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

[Andy Nunberg]

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