[Gmod-gbrowse] [Gmod-help] Re: [Gmod-schema] Error loading GFF3 file into chado

Fri Aug 14 16:52:02 EDT 2009

Hi Scott,

That was my guess on the file Manny is using.  He's actually using
ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v4.0/Sbicolor/annotation/Sbi1.4/Sbi1.4.gff3.gz

Manny explicitly said that and Shu picked up on that (Thanks for reading
Manny's response carefully!).  I'm looking at the file now.  It does not
have full-length entries, but I can's see why it complains about super_10 in
particular.

Dave C.

On Fri, Aug 14, 2009 at 1:47 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Shu,
>
> The file in question:
>
>
> ftp://ftp.jgi-psf.org/pub/JGI_data/Sorghum_bicolor/v1.0/Sorbi1_GeneModels_Sbi1_4_Sbi1_4.gff.gz
>
> is definitely not GFF3.  The first couple of lines look like this:
>
> chr_1   JGI     exon    2164    2829    .       +       .       name
> "Sb01g000200"; transcriptId 5257096
> chr_1   JGI     CDS     2164    2829    .       +       0       name
> "Sb01g000200"; proteinId 5027909; exonNumber 1
>
> The 9th column needs to be in "tag=value" format and "name" should be
> capitalized, and it would be nice to have gene and mRNA features to go
> with the exon and CDS features, rather than depending on inferring
> their existance (the Chado loader will fail to do that, and the
> Bio::DB::SeqFeature::Store will probably be successful, but getting
> GBrowse to display it properly will likely not be easy).
>
> Scott
>
>
> On Aug 14, 2009, at 4:35 PM, Shengqiang Shu wrote:
>
> > This file is in format of GFF3, Is this loading problem due to file
> > not conforming to GFF3 standard? In term of SO terms, it uses gene,
> > mRNA, exon, CDS. No problem, is there?
> >
> > Only thing looks like missing is Name attribute. Is Name attribute
> > required? From scanning through doc on sequence ontology site, it
> > did not say Name is required.
> >
> > I know this file is produced by one of our members. If you guys
> > point out what is the problem with file in term of conforming to
> > GFF3 standard, it would be very helpful.
> >
> > By the way, FASTA in GFF3 is optional, isn't? Don't know why loader
> > can not handle it? ah, the file is annotation GFF3 file, it does not
> > contain genomic features. Is this causing the loading problem?
> >
> >
> > Shu
> >
> >
> > On Aug 14, 2009, at 12:54 PM, Chris Fields wrote:
> >
> >> Yikes, another GFF2 variant?
> >>
> >> chris
> >>
> >> On Aug 14, 2009, at 2:50 PM, Jason Stajich wrote:
> >>
> >>> I also have these script jg_gff2gff3.pl in gff_tools of
> http://github.com/hyphaltip/genome-scripts/tree/master
> >>> and
> >>> gff3_to_JGIgff.pl for converting back into JGI gff from GFF3.
> >>>
> >>> -jason
> >>>
> >>> On Aug 14, 2009, at 11:01 AM, Don Gilbert wrote:
> >>>
> >>>>
> >>>>> Has anyone out there written a JGI GFF2 to GFF3 parser
> >>>>
> >>>> I've written both ways: jgi to gff3, and gff3 to jgi-gff (which
> >>>> is a
> >>>> variant of gff2).
> >>>> Find here
> >>>> http://wfleabase.org/release1/current_release/supplement/jgi_gff/
> >>>> as jgi2gff.pl  (and dpulex_gff2jgi.pl  for the other way)
> >>>>
> >>>> This script will want some revision for your data, and the variant
> >>>> of JGI's gff
> >>>> I worked with may differ from yours.  Look at the sample at the top
> >>>> of the
> >>>> script to see if it matches yours.
> >>>>
> >>>> - Don
> >>>>
> >>>>
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> >>> --
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> >>> jason.stajich at gmail.com
> >>> jason at bioperl.org
> >>>
> >>>
> >>>
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> >>
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> -----------------------------------------------------------------------
> 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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