Bio::DB::GFF(3) User Contributed Perl Documentation Bio::DB::GFF(3)NAMEBio::DB::GFF-- Storage and retrieval of sequence annotation data
SYNOPSIS
use Bio::DB::GFF;
# Open the sequence database
my $db = Bio::DB::GFF->new( -adaptor => 'dbi::mysqlopt',
-dsn => 'dbi:mysql:elegans');
# fetch a 1 megabase segment of sequence starting at landmark "ZK909"
my $segment = $db->segment('ZK909', 1 => 1000000);
# pull out all transcript features
my @transcripts = $segment->features('transcript');
# for each transcript, total the length of the introns
my %totals;
for my $t (@transcripts) {
my @introns = $t->Intron;
$totals{$t->name} += $_->length foreach @introns;
}
# Sort the exons of the first transcript by position
my @exons = sort {$a->start <=> $b->start} $transcripts[0]->Exon;
# Get a region 1000 bp upstream of first exon
my $upstream = $exons[0]->subseq(-1000,0);
# get its DNA
my $dna = $upstream->seq;
# and get all curated polymorphisms inside it
@polymorphisms = $upstream->contained_features('polymorphism:curated');
# get all feature types in the database
my @types = $db->types;
# count all feature types in the segment
my %type_counts = $segment->types(-enumerate=>1);
# get an iterator on all curated features of type 'exon' or 'intron'
my $iterator = $db->get_seq_stream(-type => ['exon:curated','intron:curated']);
while (my $s = $iterator->next_seq) {
print $s,"\n";
}
# find all transcripts annotated as having function 'kinase'
my $iterator = $db->get_seq_stream(-type=>'transcript',
-attributes=>{Function=>'kinase'});
while (my $s = $iterator->next_seq) {
print $s,"\n";
}
DESCRIPTIONBio::DB::GFF provides fast indexed access to a sequence annotation
database. It supports multiple database types (ACeDB, relational), and
multiple schemas through a system of adaptors and aggregators.
The following operations are supported by this module:
- retrieving a segment of sequence based on the ID of a landmark
- retrieving the DNA from that segment
- finding all annotations that overlap with the segment
- finding all annotations that are completely contained within the
segment
- retrieving all annotations of a particular type, either within a
segment, or globally
- conversion from absolute to relative coordinates and back again,
using any arbitrary landmark for the relative coordinates
- using a sequence segment to create new segments based on relative
offsets
The data model used by Bio::DB::GFF is compatible with the GFF flat
file format (<http://www.sequenceontology.org/gff3.shtml>). The module
can load a set of GFF files into the database, and serves objects that
have methods corresponding to GFF fields.
The objects returned by Bio::DB::GFF are compatible with the
SeqFeatureI interface, allowing their use by the Bio::Graphics and
Bio::DAS modules.
Auxiliary Scripts
The bioperl distribution includes several scripts that make it easier
to work with Bio::DB::GFF databases. They are located in the scripts
directory under a subdirectory named Bio::DB::GFF:
· bp_load_gff.pl
This script will load a Bio::DB::GFF database from a flat GFF file
of sequence annotations. Only the relational database version of
Bio::DB::GFF is supported. It can be used to create the database
from scratch, as well as to incrementally load new data.
This script takes a --fasta argument to load raw DNA into the
database as well. However, GFF databases do not require access to
the raw DNA for most of their functionality.
load_gff.pl also has a --upgrade option, which will perform a non-
destructive upgrade of older schemas to newer ones.
· bp_bulk_load_gff.pl
This script will populate a Bio::DB::GFF database from a flat GFF
file of sequence annotations. Only the MySQL database version of
Bio::DB::GFF is supported. It uses the "LOAD DATA INFILE" query in
order to accelerate loading considerably; however, it can only be
used for the initial load, and not for updates.
This script takes a --fasta argument to load raw DNA into the
database as well. However, GFF databases do not require access to
the raw DNA for most of their functionality.
· bp_fast_load_gff.pl
This script is as fast as bp_bulk_load_gff.pl but uses Unix pipe
tricks to allow for incremental updates. It only supports the
MySQL database version of Bio::DB::GFF and is guaranteed not to
work on non-Unix platforms.
