[Bioperl-l] Help needed on GFF

[Lincoln Stein]

To use this strategy first you need to create a local GFF database 
containing all the human sequences.  This probably isn't what you 
want to do.

You should go to Ensembl and fetch the sequences from there.  There is 
a nice Perl interface that you can script to.

Lincoln

On Saturday 25 September 2004 05:15 pm, Yunlong Liu wrote:
> I am new in both bioperl and database.
>
> Can anyone help me to solve this problem?
>
>
>
> I was trying to retrieve sequences from a specific region on the
> human genome, for instance, chr2, 1 - 10000.
>
> I am using Bio::DB::GFF to solve this.  I copied the following
> script from
> http://doc.bioperl.org/releases/bioperl-1.4/Bio/DB/GFF.html#SYNOPSI
>S
>
>
>
> use Bio::DB::GFF;
>
> # Open the sequence database
>   my $db      = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt',
>                                    -dsn     => 'dbi:mysql:elegans',
>                                   -fasta   =>
> '/usr/local/fasta_files' );
>   # fetch a 1 megabase segment of sequence starting at landmark
> "ZK909" my $segment = $db->segment('ZK909', 1 => 1000000);
>
>
>
>
>
> However, I got the following error message:
>
>
>
> DBI connect ('elegans', '',.) failed: Can't connect to MySQL server
> on 'localhost' <10061> at
> C:/Perl/site/lib/Bio/DB/GFF/Adaptor/dbi/caching-handle.pm line 139.
>
>
>
> Can anyone help me to solve it?
>
>
>
> Thanks,
>
>
>
> Yunlong Liu

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724