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Oct 16th, 2017
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  1. $db = Bio::DB::GFF->new(
  2. -dsn => 'dbi:mysql:driver=mysql;host=localhost;dbname=pddb_gene_models_3_26',
  3. -user => 'webuser',
  4. -pass => 'ptest',
  5. -aggregator => [
  6. 'processed_transcript',
  7. 'meta{chunk/meta}'
  8. ];
  9. );
  10.  
  11.  
  12. $attributes = { 'EntrezGene' => 7097 };
  13. @extended_types = [
  14. 'CDS:Ensembl',
  15. 'UTR:Ensembl'
  16. ];
  17.  
  18. @feature_set = $db->features( -types => \@extended_types,
  19. -attributes => $attributes );
  20.  
  21.  
  22. Database contains:
  23.  
  24. fattribute_to_feature table with
  25. +---------+---------------+------------------+
  26. | fid | fattribute_id | fattribute_value |
  27. +---------+---------------+------------------+
  28. | 1325112 | 3 | 7097 |
  29. | 1325113 | 3 | 7097 |
  30. | 1325114 | 3 | 7097 |
  31. | 1344783 | 3 | 7097 |
  32. | 1344784 | 3 | 7097 |
  33. | 2329797 | 3 | 7097 |
  34. | 2596692 | 3 | 7097 |
  35. | 2802692 | 3 | 7097 |
  36. +---------+---------------+------------------+
  37.  
  38. fdata table with:
  39. +---------+------+-----------+-----------+--------------+---------+--------+---------+--------+--------+---------------+--------------+---------+---------------+------------------+
  40. | fid | fref | fstart | fstop | fbin | ftypeid | fscore | fstrand | fphase | gid | ftarget_start | ftarget_stop | fid | fattribute_id | fattribute_value |
  41. +---------+------+-----------+-----------+--------------+---------+--------+---------+--------+--------+---------------+--------------+---------+---------------+------------------+
  42. | 2802692 | chr4 | 154622652 | 154626851 | 10000.015462 | 3 | NULL | + | NULL | 422357 | NULL | NULL | 2802692 | 3 | 7097 |
  43. +---------+------+-----------+-----------+--------------+---------+--------+---------+--------+--------+---------------+--------------+---------+---------------+------------------+
  44.  
  45. where ftype_id of 6 is CDS:Ensembl
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