Arguments are the same as bp_load_gff.pl
· gadfly_to_gff.pl
This script will convert the GFF-like format used by the Berkeley
Drosophila Sequencing project into a format suitable for use with
this module.
· sgd_to_gff.pl
This script will convert the tab-delimited feature files used by
the Saccharomyces Genome Database into a format suitable for use
with this module.
GFF Fundamentals
The GFF format is a flat tab-delimited file, each line of which
corresponds to an annotation, or feature. Each line has nine columns
and looks like this:
Chr1 curated CDS 365647 365963 . + 1 Transcript "R119.7"
The 9 columns are as follows:
1. reference sequence
This is the ID of the sequence that is used to establish the
coordinate system of the annotation. In the example above, the
reference sequence is "Chr1".
2. source
The source of the annotation. This field describes how the
annotation was derived. In the example above, the source is
"curated" to indicate that the feature is the result of human
curation. The names and versions of software programs are often
used for the source field, as in "tRNAScan-SE/1.2".
3. method
The annotation method. This field describes the type of the
annotation, such as "CDS". Together the method and source describe
the annotation type.
4. start position
The start of the annotation relative to the reference sequence.
5. stop position
The stop of the annotation relative to the reference sequence.
Start is always less than or equal to stop.
6. score
For annotations that are associated with a numeric score (for
example, a sequence similarity), this field describes the score.
The score units are completely unspecified, but for sequence
similarities, it is typically percent identity. Annotations that
don't have a score can use "."
7. strand
For those annotations which are strand-specific, this field is the
strand on which the annotation resides. It is "+" for the forward
strand, "-" for the reverse strand, or "." for annotations that are
not stranded.
8. phase
For annotations that are linked to proteins, this field describes
the phase of the annotation on the codons. It is a number from 0
to 2, or "." for features that have no phase.
9. group
GFF provides a simple way of generating annotation hierarchies ("is
composed of" relationships) by providing a group field. The group
field contains the class and ID of an annotation which is the
logical parent of the current one. In the example given above, the
group is the Transcript named "R119.7".
The group field is also used to store information about the target
of sequence similarity hits, and miscellaneous notes. See the next
section for a description of how to describe similarity targets.
The format of the group fields is "Class ID" with a single space
(not a tab) separating the class from the ID. It is VERY IMPORTANT
to follow this format, or grouping will not work properly.
The sequences used to establish the coordinate system for annotations
can correspond to sequenced clones, clone fragments, contigs or super-
contigs. Thus, this module can be used throughout the lifecycle of a
sequencing project.
In addition to a group ID, the GFF format allows annotations to have a
group class. For example, in the ACeDB representation, RNA
interference experiments have a class of "RNAi" and an ID that is
unique among the RNAi experiments. Since not all databases support
this notion, the class is optional in all calls to this module, and
defaults to "Sequence" when not provided.
Double-quotes are sometimes used in GFF files around components of the
group field. Strictly, this is only necessary if the group name or
class contains whitespace.
Making GFF files work with this module
Some annotations do not need to be individually named. For example, it
is probably not useful to assign a unique name to each ALU repeat in a
vertebrate genome. Others, such as predicted genes, correspond to
named biological objects; you probably want to be able to fetch the
positions of these objects by referring to them by name.
To accomodate named annotations, the GFF format places the object class
and name in the group field. The name identifies the object, and the
class prevents similarly-named objects, for example clones and
sequences, from collding.
A named object is shown in the following excerpt from a GFF file:
Chr1 curated transcript 939627 942410 . + . Transcript Y95B8A.2
This object is a predicted transcript named Y95BA.2. In this case, the
group field is used to identify the class and name of the object, even
though no other annotation belongs to that group.
It now becomes possible to retrieve the region of the genome covered by
transcript Y95B8A.2 using the segment() method:
$segment = $db->segment(-class=>'Transcript',-name=>'Y95B8A.2');
It is not necessary for the annotation's method to correspond to the
object class, although this is commonly the case.
