[Bioperl-l] Help needed on GFF

[Jason Stajich]

On Sep 25, 2004, at 5:15 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#SYNOPSIS
>
>
Add
-user and -pass options when you initialize the DB::GFF object or have 
your mysql server accept connections to the elegans database with

>

> 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'
                                      -user   => $username, -pass => 
$password,
>                                 );
>   # 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.
>
And of course you have already loaded the celegans data into a database 
called 'elegans' ?

>
>
> Can anyone help me to solve it?
>
>
>
> Thanks,
>
>
>
> Yunlong Liu
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/