package Bio::DB::GFF::Adaptor::dbi::pg;
=head1 NAME
Bio::DB::GFF::Adaptor::dbi::pg -- Database adaptor for a specific postgres schema
=head1 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;
=head2 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:
=over
=item 1
Set 'enable_seqscan = false' in your postgresql.conf file (and restart
your server).
=item 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.
=back
=cut
# a simple postgres adaptor
use strict;
use Bio::DB::GFF::Util::Binning;
use Bio::DB::GFF::Util::Rearrange; # for rearrange()
use base qw(Bio::DB::GFF::Adaptor::dbi);
use constant MAX_SEGMENT => 100_000_000; # the largest a segment can get
use constant DEFAULT_CHUNK => 2000;
use constant GETSEQCOORDS =><<END;
SELECT fref,
COALESCE(gclass,'Sequence'),
min(fstart),
max(fstop),
fstrand,
gname
FROM fdata,fgroup
WHERE lower(fgroup.gname) = lower(?)
AND fgroup.gclass=?
AND fgroup.gid=fdata.gid
GROUP BY fref,fstrand,gclass,gname
END
;
use constant GETALIASCOORDS =><<END;
SELECT fref,
COALESCE(gclass,'Sequence'),
min(fstart),
max(fstop),
fstrand,
gname
FROM fdata,fgroup,fattribute,fattribute_to_feature
WHERE lower(fattribute_to_feature.fattribute_value)=lower(?)
AND fgroup.gclass=?
AND fgroup.gid=fdata.gid
AND fattribute.fattribute_name='Alias'
AND fattribute_to_feature.fattribute_id=fattribute.fattribute_id
AND fattribute_to_feature.fid=fdata.fid
GROUP BY fref,fstrand,gclass,gname
END
;
use constant GETALIASLIKE =><<END;
SELECT fref,
COALESCE(gclass,'Sequence'),
min(fstart),
max(fstop),
fstrand,
gname
FROM fdata,fgroup,fattribute,fattribute_to_feature
WHERE lower(fattribute_to_feature.fattribute_value) LIKE lower(?)
AND fgroup.gclass=?
AND fgroup.gid=fdata.gid
AND fattribute.fattribute_name='Alias'
AND fattribute_to_feature.fattribute_id=fattribute.fattribute_id
AND fattribute_to_feature.fid=fdata.fid
GROUP BY fref,fstrand,gname
END
;
use constant GETFORCEDSEQCOORDS =><<END;
SELECT fref,
COALESCE(gclass,'Sequence'),
min(fstart),
max(fstop),
fstrand
FROM fdata,fgroup
WHERE lower(fgroup.gname) = lower(?)
AND fgroup.gclass=?
AND lower(fdata.fref) = lower(?)
AND fgroup.gid=fdata.gid
GROUP BY fref,fstrand,gclass
END
;
use constant FULLTEXTWILDCARD => <<END;
SELECT distinct gclass,gname,fattribute_value
FROM fgroup,fattribute_to_feature,fdata
WHERE fgroup.gid=fdata.gid
AND fdata.fid=fattribute_to_feature.fid
AND lower(fattribute_to_feature.fattribute_value) LIKE lower(?)
END
;
########################
# moved from mysqlopt.pm
########################
# this is the largest that any reference sequence can be (100 megabases)
use constant MAX_BIN => 100_000_000;
# this is the smallest bin (1 K)
use constant MIN_BIN => 1000;
# size of range over which it is faster to force mysql to use the range for indexing
use constant STRAIGHT_JOIN_LIMIT => 200_000;
##############################################################################
=head1 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:
=over 4
=item 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.
=item 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)
=item 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)
=item 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.
=item 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.
=item 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)
=back
=head2 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.
=cut
=head2 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
=cut
#'
sub new {
my $class = shift;
my ($dsn,$other) = rearrange([
[qw(FEATUREDB DB DSN)],
],@_);
$dsn = "dbi:Pg:dbname=$dsn" if !ref($dsn) && $dsn !~ /^(dbi|DBI):/;
my $self = $class->SUPER::new(-dsn=>$dsn,%$other);
$self;
}
=head2 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.