As explained above, each annotation in a GFF file refers to a reference
sequence. It is important that each reference sequence also be
identified by a line in the GFF file. This allows the Bio::DB::GFF
module to determine the length and class of the reference sequence, and
makes it possible to do relative arithmetic.
For example, if "Chr1" is used as a reference sequence, then it should
have an entry in the GFF file similar to this one:
Chr1 assembly chromosome 1 14972282 . + . Sequence Chr1
This indicates that the reference sequence named "Chr1" has length
14972282 bp, method "chromosome" and source "assembly". In addition,
as indicated by the group field, Chr1 has class "Sequence" and name
"Chr1".
The object class "Sequence" is used by default when the class is not
specified in the segment() call. This allows you to use a shortcut
form of the segment() method:
$segment = $db->segment('Chr1'); # whole chromosome
$segment = $db->segment('Chr1',1=>1000); # first 1000 bp
For your convenience, if, during loading a GFF file, Bio::DB::GFF
encounters a line like the following:
##sequence-region Chr1 1 14972282
It will automatically generate the following entry:
Chr1 reference Component 1 14972282 . + . Sequence Chr1
This is sufficient to use Chr1 as a reference point. The
##sequence-region line is frequently found in the GFF files distributed
by annotation groups.
Specifying the group tag
A frequent problem with GFF files is the problem distinguishing which
of the several tag/value pairs in the 9th column is the grouping pair.
Ordinarily the first tag will be used for grouping, but some GFF
manipulating tools do not preserve the order of attributes. To
eliminate this ambiguity, this module provides two ways of explicitly
specifying which tag to group on:
· Using -preferred_groups
When you create a Bio::DB::GFF object, pass it a
-preferred_groups=> argument. This specifies a tag that will be
used for grouping. You can pass an array reference to specify a
list of such tags.
· In the GFF header
The GFF file itself can specify which tags are to be used for
grouping. Insert a comment like the following:
##group-tags Accession Locus
This says to use the Accession tag for grouping. If it is not
available, use the Locus tag. If neither tag is available, use the
first pair to appear.
These options only apply when loading a GFF file into the database, and
have no effect on existing databases.
The group-tags comment in the GFF file will *override* the preferred
groups set when you create the Bio::DB::GFF object.
For backward compatibility, the tags Sequence and Transcript are always
treated as grouping tags unless preferred_tags are specified. The
"Target" tag is always used for grouping regardless of the
preferred_groups() setting, and the tags "tstart", "tend" and "Note"
cannot be used for grouping. These are historical artefacts coming
from various interpretations of GFF2, and cannot be changed.
Sequence alignments
There are two cases in which an annotation indicates the relationship
between two sequences. The first case is a similarity hit, where the
annotation indicates an alignment. The second case is a map assembly,
in which the annotation indicates that a portion of a larger sequence
is built up from one or more smaller ones.
Both cases are indicated by using the Target tag in the group field.
For example, a typical similarity hit will look like this:
Chr1 BLASTX similarity 76953 77108 132 + 0 Target Protein:SW:ABL_DROME 493 544
The group field contains the Target tag, followed by an identifier for
the biological object referred to. The GFF format uses the notation
Class:Name for the biological object, and even though this is
stylistically inconsistent, that's the way it's done. The object
identifier is followed by two integers indicating the start and stop of
the alignment on the target sequence.
Unlike the main start and stop columns, it is possible for the target
start to be greater than the target end. The previous example
indicates that the the section of Chr1 from 76,953 to 77,108 aligns to
the protein SW:ABL_DROME starting at position 493 and extending to
position 544.
A similar notation is used for sequence assembly information as shown
in this example:
Chr1 assembly Link 10922906 11177731 . . . Target Sequence:LINK_H06O01 1 254826
LINK_H06O01 assembly Cosmid 32386 64122 . . . Target Sequence:F49B2 6 31742
This indicates that the region between bases 10922906 and 11177731 of
Chr1 are composed of LINK_H06O01 from bp 1 to bp 254826. The region of
LINK_H0601 between 32386 and 64122 is, in turn, composed of the bases 5
to 31742 of cosmid F49B2.
