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.IX Title "Bio::DB::GFF::Adaptor::dbi::pg 3pm"
.TH Bio::DB::GFF::Adaptor::dbi::pg 3pm "2020-01-13" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::DB::GFF::Adaptor::dbi::pg \-\- Database adaptor for a specific postgres schema
.SH "NOTES"
.IX Header "NOTES"
\&\s-1SQL\s0 commands that need to be executed before this adaptor will work:
.PP
.Vb 1
\&  CREATE DATABASE <dbname>;
.Ve
.PP
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):
.PP
.Vb 8
\&  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;
.Ve
.SS "Optimizing the database"
.IX Subsection "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 \s-1VACUUM FULL ANALYZE\s0 whenever
you change the database.
.PP
Additionally, for a \s-1GFF\s0 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:
.IP "1." 4
Set 'enable_seqscan = false' in your postgresql.conf file (and restart
your server).
.IP "2." 4
Create 'partial' indexes for each automatic class, doing this for the
example class 'Allele':
.Sp
.Vb 2
\&  CREATE INDEX partial_allele_gclass ON 
\&    fgroup (lower(\*(Aqgname\*(Aq)) WHERE gclass=\*(AqAllele\*(Aq;
.Ve
.Sp
And be sure to run \s-1VACUUM FULL ANALYZE\s0 after creating the indexes.
.SH "DESCRIPTION"
.IX Header "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.
.PP
The schema uses several tables:
.IP "fdata" 4
.IX Item "fdata"
This is the feature data table.  Its columns are:
.Sp
.Vb 11
\&    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)
.Ve
.Sp
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.
.IP "fgroup" 4
.IX Item "fgroup"
This is the group table. There is one row for each group.  Columns:
.Sp
.Vb 3
\&    gid       the group ID (integer)
\&    gclass    the class of the group (string)
\&    gname     the name of the group (string)
.Ve
.Sp
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 \s-1GFF\s0 version 2
format.
.Sp
The fgroup.gid field joins with the fdata.gid field.
.Sp
Examples:
.Sp
.Vb 7
\&  sql> select * from fgroup where gname=\*(Aqsjj_2L52.1\*(Aq;
\&  +\-\-\-\-\-\-\-+\-\-\-\-\-\-\-\-\-\-\-\-\-+\-\-\-\-\-\-\-\-\-\-\-\-+
\&  | 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=\*(AqPCR_product\*(Aq and gname = \*(Aqsjj_2L52.1\*(Aq 
\&                  and fdata.gid=fgroup.gid;
\&  +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+\-\-\-\-\-\-\-\-+\-\-\-\-\-\-\-+
\&  | fref          | fstart | fstop |
\&  +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+\-\-\-\-\-\-\-\-+\-\-\-\-\-\-\-+
\&  | CHROMOSOME_II |   1586 |  2355 |
\&  +\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-+\-\-\-\-\-\-\-\-+\-\-\-\-\-\-\-+
\&  1 row in set (0.03 sec)
.Ve
.IP "ftype" 4
.IX Item "ftype"
This table contains the feature types, one per row.  Columns are:
.Sp
.Vb 3
\&    ftypeid      the feature type ID (integer)
\&    fmethod      the feature type method name (string)
\&    fsource      the feature type source name (string)
.Ve
.Sp
The ftype.ftypeid field joins with the fdata.ftypeid field.  Example:
.Sp
.Vb 11
\&  sql> select fref,fstart,fstop,fmethod,fsource from fdata,fgroup,ftype 
\&         where gclass=\*(AqPCR_product\*(Aq 
\&               and gname = \*(Aqsjj_2L52.1\*(Aq
\&               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)
.Ve
.IP "fdna" 4
.IX Item "fdna"
This table holds the raw \s-1DNA\s0 of the reference sequences.  It has three
columns:
.Sp
.Vb 3
\&    fref          reference sequence name (string)
\&    foffset       offset of this sequence
\&    fdna          the DNA sequence (longblob)
.Ve
.Sp
To overcome problems loading large blobs, \s-1DNA\s0 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.
.IP "fattribute_to_feature" 4
.IX Item "fattribute_to_feature"
This table holds \*(L"attributes\*(R", which are tag/value pairs stuffed into
the \s-1GFF\s0 line.  The first tag/value pair is treated as the group, and
anything else is treated as an attribute (weird, huh?).