=cut
sub schema {
my %schema = (
fdata =>{
table=> q{
CREATE TABLE "fdata" (
"fid" serial NOT NULL,
"fref" character varying(100) DEFAULT '' NOT NULL,
"fstart" integer DEFAULT '0' NOT NULL,
"fstop" integer DEFAULT '0' NOT NULL,
"fbin" double precision DEFAULT '0.000000' NOT NULL,
"ftypeid" integer DEFAULT '0' NOT NULL,
"fscore" double precision DEFAULT NULL,
"fstrand" character varying(3) DEFAULT NULL,
"fphase" character varying(3) DEFAULT NULL,
"gid" integer DEFAULT '0' NOT NULL,
"ftarget_start" integer DEFAULT NULL,
"ftarget_stop" integer DEFAULT NULL,
CONSTRAINT chk_fdata_fstrand CHECK (fstrand IN ('+','-')),
CONSTRAINT chk_fdata_fphase CHECK (fphase IN ('0','1','2')),
CONSTRAINT pk_fdata PRIMARY KEY (fid)
)
}, # fdata table
#CONSTRAINT fref_fdata UNIQUE (fref, fbin, fstart, fstop, ftypeid, gid)
# fdata_fref_idx => q{ CREATE UNIQUE INDEX fdata_fref_idx ON fdata (fref,fbin,fstart,fstop,ftypeid,gid)},
index=>{
fdata_fref_idx => q{
CREATE INDEX fdata_fref_idx ON fdata (fref,fbin,fstart,fstop,ftypeid,gid)
},
fdata_ftypeid_idx => q{
CREATE INDEX fdata_ftypeid_idx ON fdata (ftypeid)
},
fdata_gid_idx => q{
CREATE INDEX fdata_gid_idx ON fdata (gid)
}
}, # fdata indexes
}, # fdata
fgroup => {
table => q{
CREATE TABLE "fgroup" (
"gid" serial NOT NULL,
"gclass" character varying(100) DEFAULT NULL,
"gname" character varying(100) DEFAULT NULL,
CONSTRAINT pk_fgroup PRIMARY KEY (gid)
)
}, # fgroup table
index => {
fgroup_gclass_idx => q{
CREATE UNIQUE INDEX fgroup_gclass_idx ON fgroup (gclass,gname)
},
fgroup_gname_idx => q{
CREATE INDEX fgroup_gname_idx ON fgroup(gname)
},
fgroup_lower_gname_idx => q{
CREATE INDEX fgroup_lower_gname_idx ON fgroup (lower(gname))
},
}, # fgroup indexes
}, # fgroup
ftype => {
table => q{
CREATE TABLE "ftype" (
"ftypeid" serial NOT NULL,
"fmethod" character varying(100) DEFAULT '' NOT NULL,
"fsource" character varying(100) DEFAULT NULL,
CONSTRAINT pk_ftype PRIMARY KEY (ftypeid),
CONSTRAINT ftype_ftype UNIQUE (fmethod, fsource)
)
}, # ftype table
index => {
ftype_fmethod_idx => q{
CREATE INDEX ftype_fmethod_idx ON ftype (fmethod)
},
ftype_fsource_idx => q{
CREATE INDEX ftype_fsource_idx ON ftype (fsource)
},
ftype_ftype_idx => q{
CREATE UNIQUE INDEX ftype_ftype_idx ON ftype (fmethod,fsource)
}
}, # ftype indexes
}, # ftype
fdna => {
table => q{
CREATE TABLE "fdna" (
"fref" character varying(100) DEFAULT '' NOT NULL,
"foffset" integer DEFAULT '0' NOT NULL,
"fdna" bytea,
CONSTRAINT pk_fdna PRIMARY KEY (fref, foffset)
)
} #fdna table
}, #fdna
fmeta => {
table => q{
CREATE TABLE "fmeta" (
"fname" character varying(255) DEFAULT '' NOT NULL,
"fvalue" character varying(255) DEFAULT '' NOT NULL,
CONSTRAINT pk_fmeta PRIMARY KEY (fname)
)
} # fmeta table
}, # fmeta