Attributes
While not intended to serve as a general-purpose sequence database (see
bioperl-db for that), GFF allows you to tag features with arbitrary
attributes. Attributes appear in the Group field following the initial
class/name pair. For example:
Chr1 cur trans 939 942 . + . Transcript Y95B8A.2 ; Gene sma-3 ; Alias sma3
This line tags the feature named Transcript Y95B8A.2 as being "Gene"
named sma-3 and having the Alias "sma3". Features having these
attributes can be looked up using the fetch_feature_by_attribute()
method.
Two attributes have special meaning: "Note" is for backward
compatibility and is used for unstructured text remarks. "Alias" is
considered as a synonym for the feature name and will be consulted when
looking up a feature by its name.
Adaptors and Aggregators
This module uses a system of adaptors and aggregators in order to make
it adaptable to use with a variety of databases.
· Adaptors
The core of the module handles the user API, annotation coordinate
arithmetic, and other common issues. The details of fetching
information from databases is handled by an adaptor, which is
specified during Bio::DB::GFF construction. The adaptor
encapsulates database-specific information such as the schema, user
authentication and access methods.
There are currently five adaptors recommended for general use:
Adaptor Name Description
-----------------------
memory A simple in-memory database suitable for testing
and small data sets.
berkeleydb An indexed file database based on the DB_File module,
suitable for medium-sized read-only data sets.
dbi::mysql An interface to a schema implemented in the Mysql
relational database management system.
dbi::oracle An interface to a schema implemented in the Oracle
relational database management system.
dbi::pg An interface to a schema implemented in the PostgreSQL
relational database management system.
Check the Bio/DB/GFF/Adaptor directory and subdirectories for
other, more specialized adaptors, as well as experimental ones.
· Aggregators
The GFF format uses a "group" field to indicate aggregation
properties of individual features. For example, a set of exons and
introns may share a common transcript group, and multiple
transcripts may share the same gene group.
Aggregators are small modules that use the group information to
rebuild the hierarchy. When a Bio::DB::GFF object is created, you
indicate that it use a set of one or more aggregators. Each
aggregator provides a new composite annotation type. Before the
database query is generated each aggregator is called to
"disaggregate" its annotation type into list of component types
contained in the database. After the query is generated, each
aggregator is called again in order to build composite annotations
from the returned components.
For example, during disaggregation, the standard
"processed_transcript" aggregator generates a list of component
feature types including "UTR", "CDS", and "polyA_site". Later, it
aggregates these features into a set of annotations of type
"processed_transcript".
During aggregation, the list of aggregators is called in reverse
order. This allows aggregators to collaborate to create multi-
level structures: the transcript aggregator assembles transcripts
from introns and exons; the gene aggregator then assembles genes
from sets of transcripts.
Three default aggregators are provided:
transcript assembles transcripts from features of type
exon, CDS, 5'UTR, 3'UTR, TSS, and PolyA
clone assembles clones from Clone_left_end, Clone_right_end
and Sequence features.
alignment assembles gapped alignments from features of type
"similarity".
In addition, this module provides the optional "wormbase_gene"
aggregator, which accomodates the WormBase representation of genes.
This aggregator aggregates features of method "exon", "CDS",
"5'UTR", "3'UTR", "polyA" and "TSS" into a single object. It also
expects to find a single feature of type "Sequence" that spans the
entire gene.
The existing aggregators are easily customized.
Note that aggregation will not occur unless you specifically
request the aggregation type. For example, this call:
@features = $segment->features('alignment');
will generate an array of aggregated alignment features. However,
this call:
@features = $segment->features();
will return a list of unaggregated similarity segments.
For more informnation, see the manual pages for
Bio::DB::GFF::Aggregator::processed_transcript,
Bio::DB::GFF::Aggregator::clone, etc.
Loading GFF3 Files
This module will accept GFF3 files, as described at
http://song.sourceforge.net/gff3.shtml. However, the implementation has
some limitations.