.Sp
.Vb 2
\& CHR_I assembly_tag Finished     2032 2036 . + . Note "Right: cTel33B"
\& CHR_I assembly_tag Polymorphism 668  668  . + . Note "A\->C in cTel33B"
.Ve
.Sp
The columns of this table are:
.Sp
.Vb 3
\&    fid                 feature ID (integer)
\&    fattribute_id       ID of the attribute (integer)
\&    fattribute_value    text of the attribute (text)
.Ve
.Sp
The fdata.fid column joins with fattribute_to_feature.fid.
.IP "fattribute" 4
.IX Item "fattribute"
This table holds the normalized names of the attributes.  Fields are:
.Sp
.Vb 2
\&  fattribute_id      ID of the attribute (integer)
\&  fattribute_name    Name of the attribute (varchar)
.Ve
.SS "Data Loading Methods"
.IX Subsection "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.
.SS "new"
.IX Subsection "new"
.Vb 6
\& 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
.Ve
.PP
The new constructor is identical to the \*(L"dbi\*(R" adaptor's \fBnew()\fR method,
except that the prefix \*(L"dbi:pg\*(R" is added to the database \s-1DSN\s0 identifier
automatically if it is not there already.
.PP
.Vb 2
\&  Argument       Description
\&  \-\-\-\-\-\-\-\-       \-\-\-\-\-\-\-\-\-\-\-
\&
\&  \-dsn           the DBI data source, e.g. \*(Aqdbi:Pg:dbname=:ens0040\*(Aq or "ens0040"
\&
\&  \-user          username for authentication
\&
\&  \-pass          the password for authentication
.Ve
.SS "schema"
.IX Subsection "schema"
.Vb 6
\& Title   : schema
\& Usage   : $schema = $db\->schema
\& Function: return the CREATE script for the schema
\& Returns : a list of CREATE statemetns
\& Args    : none
\& Status  : protected
.Ve
.PP
This method returns a list containing the various \s-1CREATE\s0 statements
needed to initialize the database tables.
.SS "setup_load"
.IX Subsection "setup_load"
.Vb 6
\& Title   : setup_load
\& Usage   : $db\->setup_load
\& Function: called before load_gff_line()
\& Returns : void
\& Args    : none
\& Status  : protected
.Ve
.PP
This method performs schema-specific initialization prior to loading a
set of \s-1GFF\s0 records.  It prepares a set of \s-1DBI\s0 statement handlers to be 
used in loading the data.
.SS "load_gff_line"
.IX Subsection "load_gff_line"
.Vb 6
\& 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
.Ve
.PP
This method is called once per line of the \s-1GFF\s0 and passed a series of
parsed data items that are stored into the hashref \f(CW$fields\fR.  The keys are:
.PP
.Vb 10
\& 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\*(Aqs group (may be undef)
\& group_name   ID of annotation\*(Aqs 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
.Ve
.SS "get_table_id"
.IX Subsection "get_table_id"
.Vb 6
\& 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
.Ve
.PP
This internal method is called by load_gff_line to look up the integer
\&\s-1ID\s0 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.
.PP
This method requires that a statement handler named \fIlookup_$table\fR,
have been created previously by \fBsetup_load()\fR.  It is here to overcome
deficiencies in mysql's \s-1INSERT\s0 syntax.
.SS "range_query"
.IX Subsection "range_query"
.Vb 6
\& 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
.Ve
.PP
This method constructs the statement handle for this module's central
query: given a range and/or a list of feature types, fetch their \s-1GFF\s0
records.  It overrides a method in dbi.pm so that the overlaps query
can write \s-1SQL\s0 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 
\&\*(L"pg_\*(R".
.PP
The positional arguments are as follows:
.PP
.Vb 1
\&  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.
.Ve
.SS "search_notes"
.IX Subsection "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.
.PP
See also Bio::DB::GFF
.PP
.Vb 6
\& 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
.Ve
.PP
This is a replacement for the mysql-specific method.  Given a search string, it
performs a \s-1ILIKE\s0 search of the notes table and returns an array of results.
Each row of the returned array is a arrayref containing the following fields:
.PP
.Vb 3
\&  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.
.Ve
.PP
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.
.SS "make_meta_set_query"
.IX Subsection "make_meta_set_query"
.Vb 6
\& 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
.Ve
.PP
By default this does nothing; meta parameters are not stored or
retrieved.
.SS "make_features_by_name_where_part"
.IX Subsection "make_features_by_name_where_part"
.Vb 8
\& 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
.Ve