fattribute => {
table => q{
CREATE TABLE "fattribute" (
"fattribute_id" serial NOT NULL,
"fattribute_name" character varying(255) DEFAULT '' NOT NULL,
CONSTRAINT pk_fattribute PRIMARY KEY (fattribute_id)
)
}, # fattribute table
}, # fattribute
fattribute_to_feature => {
table => q{
CREATE TABLE "fattribute_to_feature" (
"fid" integer DEFAULT '0' NOT NULL,
"fattribute_id" integer DEFAULT '0' NOT NULL,
"fattribute_value" text
)
}, # fattribute_to_feature table
index => {
fattribute_to_feature_fid => q{
CREATE INDEX fattribute_to_feature_fid ON fattribute_to_feature (fid,fattribute_id)
},
fattribute_txt_idx => q{
CREATE INDEX fattribute_txt_idx ON fattribute_to_feature (fattribute_value)
},
fattribute_lower_idx => q{
CREATE INDEX fattribute_lower_idx ON fattribute_to_feature (lower(fattribute_value))
},
} # fattribute_to_feature indexes
}, # fattribute_to_feature
finterval_stats => {
table=> q{
CREATE TABLE "finterval_stats" (
"ftypeid" integer DEFAULT '0' NOT NULL,
"fref" character varying(100) DEFAULT '' NOT NULL,
"fbin" integer DEFAULT '0' NOT NULL,
"fcum_count" integer DEFAULT '0' NOT NULL,
CONSTRAINT pk_finterval_stats PRIMARY KEY (ftypeid,fref,fbin)
)
} # finterval_stats table
},# finterval_stats
);
return \%schema;
}
=head2 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.
=cut
sub setup_load {
my $self = shift;
my $schema = $self->schema;
my $dbh = $self->features_db;
if ($self->lock_on_load) {
my @tables = map { "$_ WRITE"} $self->tables;
my $tables = join ', ',@tables;
$dbh->do("LOCK TABLES $tables");
}
my $lookup_type = $dbh->prepare_delayed('SELECT ftypeid FROM ftype WHERE fmethod=? AND fsource=?');
my $insert_type = $dbh->prepare_delayed('INSERT INTO ftype (fmethod,fsource) VALUES (?,?)');
my $insertid_type = $dbh->prepare_delayed("SELECT currval('ftype_ftypeid_seq')");
my $lookup_group = $dbh->prepare_delayed('SELECT gid FROM fgroup WHERE lower(gname)=lower(?) AND gclass=?');
my $insert_group = $dbh->prepare_delayed('INSERT INTO fgroup (gname,gclass) VALUES (?,?)');
my $insertid_group = $dbh->prepare_delayed("SELECT currval('fgroup_gid_seq')");
my $lookup_attribute = $dbh->prepare_delayed('SELECT fattribute_id FROM fattribute WHERE fattribute_name=?');
my $insert_attribute = $dbh->prepare_delayed('INSERT INTO fattribute (fattribute_name) VALUES (?)');
my $insertid_attribute = $dbh->prepare_delayed("SELECT currval('fattribute_fattribute_id_seq')");
my $insert_attribute_value = $dbh->prepare_delayed('INSERT INTO fattribute_to_feature (fid,fattribute_id,fattribute_value) VALUES (?,?,?)');
my $insert_data = $dbh->prepare_delayed(<<END);
INSERT INTO fdata (fref,fstart,fstop,fbin,ftypeid,fscore,
fstrand,fphase,gid,ftarget_start,ftarget_stop)
VALUES(?,?,?,?,?,?,?,?,?,?,?)
