loading data into chado

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loading data into chado

claudia

To whom it may concern,

 I am attempting to load a preproccessed gff3 file that is a merged gff3 from a maker output and I am getting this response (below) when I use the gmod bulk load script. Could you shed some light for me in solving this problem?

Thank you,

Claudia DiNatale

contig00562    blastx    protein_match    24    422    187    -    .    ID=contig00562:hit:365;Name=30128.m008887#Guanosine-5'-triphosphate,3'-diphosphate;

A feature may have at most one Name value
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::FeatureIO::gff::_handle_feature /usr/share/perl5/Bio/FeatureIO/gff.pm:729
STACK: Bio::FeatureIO::gff::next_feature /usr/share/perl5/Bio/FeatureIO/gff.pm:172
STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:777


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Re: loading data into chado

Scott Cain
Hi Claudia,

Questions about Chado are best sent to the schema mailing list, which
I cc'ed here.

The problem you are having is that the comma has special meaning in
column nine of a GFF3 file, indicating more than one value, so that
feature really has two names,
"30128.m008887#Guanosine-5'-triphosphate" and "3'-diphosphate", which
isn't allowed.  In order for that to be the name, the comma needs to
be URI escaped, which is to say, replaced with "%2C".

Scott


On Tue, Dec 7, 2010 at 2:54 PM, Dinatale C <[hidden email]> wrote:

> To whom it may concern,
>
>  I am attempting to load a preproccessed gff3 file that is a merged gff3
> from a maker output and I am getting this response (below) when I use the
> gmod bulk load script. Could you shed some light for me in solving this
> problem?
>
> Thank you,
>
> Claudia DiNatale
>
> contig00562    blastx    protein_match    24    422    187    -    .
>  ID=contig00562:hit:365;Name=30128.m008887#Guanosine-5'-triphosphate,3'-diphosphate;
>
> A feature may have at most one Name value
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368
> STACK: Bio::FeatureIO::gff::_handle_feature
> /usr/share/perl5/Bio/FeatureIO/gff.pm:729
> STACK: Bio::FeatureIO::gff::next_feature
> /usr/share/perl5/Bio/FeatureIO/gff.pm:172
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:777
>
> ------------------------------------------------------------------------------
> What happens now with your Lotus Notes apps - do you make another costly
> upgrade, or settle for being marooned without product support? Time to move
> off Lotus Notes and onto the cloud with Force.com, apps are easier to build,
> use, and manage than apps on traditional platforms. Sign up for the Lotus
> Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>



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

------------------------------------------------------------------------------
What happens now with your Lotus Notes apps - do you make another costly
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off Lotus Notes and onto the cloud with Force.com, apps are easier to build,
use, and manage than apps on traditional platforms. Sign up for the Lotus
Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d
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