GFF version string is required
The GFF file must contain the version comment:
##gff-version 3
Unless this version string is present at the top of the GFF file,
the loader will attempt to parse the file in GFF2 format, with
less-than-desirable results.
Only one level of nesting allowed
A major restriction is that Bio::DB::GFF only allows one level of
nesting of features. For nesting, the Target tag will be used
preferentially followed by the ID tag, followed by the Parent tag.
This means that if genes are represented like this:
XXXX XXXX gene XXXX XXXX XXXX ID=myGene
XXXX XXXX mRNA XXXX XXXX XXXX ID=myTranscript;Parent=myGene
XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript
XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript
Then there will be one group called myGene containing the "gene"
feature and one group called myTranscript containing the mRNA, and
two exons.
You can work around this restriction to some extent by using the
Alias attribute literally:
XXXX XXXX gene XXXX XXXX XXXX ID=myGene
XXXX XXXX mRNA XXXX XXXX XXXX ID=myTranscript;Parent=myGene;Alias=myGene
XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript;Alias=myGene
XXXX XXXX exon XXXX XXXX XXXX Parent=myTranscript;Alias=myGene
This limitation will be corrected in the next version of
Bio::DB::GFF.
API
The following is the API for Bio::DB::GFF.
Querying GFF Databases
new
Title : new
Usage : my $db = Bio::DB::GFF->new(@args);
Function: create a new Bio::DB::GFF object
Returns : new Bio::DB::GFF object
Args : lists of adaptors and aggregators
Status : Public
These are the arguments:
-adaptor Name of the adaptor module to use. If none
provided, defaults to "dbi::mysqlopt".
-aggregator Array reference to a list of aggregators
to apply to the database. If none provided,
defaults to ['processed_transcript','alignment'].
-preferred_groups When interpreteting the 9th column of a GFF2 file,
the indicated group names will have preference over
other attributes, even if they do not come first in
the list of attributes. This can be a scalar value
or an array reference.
<other> Any other named argument pairs are passed to
the adaptor for processing.
The adaptor argument must correspond to a module contained within the
Bio::DB::GFF::Adaptor namespace. For example, the
Bio::DB::GFF::Adaptor::dbi::mysql adaptor is loaded by specifying
'dbi::mysql'. By Perl convention, the adaptors names are lower case
because they are loaded at run time.
The aggregator array may contain a list of aggregator names, a list of
initialized aggregator objects, or a string in the form
"aggregator_name{subpart1,subpart2,subpart3/main_method}" (the
"/main_method" part is optional, but if present a feature with the
main_method must be present in order for aggregation to occur). For
example, if you wish to change the components aggregated by the
transcript aggregator, you could pass it to the GFF constructor this
way:
my $transcript =
Bio::DB::Aggregator::transcript->new(-sub_parts=>[qw(exon intron utr
polyA spliced_leader)]);
my $db = Bio::DB::GFF->new(-aggregator=>[$transcript,'clone','alignment],
-adaptor => 'dbi::mysql',
-dsn => 'dbi:mysql:elegans42');
Alternatively, you could create an entirely new transcript aggregator
this way:
my $new_agg = 'transcript{exon,intron,utr,polyA,spliced_leader}';
my $db = Bio::DB::GFF->new(-aggregator=>[$new_agg,'clone','alignment],
-adaptor => 'dbi::mysql',
-dsn => 'dbi:mysql:elegans42');
See Bio::DB::GFF::Aggregator for more details.
The -preferred_groups argument is used to change the default processing
of the 9th column of GFF version 2 files. By default, the first
tag/value pair is used to establish the group class and name. If you
pass -preferred_groups a scalar, the parser will look for a tag of the
indicated type and use it as the group even if it is not first in the
file. If you pass this argument a list of group classes as an array
ref, then the list will establish the precedence for searching.
The commonly used 'dbi::mysql' adaptor recognizes the following
adaptor-specific arguments:
Argument Description
-------- -----------
-dsn the DBI data source, e.g. 'dbi:mysql:ens0040'
If a partial name is given, such as "ens0040", the
"dbi:mysql:" prefix will be added automatically.
