[Bioperl-pipeline] Re: load_contig.pl almost works!
Andy Nunberg
anunberg@oriongenomics.com
Wed, 23 Oct 2002 13:41:44 -0500
I think everyone knows about this but just in case you dont...
I installed the XML::Parser module today and there seems to be a 'feature'
with the makefile.
Basically it was looking for Parser/Expat.pm but this file exists in
Expat/, I made a hardlink to Parser/
that seems to fix it.
This is similar to the problem I had before when trying to run the xml
script with these directories without installing them(just making them)
where a Module was called from a location (directory path) that is no
longer valid.
Andy
At 11:24 PM 10/14/2002 +0800, you wrote:
>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
>>
>> _______________________________________________
>> bioperl-pipeline mailing list
>> bioperl-pipeline@bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>>
*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC
(314) 615-6989
http://www.oriongenomics.com