END
;
my $delete_existing_data = $dbh->prepare_delayed('DELETE FROM fdata WHERE fref=? AND fstart=? AND fstop=? AND fbin=? AND ftypeid=? AND GID=?');
my $insertid_data = $dbh->prepare_delayed("SELECT currval('fdata_fid_seq')");
$self->{load_stuff}{sth}{lookup_ftype} = $lookup_type;
$self->{load_stuff}{sth}{insert_ftype} = $insert_type;
$self->{load_stuff}{sth}{insertid_ftype} = $insertid_type;
$self->{load_stuff}{sth}{lookup_fgroup} = $lookup_group;
$self->{load_stuff}{sth}{insert_fgroup} = $insert_group;
$self->{load_stuff}{sth}{insertid_fgroup} = $insertid_group;
$self->{load_stuff}{sth}{insertid_fdata} = $insertid_data;
$self->{load_stuff}{sth}{insert_fdata} = $insert_data;
$self->{load_stuff}{sth}{delete_existing_fdata} = $delete_existing_data;
$self->{load_stuff}{sth}{lookup_fattribute} = $lookup_attribute;
$self->{load_stuff}{sth}{insert_fattribute} = $insert_attribute;
$self->{load_stuff}{sth}{insertid_fattribute} = $insertid_attribute;
$self->{load_stuff}{sth}{insert_fattribute_value} = $insert_attribute_value;
$self->{load_stuff}{types} = {};
$self->{load_stuff}{groups} = {};
$self->{load_stuff}{counter} = 0;
}
=head2 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
=cut
sub load_gff_line {
my $self = shift;
my $gff = shift;
if (defined $gff->{phase}){
chomp($gff->{phase});
undef($gff->{phase}) if $gff->{phase} eq '.';
}
if (defined $gff->{strand} && $gff->{strand} eq '.'){undef($gff->{strand})};
if (defined $gff->{score} && $gff->{score} eq '.'){undef($gff->{score})};
my $s = $self->{load_stuff};
my $dbh = $self->features_db;
local $dbh->{PrintError} = 0;
defined(my $typeid = $self->get_table_id('ftype', $gff->{method} => $gff->{source})) or return;
defined(my $groupid = $self->get_table_id('fgroup',$gff->{gname} => $gff->{gclass})) or return;
my $bin = bin($gff->{start},$gff->{stop},$self->min_bin);
my $result = $s->{sth}{insert_fdata}->execute($gff->{ref},
$gff->{start},$gff->{stop},$bin,
$typeid,
$gff->{score},$gff->{strand},$gff->{phase},
$groupid,
$gff->{tstart},$gff->{tstop});
warn $dbh->errstr,"\n" and print "ref=",$gff->{ref}," start=",$gff->{start}," stop=",$gff->{stop}," bin=",$bin," typeid=",$typeid," groupid=",$groupid,"\n"
and return unless $result;
my $fid = $self->insertid($s->{sth},'fdata')
|| $self->get_feature_id($gff->{ref},$gff->{start},$gff->{stop},$typeid,$groupid);
# insert attributes
foreach (@{$gff->{attributes}}) {
defined(my $attribute_id = $self->get_table_id('fattribute',$_->[0])) or return;
$s->{sth}{insert_fattribute_value}->execute($fid,$attribute_id,$_->[1]);
}
if ( (++$s->{counter} % 1000) == 0) {
print STDERR "$s->{counter} records loaded...";
print STDERR -t STDOUT && !$ENV{EMACS} ? "\r" : "\n";
}
$fid;
}
sub insertid {
my $self = shift;
my $sth = shift ;
my $table = shift;
my $insert_id;
if ($sth->{"insertid_$table"}->execute()){
$insert_id = ($sth->{"insertid_$table"}->fetchrow_array)[0];
}
else{
warn "No CURRVAL for SEQUENCE of table $table ",$sth->errstr,"\n";
return;
}
return $insert_id;
}
=head2 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 I<lookup_$table>,
have been created previously by setup_load(). It is here to overcome
deficiencies in mysql's INSERT syntax.
=cut
#'
# get the object ID from a named table
sub get_table_id {
my $self = shift;
my $table = shift;
my @ids = @_;
# irritating warning for null id
my $id_key;
{
local $^W=0;
$id_key = join ':',@ids;
}
my $s = $self->{load_stuff};
my $sth = $s->{sth};
my $dbh = $self->features_db;
unless (defined($s->{$table}{$id_key})) {
$sth->{"lookup_$table"}->execute(@ids);
my @result = $sth->{"lookup_$table"}->fetchrow_array;
if (@result > 0) {
$s->{$table}{$id_key} = $result[0];
} else {
$sth->{"insert_$table"}->execute(@ids)
&& ($s->{$table}{$id_key} = $self->insertid($sth,$table));
#&& ($s->{$table}{$id_key} = $self->insertid($sth->{"insertid_$table"}));
#&& ($s->{$table}{$id_key} = $sth->{"insert_$table"}->insertid);
}
}
my $id = $s->{$table}{$id_key};
unless (defined $id) {
warn "No $table id for $id_key ",$dbh->errstr," Record skipped.\n";
return;
}
$id;
}
#sub insertid {
# my $self = shift;
# my $insertid_sth = shift ;
# my $insert_id;
# if ($insertid_sth->execute){
# $insert_id = ($insertid_sth->fetchrow_array)[0];
# }
# else{
# warn "No CURRVAL for SEQUENCE ",$insertid_sth->errstr,"\n";
# return;
# }
# return $insert_id;
#}
sub insert_sequence {
my $self = shift;
my($id,$offset,$seq) = @_;
my $sth = $self->{_insert_sequence}
||= $self->dbh->prepare_delayed('insert into fdna values (?,?,?)');
$sth->execute($id,$offset,$seq) or $self->throw($sth->errstr);
}
=head2 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.
