Provided by: libbio-db-gff-perl_1.7.4-1_all 
NAME
Bio::DB::GFF::Adaptor::dbi::pg -- Database adaptor for a specific postgres schema
NOTES
SQL commands that need to be executed before this adaptor will work:
CREATE DATABASE <dbname>;
Also, select permission needs to be granted for each table in the database to the owner of
the httpd process (usually 'nobody', but for some RedHat systems it is 'apache') if this
adaptor is to be used with the Generic Genome Browser (gbrowse):
CREATE USER nobody;
GRANT SELECT ON TABLE fmeta TO nobody;
GRANT SELECT ON TABLE fgroup TO nobody;
GRANT SELECT ON TABLE fdata TO nobody;
GRANT SELECT ON TABLE fattribute_to_feature TO nobody;
GRANT SELECT ON TABLE fdna TO nobody;
GRANT SELECT ON TABLE fattribute TO nobody;
GRANT SELECT ON TABLE ftype TO nobody;
Optimizing the database
PostgreSQL generally requires some tuning before you get very good performance for large
databases. For general information on tuning a PostgreSQL server, see
http://www.varlena.com/GeneralBits/Tidbits/perf.html Of particular importance is executing
VACUUM FULL ANALYZE whenever you change the database.
Additionally, for a GFF database, there are a few items you can tune. For each automatic
class in your GBrowse conf file, there will be one or two searches done when searching for
a feature. If there are lots of features, these search can take several seconds. To
speed these searches, do two things:
1. Set 'enable_seqscan = false' in your postgresql.conf file (and restart your server).
2. Create 'partial' indexes for each automatic class, doing this for the example class
'Allele':
CREATE INDEX partial_allele_gclass ON
fgroup (lower('gname')) WHERE gclass='Allele';
And be sure to run VACUUM FULL ANALYZE after creating the indexes.
DESCRIPTION
This adaptor implements a specific postgres 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)
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:pg" is added to the database DSN identifier automatically if it is not there
already.
Argument Description
-------- -----------
-dsn the DBI data source, e.g. 'dbi:Pg:dbname=: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.
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.
range_query
Title : range_query
Usage : $db->range_query($range_type,$refseq,$refclass,$start,$stop,$types,$order_by_group,$attributes,$binsize)
Function: create statement handle for range/overlap queries
Returns : a DBI statement handle
Args : see below
Status : Protected
This method constructs the statement handle for this module's central query: given a range
and/or a list of feature types, fetch their GFF records. It overrides a method in dbi.pm
so that the overlaps query can write SQL optimized for Postgres. Specifically, instead of
writing the bin related section as a set of ORs, each bin piece is place in a separate
select and then they are UNIONed together. This subroutine requires several replacements
for other subroutines in dbi.pm. In this module, they are named the same as those in
dbi.pm but prefixed with "pg_".
The positional arguments are as follows:
Argument Description
$isrange A flag indicating that this is a range.
query. Otherwise an overlap query is
assumed.
$refseq The reference sequence name (undef if no range).
$refclass The reference sequence class (undef if no range).
$start The start of the range (undef if none).
$stop The stop of the range (undef if none).
$types Array ref containing zero or feature types in the
format [method,source].
$order_by_group A flag indicating that statement handler should group
the features by group id (handy for iterative fetches)
$attributes A hash containing select attributes.
$binsize A bin size for generating tables of feature density.
search_notes
This PostgreSQL adaptor does not implement the search notes method because it can be very
slow (although the code for the method is contained in this method but commented out).
There is, however, a PostgreSQL adaptor that does implement it in a more efficient way:
Bio::DB::GFF::Adaptor::dbi::pg_fts, which inherits from this adaptor and uses the optional
PostgreSQL module TSearch2 for full text indexing. See that adaptor's documentation for
more information.
See also Bio::DB::GFF
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 replacement for the mysql-specific method. Given a search string, it performs a
ILIKE 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.
Note that for large databases this can be very slow and may result in time out or 500-cgi
errors. If this is happening on a regular basis, you should look into using
Bio::DB::GFF::Adaptor::dbi::pg_fts which implements the TSearch2 full text indexing
scheme.
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.
make_features_by_name_where_part
Title : make_features_by_name_where_part
Usage : $db->make_features_by_name_where_part
Function: Overrides a function in Bio::DB::GFF::Adaptor::dbi to insure
that searches will be case insensitive. It creates the SQL
fragment needed to select a feature by its group name & class
Returns : a SQL fragment and bind arguments
Args : see below
Status : Protected