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- $db = Bio::DB::GFF->new(
- -dsn => 'dbi:mysql:driver=mysql;host=localhost;dbname=pddb_gene_models_3_26',
- -user => 'webuser',
- -pass => 'ptest',
- -aggregator => [
- 'processed_transcript',
- 'meta{chunk/meta}'
- ];
- );
- $attributes = { 'EntrezGene' => 7097 };
- @extended_types = [
- 'CDS:Ensembl',
- 'UTR:Ensembl'
- ];
- @feature_set = $db->features( -types => \@extended_types,
- -attributes => $attributes );
- Database contains:
- fattribute_to_feature table with
- +---------+---------------+------------------+
- | fid | fattribute_id | fattribute_value |
- +---------+---------------+------------------+
- | 1325112 | 3 | 7097 |
- | 1325113 | 3 | 7097 |
- | 1325114 | 3 | 7097 |
- | 1344783 | 3 | 7097 |
- | 1344784 | 3 | 7097 |
- | 2329797 | 3 | 7097 |
- | 2596692 | 3 | 7097 |
- | 2802692 | 3 | 7097 |
- +---------+---------------+------------------+
- fdata table with:
- +---------+------+-----------+-----------+--------------+---------+--------+---------+--------+--------+---------------+--------------+---------+---------------+------------------+
- | fid | fref | fstart | fstop | fbin | ftypeid | fscore | fstrand | fphase | gid | ftarget_start | ftarget_stop | fid | fattribute_id | fattribute_value |
- +---------+------+-----------+-----------+--------------+---------+--------+---------+--------+--------+---------------+--------------+---------+---------------+------------------+
- | 2802692 | chr4 | 154622652 | 154626851 | 10000.015462 | 3 | NULL | + | NULL | 422357 | NULL | NULL | 2802692 | 3 | 7097 |
- +---------+------+-----------+-----------+--------------+---------+--------+---------+--------+--------+---------------+--------------+---------+---------------+------------------+
- where ftype_id of 6 is CDS:Ensembl
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