=cut
sub range_query {
my $self = shift;
my($rangetype,$refseq,$class,$start,$stop,$types,$sparse,$order_by_group,$attributes,$bin) = @_;
my $dbh = $self->features_db;
# my @bin_parts = split /\n\s+OR/, $self->bin_query($start,$stop);
# warn "bin_part: @bin_parts\n";
my %a = (refseq=>$refseq,class=>$class,start=>$start,stop=>$stop,types=>$types,attributes=>$attributes,bin_width=>$bin);
my ($query, @args, $order_by);
if ($rangetype ne 'overlaps') {
my $select = $self->make_features_select_part(\%a);
my $from = $self->make_features_from_part($sparse,\%a);
my $join = $self->make_features_join_part(\%a);
my $where;
($where,@args) = $self->make_features_by_range_where_part($rangetype,\%a);
my ($group_by,@more_args) = $self->make_features_group_by_part(\%a);
$order_by = $self->make_features_order_by_part(\%a) if $order_by_group;
$query = "SELECT $select FROM $from WHERE $join";
$query .= " AND $where" if $where;
if ($group_by) {
$query .= " GROUP BY $group_by";
push @args,@more_args;
}
} else { # most common case: overlaps query
my @bin_parts = split /\s*OR/, $self->bin_query($start,$stop);
my $select = $self->make_features_select_part(\%a);
my $from = $self->make_features_from_part($sparse,\%a);
my $join = $self->make_features_join_part(\%a);
my $where;
($where,@args) = $self->pg_make_features_by_range_where_part($rangetype,\%a);
my ($group_by,@more_args)= $self->make_features_group_by_part(\%a);
$order_by = $self->pg_make_features_order_by_part(\%a) if $order_by_group;
my @temp_args;
my @query_pieces;
foreach my $bin (@bin_parts) {
my $temp_query = "SELECT $select FROM $from WHERE $join AND $where AND $bin\n";
push @temp_args, @args;
if ($group_by) {
$temp_query .= " GROUP BY $group_by";
push @temp_args,@more_args;
}
push @query_pieces, $temp_query;
}
@args = @temp_args;
$query = join("UNION\n", @query_pieces);
}
$query .= " ORDER BY $order_by" if $order_by;
$self->dbh->do('set enable_seqscan=off');
my $sth = $self->dbh->do_query($query,@args);
$sth;
}
sub pg_make_features_by_range_where_part {
my $self = shift;
my ($rangetype,$options) = @_;
return unless $rangetype eq 'overlaps';
$options ||= {};
my ($refseq,$class,$start,$stop,$types,$attributes) =
@{$options}{qw(refseq class start stop types attributes)};
my (@query,@args);
if ($refseq) {
my ($q,@a) = $self->refseq_query($refseq,$class);
push @query,$q;
push @args,@a;
}
if (defined $start or defined $stop) {
$start = 0 unless defined($start);
$stop = MAX_SEGMENT unless defined($stop);
my ($range_query,@range_args) = $self->pg_overlap_query($start,$stop);
push @query,$range_query;
push @args,@range_args;
}
if (defined $types && @$types) {
my ($type_query,@type_args) = $self->types_query($types);
push @query,$type_query;
push @args,@type_args;
}
if ($attributes) {
my ($attribute_query,@attribute_args) = $self->make_features_by_attribute_where_part($attributes);
push @query,"($attribute_query)";
push @args,@attribute_args;
}
my $query = join "AND",@query;
return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args);
}
sub pg_overlap_query {
my $self = shift;
my ($start,$stop) = @_;
my ($iq,@iargs) = $self->overlap_query_nobin($start,$stop);
my $query = "\n$iq\n";
my @args = @iargs;
return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args);
}
sub pg_make_features_order_by_part {
my $self = shift;
my $options = shift || {};
return "gname";
}
=head2 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: L<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 L<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 L<Bio::DB::GFF::Adaptor::dbi::pg_fts> which
implements the TSearch2 full text indexing scheme.
