[Bioperl-l] GFF file and load_gff.pl

Dan Bolser dan.bolser at gmail.com
Fri May 22 08:42:17 EDT 2009


2009/1/28 Richard Harrison <richard.harrison at edinburgh.ac.uk>:

...

> These are the commands that I'm using to populate two different databases,
> so I can work out which method is best:
>
> ./bp_seqfeature_load.pl -d cere_seqfeat -s Bio::DB::SeqFeature -a DBI::mysql
> -user root -pass pwd -v --verbose -c genome.gff
>
> ./bp_load_gff.pl -d cere_gffdb -user root -pass pwd --adaptor=dbi::mysql
> --create --gff3_munge genome.gff
>
> Both databases seem to load the data ok and don't give error messages..
>
>
> Then in bioperl:
>
> #use Bio::DB::SeqFeature;
>
>  # Open the feature database
>  my $db     = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
>                                                                 -dsn     =>
> 'dbi:mysql:cere_seqfeat',
>
>                     -user => 'root',
>
>                     -pass => 'pwd',
>
>                     -create => 1
>
>                    );
> my @types = $db->types;
>        foreach (@types){
>        print "$_\n";
>        }
>
>
> I GET NO OUTPUT

I don't think you should be using the '-create' option here. You need
to use it when loading data for the first time, but not when
subsequently connecting to the database to read the data (I believe).
If I'm right, this second use of -create is deleting all the data that
you loaded when calling bp_seqfeature_load.pl (where you correctly
used -c to create a 'fresh' database). This would explain why you get
no output from the types method.


Dan.



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