( 4 records )
> ftype ( 4 records )
>
>
>> bp_seqfeature_load.pl -d gb_bt -c -f Chr1.gff3 Chr1.fa
>
> -- result in following mysql tables (note different from above):
>
> attribute ( 2218 records )
> attributelist ( 5 records )
> feature ( 16883 records )
> locationlist ( 1 records )
> meta ( 4 records )
> name ( 893 records )
> parent2child ( 15990 records )
> sequence ( 78796 records )
> typelist ( 4 records )
>
> I wonder why? Should they both work? .. I see there are a number of
> gbrowse data load tools (bp_load_gff.pl, bp_bulk_load_gff.pl,
> bp_seqfeature_load.pl, bp_fast_load_gff.pl) in various GBrowse
> documentations but am kind confused to clearly distinguish them (they have
> good man pages though).  Is there a web page listing their differences
> and/or best fit situations?
>
> Thank you,
> Zhiliang
>
> ------------------------------------------------------------------------------
> OpenSolaris 2009.06 is a cutting edge operating system for enterprises
> looking to deploy the next generation of Solaris that includes the latest
> innovations from Sun and the OpenSource community. Download a copy and
> enjoy capabilities such as Networking, Storage and Virtualization.
> Go to: http://p.sf.net/sfu/opensolaris-get
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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