[Bioperl-pipeline] Re: load_contig.pl almost works!

[Shawn]

Hi Andy,
	not that I putting any pressure on Kiran who is working on the XML :)
We are working hard to get the XML ready. The dtd for the XML has
changed a bit due to some major pipeline changes and the current script
simply won't work with the latest pipeline. As we didn't do a branch on
the pipeline, it being too immature then, I can't tell you which
pipeline version to use with the XML I afraid. As for the XML parser,
Kiran can probably elaborate on the choice of that and the module to
use. I urge your patience as we try and get this out soon. Kiran could
probably give a better estimate on this. 


shawn



On Thu, 2002-10-03 at 03:40, Andy Nunberg wrote:
> Thanks..
> I will try to make those changes in the bioperl trunk.
> 
> Next step is to get the XML2Db.pl script to work. I dont know if you saw
> the previous message to Elia, but the new XML parser module has a different
> directory structure, so calls to XML will not work.  Can you send or just
> tell us what version of XML parser and XML simple object you are using so I
> can install it?
> Thanks
> Andy
> At 12:47 AM 10/3/2002 +0800, you wrote:
> >> 
> >> But at the end I get this...
> >> -------------------- EXCEPTION --------------------
> >> MSG: -text
> >> STACK Bio::Root::RootI::throw_not_implemented
> >> /compbio/dev/bioperl-live/Bio/Root/RootI.pm:574
> >> STACK Bio::Root::RootI::verbose 
> >/compbio/dev/bioperl-live/Bio/Root/RootI.pm:281
> >> STACK Bio::Root::RootI::_cleanup_methods
> >> /compbio/dev/bioperl-live/Bio/Root/RootI.pm:522
> >> STACK Bio::Root::RootI::DESTROY 
> >/compbio/dev/bioperl-live/Bio/Root/RootI.pm:627
> >> STACK (eval) /nfs/orion2/anunberg/CVS/andy/load_contigs.pl:77
> >> STACK toplevel /nfs/orion2/anunberg/CVS/andy/load_contigs.pl:77
> >> -------------------------------------------
> >>         (in cleanup) 
> >> -------------------- EXCEPTION --------------------
> >> MSG: -text
> >> STACK Bio::Root::RootI::throw_not_implemented
> >> /compbio/dev/bioperl-live/Bio/Root/RootI.pm:574
> >> STACK Bio::Root::RootI::verbose 
> >/compbio/dev/bioperl-live/Bio/Root/RootI.pm:281
> >> STACK Bio::Root::RootI::_cleanup_methods
> >> /compbio/dev/bioperl-live/Bio/Root/RootI.pm:522
> >> STACK Bio::Root::RootI::DESTROY 
> >/compbio/dev/bioperl-live/Bio/Root/RootI.pm:627
> >> STACK (eval) /nfs/orion2/anunberg/CVS/andy/load_contigs.pl:0
> >> STACK toplevel /nfs/orion2/anunberg/CVS/andy/load_contigs.pl:0
> >> -------------------------------------------
> >
> >This is the problem with Ensembl being compatible with bioperl-072 and not 
> >the main trunk.
> >A classic headache we face with the pipeline. You can try the script with 
> >bioperl-072, and hopefully that will work. Else, do what I do, modify 
> >Bio::Root::RootI
> >as follows:
> >
> >
> >sub verbose{
> >   my ($self,$value) = @_;
> >   #comment out to work with Ensembl
> >   #$self->throw_not_implemented();
> >}
> >
> >> If I look in mysql I can see the contig entry in the contig table and
> >> features for it in the features table.
> >> This script only updates the dna,contig and features table?  Just wanted
> >> tto know in case something goes wrong and I need to delete the entries.
> >
> >It shoudl update dna,contig,clone and feature tables.
> >
> >cheers,
> >
> >
> >shawn
> >
> >> 
> >> 
> >> Andy
> >> 
> >> At 12:16 AM 10/3/2002 +0800, you wrote:
> >> >> in fact all my features do not contain seqname.  So the question is do I
> >> >> need it?  If not can i just put in the name of teh BAC as the the
> seqname?
> >> >
> >> >oops. I think I sent u the wrong version.
> >> >replace $feat->seqname with $seq->id in the sub convert_seq_features
> >> >
> >> >that should work.
> >> >
> >> >Seqname is  the reference seq on which the feature resides. In this
> >> >case, the BAC name would be right.
> >> >
> >> >`
> >> >shawn
> >> >
> >> >> 
> >> >> Thanks
> >> >> Andy
> >> >> *******************************************************************
> >> >> Andy Nunberg, Ph.D
> >> >> Computational Biologist
> >> >> Orion Genomics, LLC 
> >> >> (314) 615-6989
> >> >> http://www.oriongenomics.com
> >> >> 
> >> >
> >> 
> >> *******************************************************************
> >> Andy Nunberg, Ph.D
> >> Computational Biologist
> >> Orion Genomics, LLC 
> >> (314) 615-6989
> >> http://www.oriongenomics.com
> >> 
> >
> >-- 
> >********************************
> >* Shawn Hoon
> >* http://www.fugu-sg.org/~shawnh
> >********************************
> 
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC 
> (314) 615-6989
> http://www.oriongenomics.com
> 
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