=cut
sub search_notes{
# my $self = shift;
# my ($search_string,$limit) = @_;
#
# $search_string =~ tr/*/%/s;
# $search_string = '%'.$search_string unless $search_string =~ /^\%/;
# $search_string = $search_string.'%' unless $search_string =~ /\%$/;
# warn "search_string:$search_string";
# my $query = FULLTEXTWILDCARD;
# $query .= " limit $limit" if defined $limit;
# my $sth = $self->dbh->do_query($query,$search_string);
#
# my @results;
# while (my ($class,$name,$note) = $sth->fetchrow_array) {
#
# next unless $class && $name; # sorry, ignore NULL objects
# my $featname = Bio::DB::GFF::Featname->new($class=>$name);
#
# push @results,[$featname,$note,0]; #gbrowse expects a score, but
# #pg doesn't give one, thus the 0
# }
# warn @results;
#
# return @results;
}
=head2 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.
=cut
sub make_meta_set_query {
return 'INSERT INTO fmeta VALUES (?,?)';
}
sub make_classes_query {
my $self = shift;
return 'SELECT DISTINCT gclass FROM fgroup WHERE NOT gclass IS NULL';
}
sub chunk_size {
my $self = shift;
$self->meta('chunk_size') || DEFAULT_CHUNK;
}
sub getseqcoords_query {
my $self = shift;
return GETSEQCOORDS ;
}
sub getaliascoords_query{
my $self = shift;
return GETALIASCOORDS ;
}
sub getforcedseqcoords_query{
my $self = shift;
return GETFORCEDSEQCOORDS ;
}
sub getaliaslike_query{
my $self = shift;
return GETALIASLIKE ;
}
sub make_features_select_part {
my $self = shift;
my $options = shift || {};
my $s;
if (my $b = $options->{bin_width}) {
$s = <<END;
fref,
1+$b*floor(fstart/$b) as fstart,
$b*(1+floor(fstart/$b)) as fstop,
CASE WHEN fsource IS NULL THEN fmethod
ELSE fmethod||':'||fsource,
'bin',
count(*) as fscore,
'.','.','bin',
CASE WHEN fsource IS NULL THEN fref||':'||fmethod
ELSE fref||':'||fmethod||':'||fsource,
NULL,NULL,NULL,NULL
END
;
} else {
$s = <<END;
fref,fstart,fstop,fsource,fmethod,fscore,fstrand,fphase,gclass,fgroup.gname,ftarget_start,ftarget_stop,fdata.fid,fdata.gid
END
;
}
$s .= ",count(fdata.fid)" if $options->{attributes} && keys %{$options->{attributes}}>1;
$s;
}
sub make_features_from_part_bkup {
my $self = shift;
my $sparse = shift;
my $options = shift || {};
#my $index = $sparse ? ' USE INDEX(ftypeid)': '';
my $index = '';
return $options->{attributes} ? "fdata${index},ftype,fgroup,fattribute,fattribute_to_feature\n"
: "fdata${index},ftype,fgroup\n";
}
####################################
# moved from mysqlopt.pm
###################################
# meta values
sub default_meta_values {
my $self = shift;
my @values = $self->SUPER::default_meta_values;
return (
@values,
max_bin => MAX_BIN,
min_bin => MIN_BIN,
straight_join_limit => STRAIGHT_JOIN_LIMIT,
);
}
sub min_bin {
my $self = shift;
return $self->meta('min_bin') || MIN_BIN;
}
sub max_bin {
my $self = shift;
return $self->meta('max_bin') || MAX_BIN;
}
sub straight_join_limit {
my $self = shift;
return $self->meta('straight_join_limit') || STRAIGHT_JOIN_LIMIT;
}
sub _feature_by_name {
my $self = shift;
my ($class,$name,$location,$callback) = @_;
$callback || $self->throw('must provide a callback argument');
my @bin_parts = split /\s*OR/, $self->bin_query($location->[1],$location->[2]) if $location;
my $select = $self->make_features_select_part;
my $from = $self->make_features_from_part(undef,{sparse_groups=>1});
my ($where,@args) = $self->make_features_by_name_where_part($class,$name);
