[Bioperl-pipeline] any hope of getting the example to work?

[Andy Nunberg]

At 09:58 AM 10/1/2002 +0800, you wrote:
>Hi Andy,
>
>sorry we have been tied up with the ciona genome work.
>
>
>> Hi all,
>> since I cant get the first script in your example to work because of the
>> XML module, do you have any ideas how to fix this?  can you send an older
>> verision that works?
>
>give me a day or 2 ( I know I have been saying this) and I will create a
>dump of a blast pipeline for you. Kiran is working hard on the XML.
>
>I'm assuming you will want to store your features in Ensembl to view them.
>
>This will be the layout:
>
>You have your BACs stored in Ensembl (the reason why this is needed is because
>				     the features need a reference sequence for viewing them on the 
>browser)
>
>Contigs will be retrieved from EnsEMBL and blast against dbfiles in the 
>bioperl-pipeline.
>(Your dbfiles will be your proprietary data).
>
>Features are stored into the contig table in Ensembl.
>
>> website not theirs) and how to load genbank files into it.  
>
>in the ensembl-pipeline/scripts directory, there is a load_scaffolds.pl 
>script which
>works on fasta files. You could convert your genbank files to fasta and load 
>them or
>just replace the following line:
>
>my $seqio = new Bio::SeqIO(-format=>'Fasta',
>                           -file=>$seqfile);
>with
>
>my $seqio = new Bio::SeqIO(-format=>'genbank',
>                           -file=>$seqfile);
>
>this should work with the stable release of  ensembl
>
>Note though, with genbank, the script will try and store the features as
well, 
>and you will get a bunch of errors for that since the ensembl and bioperl 
>features
>aren't really compatible. You can ignore them since you are only interested in
>the sequences. Or  you could just comment out the storing of features.
Actually I want the features from Genbank, because I want to see where my
sequences are hitting what features
on the BAC. Is this possible to do?

>
>> I'd love to see a course at the O'Reilly meeting where I can learn to do
>> these basic things. (IE How to set up EnsEMBL database and populate with
>> your own data..  How to setup a basic bioperl-pipeline..I'd be happy just
>> setting up a couple of BLASTs!)
>
>when we get stable hopefully :)
>
>
>shawn
>
>-- 
>********************************
>* Shawn Hoon
>* http://www.fugu-sg.org/~shawnh
>********************************

*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com