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

[shawnh@worf.fugu-sg.org]

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.

> 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
********************************