NAME¶

Bio::DB::GFF::Adaptor::dbi::oracle -- Database adaptor for a specific oracle schema

SYNOPSIS¶

See Bio::DB::GFF

DESCRIPTION¶

This adaptor implements a specific oracle database schema that is compatible with Bio::DB::GFF. It inherits from Bio::DB::GFF::Adaptor::dbi, which itself inherits from Bio::DB::GFF.

The schema uses several tables:

fdata

This is the feature data table. Its columns are:

    fid            feature ID (integer)
    fref           reference sequence name (string)
    fstart         start position relative to reference (integer)
    fstop          stop position relative to reference (integer)
    ftypeid        feature type ID (integer)
    fscore         feature score (float); may be null
    fstrand        strand; one of "+" or "-"; may be null
    fphase         phase; one of 0, 1 or 2; may be null
    gid            group ID (integer)
    ftarget_start  for similarity features, the target start position (integer)
    ftarget_stop   for similarity features, the target stop position (integer)
    

Note that it would be desirable to normalize the reference sequence name, since there are usually many features that share the same reference feature. However, in the current schema, query performance suffers dramatically when this additional join is added.

fgroup

This is the group table. There is one row for each group. Columns:

    gid       the group ID (integer)
    gclass    the class of the group (string)
    gname     the name of the group (string)
    

The group table serves multiple purposes. As you might expect, it is used to cluster features that logically belong together, such as the multiple exons of the same transcript. It is also used to assign a name and class to a singleton feature. Finally, the group table is used to identify the target of a similarity hit. This is consistent with the way in which the group field is used in the GFF version 2 format.

The fgroup.gid field joins with the fdata.gid field.

Examples:

  sql> select * from fgroup where gname='sjj_2L52.1';
  +-------+-------------+------------+
  | gid   | gclass      | gname      |
  +-------+-------------+------------+
  | 69736 | PCR_product | sjj_2L52.1 |
  +-------+-------------+------------+
  1 row in set (0.70 sec)
  sql> select fref,fstart,fstop from fdata,fgroup 
            where gclass='PCR_product' and gname = 'sjj_2L52.1' 
                  and fdata.gid=fgroup.gid;
  +---------------+--------+-------+
  | fref          | fstart | fstop |
  +---------------+--------+-------+
  | CHROMOSOME_II |   1586 |  2355 |
  +---------------+--------+-------+
  1 row in set (0.03 sec)
    

ftype

This table contains the feature types, one per row. Columns are:

    ftypeid      the feature type ID (integer)
    fmethod      the feature type method name (string)
    fsource      the feature type source name (string)
    

The ftype.ftypeid field joins with the fdata.ftypeid field. Example:

  sql> select fref,fstart,fstop,fmethod,fsource from fdata,fgroup,ftype 
         where gclass='PCR_product' 
               and gname = 'sjj_2L52.1'
               and fdata.gid=fgroup.gid
               and fdata.ftypeid=ftype.ftypeid;
  +---------------+--------+-------+-------------+-----------+
  | fref          | fstart | fstop | fmethod     | fsource   |
  +---------------+--------+-------+-------------+-----------+
  | CHROMOSOME_II |   1586 |  2355 | PCR_product | GenePairs |
  +---------------+--------+-------+-------------+-----------+
  1 row in set (0.08 sec)
    

fdna

This table holds the raw DNA of the reference sequences. It has three columns:

    fref          reference sequence name (string)
    foffset       offset of this sequence
    fdna          the DNA sequence (longblob)
    

To overcome problems loading large blobs, DNA is automatically fragmented into multiple segments when loading, and the position of each segment is stored in foffset. The fragment size is controlled by the -clump_size argument during initialization.

fattribute_to_feature

This table holds "attributes", which are tag/value pairs stuffed into the GFF line. The first tag/value pair is treated as the group, and anything else is treated as an attribute (weird, huh?).

 CHR_I assembly_tag Finished     2032 2036 . + . Note "Right: cTel33B"
 CHR_I assembly_tag Polymorphism 668  668  . + . Note "A->C in cTel33B"
    

The columns of this table are:

    fid                 feature ID (integer)
    fattribute_id       ID of the attribute (integer)
    fattribute_value    text of the attribute (text)
    

The fdata.fid column joins with fattribute_to_feature.fid.

fattribute

This table holds the normalized names of the attributes. Fields are:

  fattribute_id      ID of the attribute (integer)
  fattribute_name    Name of the attribute (varchar)
    

 Title   : new
 Usage   : $db = Bio::DB::GFF->new(@args)
 Function: create a new adaptor
 Returns : a Bio::DB::GFF object
 Args    : see below
 Status  : Public

  Argument       Description
  --------       -----------
  -dsn           the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040"
  -user          username for authentication
  -pass          the password for authentication

 Title   : schema
 Usage   : $schema = $db->schema
 Function: return the CREATE script for the schema
 Returns : a list of CREATE statemetns
 Args    : none
 Status  : protected

 Title   : do_initialize
 Usage   : $success = $db->do_initialize($drop_all)
 Function: initialize the database
 Returns : a boolean indicating the success of the operation
 Args    : a boolean indicating whether to delete existing data
 Status  : protected

 Title   : drop_all
 Usage   : $db->drop_all
 Function: empty the database
 Returns : void
 Args    : none
 Status  : protected

 Title   : setup_load
 Usage   : $db->setup_load
 Function: called before load_gff_line()
 Returns : void
 Args    : none
 Status  : protected

 Title   : load_gff_line
 Usage   : $db->load_gff_line($fields)
 Function: called to load one parsed line of GFF
 Returns : true if successfully inserted
 Args    : hashref containing GFF fields
 Status  : protected

 ref          reference sequence
 source       annotation source
 method       annotation method
 start        annotation start
 stop         annotation stop
 score        annotation score (may be undef)
 strand       annotation strand (may be undef)
 phase        annotation phase (may be undef)
 group_class  class of annotation's group (may be undef)
 group_name   ID of annotation's group (may be undef)
 target_start start of target of a similarity hit
 target_stop  stop of target of a similarity hit
 attributes   array reference of attributes, each of which is a [tag=>value] array ref

 Title   : get_table_id
 Usage   : $integer = $db->get_table_id($table,@ids)
 Function: get the ID of a group or type
 Returns : an integer ID or undef
 Args    : none
 Status  : private

 Title   : search_notes
 Usage   : @search_results = $db->search_notes("full text search string",$limit)
 Function: Search the notes for a text string, using mysql full-text search
 Returns : array of results
 Args    : full text search string, and an optional row limit
 Status  : public

  column 1     A Bio::DB::GFF::Featname object, suitable for passing to segment()
  column 2     The text of the note
  column 3     A relevance score.
  column 4     A Bio::DB::GFF::Typename object

 Title   : make_meta_set_query
 Usage   : $sql = $db->make_meta_set_query
 Function: return SQL fragment for setting a meta parameter
 Returns : SQL fragment
 Args    : none
 Status  : public