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

[kiran]

Hi Andy,
Sorted quite lot of things out.

> 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?

It is the correct directory structure only. Your installation process seems
not correct.  You seem to have forgotten to make (it will then create the
correct directory structure for the module) but instead you may have pointed
directly to the module after unzippng or untarring it. Do try it out again
and let us know.

You can download and try out the new xml files that are set up. There is a
simple blast pipeline setup (xml/templates/simple_blast_setup.xml)(it sets
up all the contigs as inputs first and then performs blast on some
database)..
More documentation coming soon. Meanwhile, do let us know if you have
problems.

Rgs,
Kiran




From: "Andy Nunberg" <anunberg@oriongenomics.com>
To: <shawnh@worf.fugu-sg.org>
Cc: <bioperl-pipeline@bioperl.org>
Sent: Thursday, October 03, 2002 3:40 AM
Subject: [Bioperl-pipeline] Re: load_contig.pl almost works!


> 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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