possible Bug in loading ?

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possible Bug in loading ?

ganeshS

I just downloaded the latest assembly of the Human Chromosome 1 (NC_000001).

 

I tried loading it into Chado and got the following error: (Looks like two values in the Name tag is causing this problem)

 

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Error in line:

NC_000001         GenBank             pseudogenic_exon         10954    11507    .               +             .                ID=LOC100506145.pseudogenic_exon;Alias=LOC100506145;Dbxref=GeneID:100506145;Name=LOC100506145,LOC100506145;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 1 Protein;exception=unclassified transcription discrepancy;number=1;pseudo=_no_value

 

A feature may have at most one Name value

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368

STACK: Bio::FeatureIO::gff::_handle_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:729

STACK: Bio::FeatureIO::gff::next_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:172

STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:785

-----------------------------------------------------------


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Re: possible Bug in loading ?

Scott Cain
Hi Ganesh,

That isn't a bug in the loader, it's a bug in the GFF3.  As the error message points out, the Name attribute for a given feature can have at most one value, but the line you pointed out has two.  One of those should be turned into an Alias, like this:

  ...   Name=LOC100506145;Alias=LOC100506145; ...

Scott


On Wed, Aug 21, 2013 at 11:29 AM, Srinivasamoorthy, Ganesh - INTL <[hidden email]> wrote:

I just downloaded the latest assembly of the Human Chromosome 1 (NC_000001).

 

I tried loading it into Chado and got the following error: (Looks like two values in the Name tag is causing this problem)

 

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Error in line:

NC_000001         GenBank             pseudogenic_exon         10954    11507    .               +             .                ID=LOC100506145.pseudogenic_exon;Alias=LOC100506145;Dbxref=GeneID:100506145;Name=LOC100506145,LOC100506145;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 1 Protein;exception=unclassified transcription discrepancy;number=1;pseudo=_no_value

 

A feature may have at most one Name value

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368

STACK: Bio::FeatureIO::gff::_handle_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:729

STACK: Bio::FeatureIO::gff::next_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:172

STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:785

-----------------------------------------------------------


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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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Re: possible Bug in loading ?

ganeshS

Thanks for the info Scott.

I think it’s the default Genbank to GFF3 converter I am using, that causes this.

 

Is there a converter that you recommend ? will save us some rewriting of converter work.

 

Thanks

Ganesh

 

From: Scott Cain [mailto:[hidden email]]
Sent: Wednesday, August 21, 2013 11:50 AM
To: Srinivasamoorthy, Ganesh - INTL
Cc: [hidden email]
Subject: Re: [Gmod-schema] possible Bug in loading ?

 

Hi Ganesh,

That isn't a bug in the loader, it's a bug in the GFF3.  As the error message points out, the Name attribute for a given feature can have at most one value, but the line you pointed out has two.  One of those should be turned into an Alias, like this:

  ...   Name=LOC100506145;Alias=LOC100506145; ...

Scott

 

On Wed, Aug 21, 2013 at 11:29 AM, Srinivasamoorthy, Ganesh - INTL <[hidden email]> wrote:

I just downloaded the latest assembly of the Human Chromosome 1 (NC_000001).

 

I tried loading it into Chado and got the following error: (Looks like two values in the Name tag is causing this problem)

 

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Error in line:

NC_000001         GenBank             pseudogenic_exon         10954    11507    .               +             .                ID=LOC100506145.pseudogenic_exon;Alias=LOC100506145;Dbxref=GeneID:100506145;Name=LOC100506145,LOC100506145;Note=Derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 1 Protein;exception=unclassified transcription discrepancy;number=1;pseudo=_no_value

 

A feature may have at most one Name value

STACK: Error::throw

STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:368

STACK: Bio::FeatureIO::gff::_handle_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:729

STACK: Bio::FeatureIO::gff::next_feature /usr/local/share/perl5/Bio/FeatureIO/gff.pm:172

STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:785

-----------------------------------------------------------


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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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