my $join = $self->make_features_join_part;
my $range = $self->pg_make_features_by_range_where_part('overlaps',
{refseq=>$location->[0],
class =>'',
start=>$location->[1],
stop =>$location->[2]}) if $location;
my @temp_args;
my @query_pieces;
my $query;
if (@bin_parts) {
foreach my $bin (@bin_parts) {
my $temp_query = "SELECT $select FROM $from WHERE $join AND $where AND $range AND $bin\n";
push @temp_args, @args;
push @query_pieces, $temp_query;
}
@args = @temp_args;
$query = join("UNION\n", @query_pieces);
} else {
$query = "SELECT $select FROM $from WHERE $where AND $join";
}
my $sth = $self->dbh->do_query($query,@args);
my $count = 0;
while (my @row = $sth->fetchrow_array) {
$callback->(@row);
$count++;
}
$sth->finish;
return $count;
}
sub update_sequences {
my $self = shift;
my $dbh = $self->features_db;
$dbh->do("SELECT setval('public.fdata_fid_seq', max(fid)+1) FROM fdata");
$dbh->do("SELECT setval('public.fattribute_fattribute_id_seq', max(fattribute_id)+1) FROM fattribute");
$dbh->do("SELECT setval('public.fgroup_gid_seq', max(gid)+1) FROM fgroup");
$dbh->do("SELECT setval('public.ftype_ftypeid_seq', max(ftypeid)+1) FROM ftype");
1;
}
=head2 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
=cut
sub make_features_by_name_where_part {
my $self = shift;
my ($class,$name) = @_;
if ($name !~ /\*/) {
#allows utilization of an index on lower(gname)
return ("fgroup.gclass=? AND lower(fgroup.gname) = lower(?)",$class,$name);
}
else {
$name =~ tr/*/%/;
return ("fgroup.gclass=? AND lower(fgroup.gname) LIKE lower(?)",$class,$name);
}
}
#
# Methods from dbi.pm that need to be overridden to make
# searching for fref case insensitive
#
#
sub get_dna {
my $self = shift;
my ($ref,$start,$stop,$class) = @_;
my ($offset_start,$offset_stop);
my $has_start = defined $start;
my $has_stop = defined $stop;
my $reversed;
if ($has_start && $has_stop && $start > $stop) {
$reversed++;
($start,$stop) = ($stop,$start);
}
# turn start and stop into 0-based offsets
my $cs = $self->dna_chunk_size;
$start -= 1; $stop -= 1;
$offset_start = int($start/$cs)*$cs;
$offset_stop = int($stop/$cs)*$cs;
my $sth;
# special case, get it all
if (!($has_start || $has_stop)) {
$sth = $self->dbh->do_query('select fdna,foffset from fdna where lower(fref)=lower(?) order by foffset',$ref);
}
elsif (!$has_stop) {
$sth = $self->dbh->do_query('select fdna,foffset from fdna where lower(fref)=lower(?) and foffset>=? order by foffset',
$ref,$offset_start);
}
else { # both start and stop defined
$sth = $self->dbh->do_query('select fdna,foffset from fdna where lower(fref)=lower(?) and foffset>=? and foffset<=? order by foffset',
$ref,$offset_start,$offset_stop);
}
my $dna = '';
while (my($frag,$offset) = $sth->fetchrow_array) {
substr($frag,0,$start-$offset) = '' if $has_start && $start > $offset;
$dna .= $frag;
}
substr($dna,$stop-$start+1) = '' if $has_stop && $stop-$start+1 < length($dna);
if ($reversed) {
$dna = reverse $dna;
$dna =~ tr/gatcGATC/ctagCTAG/;
}
$sth->finish;
$dna;
}
sub refseq_query {
my $self = shift;
my ($refseq,$refclass) = @_;
my $query = "lower(fdata.fref)=lower(?)";
return wantarray ? ($query,$refseq) : $self->dbh->dbi_quote($query,$refseq);
}
sub make_types_where_part {
my $self = shift;
my ($srcseq,$start,$stop,$want_count,$typelist) = @_;
my (@query,@args);
if (defined($srcseq)) {
