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

[Scott C. <sc...@sc...>]

Hi David,

The NCBI GFF3 is notoriously bad and doesn't pass validation at the
GFF3 validator:

  http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

The most notable problems actually have to do with the relationships
between features.  For example, in the first few lines:

NC_007777.1     RefSeq  gene    35      1723    .       +       .
 locus_tag=Francci3_0001;db_xref=GeneID:3902947
NC_007777.1     RefSeq  CDS     35      1720    .       +       0
 locus_tag=Francci3_0001;transl_table=11;product=chromosomal
replication initiator protein
DnaA;protein_id=YP_479125.1;db_xref=GI:86738725;db_xref=InterPro:IPR001957;db_xref=InterPro:IPR003593;db_xref=InterPro:IPR013159;db_xref=InterPro:IPR013317;db_xref=GeneID:3902947;exon_number=1

While there is not anything technically wrong with these two lines,
there is what you might call a logic error: the CDS should have the
gene as a parent.  Without that information, a genome browser is going
to have a difficult time displaying the data appropriately.  Feel free
to complain to the folks at NCBI that there GFF3 is really bad (I've
done that a few times, but I think they are ignoring me :-)

So, the question is, what should you use?  The best option I can
suggest to you is the genbank2gff3 script that comes with BioPerl,
called bp_genbank2gff3.pl. If you get the developers version from
github, you can use a version of that script that has been fixed to
work appropriately with bacterial/circular genomes.

Scott


On Fri, Jul 23, 2010 at 10:54 AM, David Breimann
<dav...@gm...> 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
>
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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