-user username for authentication
-pass the password for authentication
-refclass landmark Class; defaults to "Sequence"
The commonly used 'dbi::mysqlopt' adaptor also recogizes the following
arguments.
Argument Description
-------- -----------
-fasta path to a directory containing FASTA files for the DNA
contained in this database (e.g. "/usr/local/share/fasta")
-acedb an acedb URL to use when converting features into ACEDB
objects (e.g. sace://localhost:2005)
types
Title : types
Usage : $db->types(@args)
Function: return list of feature types in range or database
Returns : a list of Bio::DB::GFF::Typename objects
Args : see below
Status : public
This routine returns a list of feature types known to the database.
The list can be database-wide or restricted to a region. It is also
possible to find out how many times each feature occurs.
For range queries, it is usually more convenient to create a
Bio::DB::GFF::Segment object, and then invoke it's types() method.
Arguments are as follows:
-ref ID of reference sequence
-class class of reference sequence
-start start of segment
-stop stop of segment
-enumerate if true, count the features
The returned value will be a list of Bio::DB::GFF::Typename objects,
which if evaluated in a string context will return the feature type in
"method:source" format. This object class also has method() and
source() methods for retrieving the like-named fields.
If -enumerate is true, then the function returns a hash (not a hash
reference) in which the keys are type names in "method:source" format
and the values are the number of times each feature appears in the
database or segment.
The argument -end is a synonum for -stop, and -count is a synonym for
-enumerate.
classes
Title : classes
Usage : $db->classes
Function: return list of landmark classes in database
Returns : a list of classes
Args : none
Status : public
This routine returns the list of reference classes known to the
database, or empty if classes are not used by the database. Classes
are distinct from types, being essentially qualifiers on the reference
namespaces.
segment
Title : segment
Usage : $db->segment(@args);
Function: create a segment object
Returns : segment object(s)
Args : numerous, see below
Status : public
This method generates a segment object, which is a Perl object
subclassed from Bio::DB::GFF::Segment. The segment can be used to find
overlapping features and the raw DNA.
When making the segment() call, you specify the ID of a sequence
landmark (e.g. an accession number, a clone or contig), and a
positional range relative to the landmark. If no range is specified,
then the entire extent of the landmark is used to generate the segment.
You may also provide the ID of a "reference" sequence, which will set
the coordinate system and orientation used for all features contained
within the segment. The reference sequence can be changed later. If
no reference sequence is provided, then the coordinate system is based
on the landmark.
Arguments:
-name ID of the landmark sequence.
-class Database object class for the landmark sequence.
"Sequence" assumed if not specified. This is
irrelevant for databases which do not recognize
object classes.
-start Start of the segment relative to landmark. Positions
follow standard 1-based sequence rules. If not specified,
defaults to the beginning of the landmark.
-end Stop of the segment relative to the landmark. If not specified,
defaults to the end of the landmark.
-stop Same as -end.
-offset For those who prefer 0-based indexing, the offset specifies the
position of the new segment relative to the start of the landmark.
-length For those who prefer 0-based indexing, the length specifies the
length of the new segment.
-refseq Specifies the ID of the reference landmark used to establish the
coordinate system for the newly-created segment.
-refclass Specifies the class of the reference landmark, for those databases
that distinguish different object classes. Defaults to "Sequence".
-absolute
Return features in absolute coordinates rather than relative to the
parent segment.
-nocheck Don't check the database for the coordinates and length of this
feature. Construct a segment using the indicated name as the
reference, a start coordinate of 1, an undefined end coordinate,
and a strand of +1.
-force Same as -nocheck.
-seq,-sequence,-sourceseq Aliases for -name.
-begin,-end Aliases for -start and -stop
-off,-len Aliases for -offset and -length
-seqclass Alias for -class
Here's an example to explain how this works:
my $db = Bio::DB::GFF->new(-dsn => 'dbi:mysql:human',-adaptor=>'dbi::mysql');
If successful, $db will now hold the database accessor object. We now
try to fetch the fragment of sequence whose ID is A0000182 and class is
"Accession."
my $segment = $db->segment(-name=>'A0000182',-class=>'Accession');
If successful, $segment now holds the entire segment corresponding to
this accession number. By default, the sequence is used as its own
reference sequence, so its first base will be 1 and its last base will
be the length of the accession.