push @query,'lower(fdata.fref)=lower(?)';
push @args,$srcseq;
if (defined $start or defined $stop) {
$start = 1 unless defined $start;
$stop = MAX_SEGMENT unless defined $stop;
my ($q,@a) = $self->overlap_query($start,$stop);
push @query,"($q)";
push @args,@a;
}
}
if (defined $typelist && @$typelist) {
my ($q,@a) = $self->types_query($typelist);
push @query,($q);
push @args,@a;
}
my $query = @query ? join(' AND ',@query) : '1=1';
return wantarray ? ($query,@args) : $self->dbh->dbi_quote($query,@args);
}
sub get_feature_id {
my $self = shift;
my ($ref,$start,$stop,$typeid,$groupid) = @_;
my $s = $self->{load_stuff};
unless ($s->{get_feature_id}) {
my $dbh = $self->features_db;
$s->{get_feature_id} =
$dbh->prepare_delayed('SELECT fid FROM fdata WHERE lower(fref)=lower(?) AND fstart=? AND fstop=? AND ftypeid=? AND gid=?');
}
my $sth = $s->{get_feature_id} or return;
$sth->execute($ref,$start,$stop,$typeid,$groupid) or return;
my ($fid) = $sth->fetchrow_array;
return $fid;
}
sub _delete {
my $self = shift;
my $delete_spec = shift;
my $ranges = $delete_spec->{segments} || [];
my $types = $delete_spec->{types} || [];
my $force = $delete_spec->{force};
my $range_type = $delete_spec->{range_type};
my $dbh = $self->features_db;
my $query = 'delete from fdata';
my @where;
my @range_part;
for my $segment (@$ranges) {
my $ref = $dbh->quote($segment->abs_ref);
my $start = $segment->abs_start;
my $stop = $segment->abs_stop;
my $range = $range_type eq 'overlaps' ? $self->overlap_query($start,$stop)
: $range_type eq 'contains' ? $self->contains_query($start,$stop)
: $range_type eq 'contained_in' ? $self->contained_in_query($start,$stop)
: $self->throw("Invalid range type '$range_type'");
push @range_part,"(lower(fref)=lower($ref) AND $range)";
}
push @where,'('. join(' OR ',@range_part).')' if @range_part;
# get all the types
if (@$types) {
my $types_where = $self->types_query($types);
my $types_query = "select ftypeid from ftype where $types_where";
my $result = $dbh->selectall_arrayref($types_query);
my @typeids = map {$_->[0]} @$result;
my $typelist = join ',',map{$dbh->quote($_)} @typeids;
$typelist ||= "0"; # don't cause DBI to die with invalid SQL when
# unknown feature types were requested.
push @where,"(ftypeid in ($typelist))";
}
$self->throw("This operation would delete all feature data and -force not specified")
unless @where || $force;
$query .= " where ".join(' and ',@where) if @where;
warn "$query\n" if $self->debug;
my $result = $dbh->do($query);
defined $result or $self->throw($dbh->errstr);
$result;
}
sub make_abscoord_query {
my $self = shift;
my ($name,$class,$refseq) = @_;
#my $query = GETSEQCOORDS;
my $query = $self->getseqcoords_query();
my $getforcedseqcoords = $self->getforcedseqcoords_query() ;
if ($name =~ /\*/) {
$name =~ s/%/\\%/g;
$name =~ s/_/\\_/g;
$name =~ tr/*/%/;
$query =~ s/gname\) = lower/gname) LIKE lower/;
}
defined $refseq
? $self->dbh->do_query($getforcedseqcoords,$name,$class,$refseq)
: $self->dbh->do_query($query,$name,$class);
}
sub make_aliasabscoord_query {
my $self = shift;
my ($name,$class) = @_;
#my $query = GETALIASCOORDS;
my $query = $self->getaliascoords_query();
if ($name =~ /\*/) {
$name =~ s/%/\\%/g;
$name =~ s/_/\\_/g;
$name =~ tr/*/%/;
$query =~ s/gname\) = lower/gname) LIKE lower/;
}
$self->dbh->do_query($query,$name,$class);
}
1;