[Bioperl-l] Help needed on GFF
yunliu at iupui.edu
Sat Sep 25 17:15:08 EDT 2004
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
# 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?
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