Assuming that this sequence belongs to a longer stretch of DNA, say a
contig, we can fetch this information like so:
my $sourceseq = $segment->sourceseq;
and find the start and stop on the source like this:
my $start = $segment->abs_start;
my $stop = $segment->abs_stop;
If we had another segment, say $s2, which is on the same contiguous
piece of DNA, we can pass that to the refseq() method in order to
establish it as the coordinate reference point:
$segment->refseq($s2);
Now calling start() will return the start of the segment relative to
the beginning of $s2, accounting for differences in strandedness:
my $rel_start = $segment->start;
IMPORTANT NOTE: This method can be used to return the segment spanned
by an arbitrary named annotation. However, if the annotation appears
at multiple locations on the genome, for example an EST that maps to
multiple locations, then, provided that all locations reside on the
same physical segment, the method will return a segment that spans the
minimum and maximum positions. If the reference sequence occupies
ranges on different physical segments, then it returns them all in an
array context, and raises a "multiple segment exception" exception in a
scalar context.
features
Title : features
Usage : $db->features(@args)
Function: get all features, possibly filtered by type
Returns : a list of Bio::DB::GFF::Feature objects
Args : see below
Status : public
This routine will retrieve features in the database regardless of
position. It can be used to return all features, or a subset based on
their method and source.
Arguments are as follows:
-types List of feature types to return. Argument is an array
reference containing strings of the format "method:source"
-merge Whether to apply aggregators to the generated features.
-rare Turn on optimizations suitable for a relatively rare feature type,
where it makes more sense to filter by feature type first,
and then by position.
-attributes A hash reference containing attributes to match.
-iterator Whether to return an iterator across the features.
-binsize A true value will create a set of artificial features whose
start and stop positions indicate bins of the given size, and
whose scores are the number of features in the bin. The
class and method of the feature will be set to "bin",
its source to "method:source", and its group to "bin:method:source".
This is a handy way of generating histograms of feature density.
If -iterator is true, then the method returns a single scalar value
consisting of a Bio::SeqIO object. You can call next_seq() repeatedly
on this object to fetch each of the features in turn. If iterator is
false or absent, then all the features are returned as a list.
Currently aggregation is disabled when iterating over a series of
features.
Types are indicated using the nomenclature "method:source". Either of
these fields can be omitted, in which case a wildcard is used for the
missing field. Type names without the colon (e.g. "exon") are
interpreted as the method name and a source wild card. Regular
expressions are allowed in either field, as in: "similarity:BLAST.*".
The -attributes argument is a hashref containing one or more attributes
to match against:
-attributes => { Gene => 'abc-1',
Note => 'confirmed' }
Attribute matching is simple string matching, and multiple attributes
are ANDed together.
get_seq_stream
Title : get_seq_stream
Usage : my $seqio = $self->get_seq_sream(@args)
Function: Performs a query and returns an iterator over it
Returns : a Bio::SeqIO stream capable of producing sequence
Args : As in features()
Status : public
This routine takes the same arguments as features(), but returns a
Bio::SeqIO::Stream-compliant object. Use it like this:
$stream = $db->get_seq_stream('exon');
while (my $exon = $stream->next_seq) {
print $exon,"\n";
}
NOTE: This is also called get_feature_stream(), since that's what it
really does.
get_feature_by_name
Title : get_feature_by_name
Usage : $db->get_feature_by_name($class => $name)
Function: fetch features by their name
Returns : a list of Bio::DB::GFF::Feature objects
Args : the class and name of the desired feature
Status : public
This method can be used to fetch a named feature from the database.
GFF annotations are named using the group class and name fields, so for
features that belong to a group of size one, this method can be used to
retrieve that group (and is equivalent to the segment() method). Any
Alias attributes are also searched for matching names.
