/ 
bioperl-1.5.2_004-RCd
/ Bio::DB::GFF::Adaptor::dbi::oracle

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 postion 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)

Data Loading Methods

In addition to implementing the abstract SQL-generating methods of Bio::DB::GFF::Adaptor::dbi, this module also implements the data loading functionality of Bio::DB::GFF.

new

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

The new constructor is identical to the "dbi" adaptor's new() method, except that the prefix "dbi:oracle" is added to the database DSN identifier automatically if it is not there already.

Argument       Description
--------       -----------

-dsn           the DBI data source, e.g. 'dbi:mysql:ens0040' or "ens0040"

-user          username for authentication

-pass          the password for authentication

schema

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

This method returns a list containing the various CREATE statements needed to initialize the database tables.

do_initialize

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

This method will load the schema into the database. If $drop_all is true, then any existing data in the tables known to the schema will be deleted.

Internally, this method calls schema() to get the schema data.

drop_all

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

This method drops the tables known to this module. Internally it calls the abstract tables() method.

setup_load

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

This method performs schema-specific initialization prior to loading a set of GFF records. It prepares a set of DBI statement handlers to be used in loading the data.

load_gff_line

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

This method is called once per line of the GFF and passed a series of parsed data items that are stored into the hashref $fields. The keys are:

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

get_table_id

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

This internal method is called by load_gff_line to look up the integer ID of an existing feature type or group. The arguments are the name of the table, and two string identifiers. For feature types, the identifiers are the method and source. For groups, the identifiers are group name and class.

This method requires that a statement handler named lookup_$table, have been created previously by setup_load(). It is here to overcome deficiencies in mysql's INSERT syntax.

search_notes

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

This is a mysql-specific method. Given a search string, it performs a full-text search of the notes table and returns an array of results. Each row of the returned array is a arrayref containing the following fields:

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.

make_meta_set_query

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

By default this does nothing; meta parameters are not stored or retrieved.