[Bioperl-l] FeatureIO::gff.pm -- error fetching sofa.definition

[Scott Cain]

Hi Tanya,

The version of Bio::FeatureIO::gff in bioperl-1.5 was still a little
rough.  In particular, it required the download of SOFA from a hard coded
location to validate the types in the GFF3.  In bioperl-live, validation
has become a option you can pass to the constructor and is off by default.
I believe the location to get SOFA from is still hard coded in though.  I
would suggest using bioperl-live if you can.

Scott

----------------------------------------------------------------------
Scott Cain, Ph. D.				 	 cain at cshl.org
GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
----------------------------------------------------------------------


On Tue, 19 Jul 2005, Tanya Gray wrote:

> Hi, I have a simple test script to read a GFF3 file using FeatureIO::gff.pm. Unfortunately it is throwing errors relating to retrieval of sofa.definition file:
> MSG: failed to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, server threw 500
> 
> I am using Bioperl-1.5.0. I just wonder if anyone might know what the problem is.  Copy of the relevant script/ error messages below.
> 
> thank you
> Tanya
> 
> 
> relevant lines of script
> ---------------------------
> 
> my $file_features = "gff3.test";
> 
> my $fio = Bio::FeatureIO->new( -file =>$file_features, -format =>"GFF", -validate_terms=>0, -version=>3) or print "\nError occurred: " . $! ;
> 
> 
> gff3.test
> ----------
> 
> ##gff-version   3
> ##sequence-region   ctg123 1 1497228
> ctg123  .       gene    1000    9000    .       +       .       ID=gene00001;Name=EDEN
> 
> ERROR MESSAGES
> ---------------------
> perl gff3test.pl                                                            [11:11]
> 
> -------------------- WARNING ---------------------
> MSG: [1/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
> ---------------------------------------------------
> 
> -------------------- WARNING ---------------------
> MSG: [2/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
> ---------------------------------------------------
> 
> -------------------- WARNING ---------------------
> MSG: [3/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
> ---------------------------------------------------
> 
> -------------------- WARNING ---------------------
> MSG: [4/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
> ---------------------------------------------------
> 
> -------------------- WARNING ---------------------
> MSG: [5/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, but server threw 500.  retrying...
> ---------------------------------------------------
> 
> ------------- EXCEPTION  -------------
> MSG: failed to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition, server threw 500
> STACK Bio::Root::IO::_initialize_io /usr/local/share/perl/5.8.7/Bio/Root/IO.pm:276
> STACK Bio::Root::IO::new /usr/local/share/perl/5.8.7/Bio/Root/IO.pm:227
> STACK Bio::OntologyIO::dagflat::defs_url /usr/local/share/perl/5.8.7/Bio/OntologyIO/dagflat.pm:361
> STACK Bio::OntologyIO::dagflat::_initialize /usr/local/share/perl/5.8.7/Bio/OntologyIO/dagflat.pm:188
> STACK Bio::OntologyIO::soflat::_initialize /usr/local/share/perl/5.8.7/Bio/OntologyIO/soflat.pm:145
> STACK Bio::OntologyIO::new /usr/local/share/perl/5.8.7/Bio/OntologyIO.pm:169
> STACK Bio::OntologyIO::new /usr/local/share/perl/5.8.7/Bio/OntologyIO.pm:178
> STACK Bio::Ontology::OntologyStore::get_ontology /usr/local/share/perl/5.8.7/Bio/Ontology/OntologyStore.pm:225
> STACK Bio::FeatureIO::gff::_initialize /usr/local/share/perl/5.8.7/Bio/FeatureIO/gff.pm:110
> STACK Bio::FeatureIO::new /usr/local/share/perl/5.8.7/Bio/FeatureIO.pm:268
> STACK Bio::FeatureIO::new /usr/local/share/perl/5.8.7/Bio/FeatureIO.pm:288
> STACK toplevel gff3test.pl:15
> 
> 
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