[Bioperl-l] GFF file and load_gff.pl
richard.harrison at ed.ac.uk
Wed Jan 28 12:36:16 EST 2009
Thank you Chris, Scott and Adam,
You are right, I was confused. I have now managed to create a
Bio::DB::GFF database with my genome annotation loaded into it. One
I am having trouble retrieving the desired info from the database.
Shown below is a typical entry into the GFF file for a gene
#chr01 SGD gene 33449 34702 . + .
#chr01 SGD CDS 33449 34702 . + 0
I would like to search the database for YAL061W and retrieve the CDS
coordinates, details about introns etc. I don't need the sequence, as
I have separate multiple genome-alignments..
At present all I can work out how to do is get all feature types and
classes in the database.. (see code below)
my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysql',
-dsn => 'dbi:mysql:biosql',
user => 'root',
pass => '*******'
my @types = $db->types;
my @classes = $db->classes;
Could someone point me towards a useful set of pointers for this. I've
tried reading the documentation but it doesn't seem to illustrate what
I want to do.
Best wishes and thanks for the help so far,
On 28 Jan 2009, at 16:15, Scott Cain wrote:
> Hi Richard,
> Your mixing up two database schemas. Do you want to use a BioSQL
> database (bioperl-db) or a Bio::DB::GFF database? I'm guessing that
> you want the latter, so I'll answer that question (as it's the easier
> one anyway). You need to add the "-c" flag (for --create) to the
> load_gff.pl command to create the Bio::DB::GFF schema.
> If you really wanted a BioSQL database, you'll have to wait for help
> from someone else more knowledgeable about it.
> On Wed, Jan 28, 2009 at 10:22 AM, Richard Harrison
> <richard.harrison at ed.ac.uk> wrote:
>> Dear all,
>> I am running Bioperl 1.6 on osx- leopard on a macbook pro.
>> I have installed mysql-5.1.30-osx10.5-x86, DBD-mysql-4.010, the
>> biosql-schema for mysql and bioperl-db. As per the instructions I
>> have a
>> database called biosql which I associated the SQL dialect biosqldb-
>> After much fannying, the install seems fine....although i can't be
>> (never used mysql before)
>> I am having problems with the script load_gff.pl
>> I want to load a database with the data from a genome.gff file (for
>> saccharomyces cerevisiae). I don't want to add sequence to it, as
>> all i need
>> is the annotation.
>> I have tried the following command(s):
>> ./bp_load_gff.pl -d biosql -user root -pass mypassword genome.gff
>> ./bp_load_gff.pl -d biosql -user root -pass mypassword --
>> With both I get the following error:
>> No ftype id for CDS:SGD Table 'biosql.ftype' doesn't exist Record
>> (then another few '000 of these)
>> genome.gff: 16379 records loaded
>> Any ideas where I'm going wrong?
>> Dr Richard Harrison
>> 127 Ashworth Labs
>> Institutes of Evolutionary Biology
>> King's Buildings
>> West Mains Road
>> Edinburgh EH9 3JT
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
> Scott Cain, Ph. D. scott at
> scottcain dot net
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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