An alternative syntax allows you to search for features by name within
a circumscribed region:
@f = $db->get_feature_by_name(-class => $class,-name=>$name,
-ref => $sequence_name,
-start => $start,
-end => $end);
This method may return zero, one, or several Bio::DB::GFF::Feature
objects.
Aggregation is performed on features as usual.
NOTE: At various times, this function was called fetch_group(),
fetch_feature(), fetch_feature_by_name() and segments(). These names
are preserved for backward compatibility.
get_feature_by_target
Title : get_feature_by_target
Usage : $db->get_feature_by_target($class => $name)
Function: fetch features by their similarity target
Returns : a list of Bio::DB::GFF::Feature objects
Args : the class and name of the desired feature
Status : public
This method can be used to fetch a named feature from the database
based on its similarity hit.
get_feature_by_attribute
Title : get_feature_by_attribute
Usage : $db->get_feature_by_attribute(attribute1=>value1,attribute2=>value2)
Function: fetch segments by combinations of attribute values
Returns : a list of Bio::DB::GFF::Feature objects
Args : the class and name of the desired feature
Status : public
This method can be used to fetch a set of features from the database.
Attributes are a list of name=>value pairs. They will be logically
ANDED together.
get_feature_by_id
Title : get_feature_by_id
Usage : $db->get_feature_by_id($id)
Function: fetch segments by feature ID
Returns : a Bio::DB::GFF::Feature object
Args : the feature ID
Status : public
This method can be used to fetch a feature from the database using its
ID. Not all GFF databases support IDs, so be careful with this.
get_feature_by_gid
Title : get_feature_by_gid
Usage : $db->get_feature_by_gid($id)
Function: fetch segments by feature ID
Returns : a Bio::DB::GFF::Feature object
Args : the feature ID
Status : public
This method can be used to fetch a feature from the database using its
group ID. Not all GFF databases support IDs, so be careful with this.
The group ID is often more interesting than the feature ID, since
groups can be complex objects containing subobjects.
delete_fattribute_to_features
Title : delete_fattribute_to_features
Usage : $db->delete_fattribute_to_features(@ids_or_features)
Function: delete one or more fattribute_to_features
Returns : count of fattribute_to_features deleted
Args : list of features or feature ids
Status : public
Pass this method a list of numeric feature ids or a set of features.
It will attempt to remove the fattribute_to_features rows of those
features from the database and return a count of the rows removed.
NOTE: This method is also called delete_fattribute_to_feature(). Also
see delete_groups() and delete_features().
delete_features
Title : delete_features
Usage : $db->delete_features(@ids_or_features)
Function: delete one or more features
Returns : count of features deleted
Args : list of features or feature ids
Status : public
Pass this method a list of numeric feature ids or a set of features.
It will attempt to remove the features from the database and return a
count of the features removed.
NOTE: This method is also called delete_feature(). Also see
delete_groups().
delete_groups
Title : delete_groups
Usage : $db->delete_groups(@ids_or_features)
Function: delete one or more feature groups
Returns : count of features deleted
Args : list of features or feature group ids
Status : public
Pass this method a list of numeric group ids or a set of features. It
will attempt to recursively remove the features and ALL members of
their group from the database. It returns a count of the number of
features (not groups) returned.
NOTE: This method is also called delete_group(). Also see
delete_features().
delete
Title : delete
Usage : $db->delete(@args)
Function: delete features
Returns : count of features deleted -- if available
Args : numerous, see below
Status : public
This method deletes all features that overlap the specified region or
are of a particular type. If no arguments are provided and the -force
argument is true, then deletes ALL features.
Arguments:
-name ID of the landmark sequence.
-ref ID of the landmark sequence (synonym for -name).
-class Database object class for the landmark sequence.
"Sequence" assumed if not specified. This is
irrelevant for databases which do not recognize
object classes.
-start Start of the segment relative to landmark. Positions
follow standard 1-based sequence rules. If not specified,
defaults to the beginning of the landmark.
-end Stop of the segment relative to the landmark. If not specified,
defaults to the end of the landmark.
-offset Zero-based addressing
-length Length of region
-type,-types Either a single scalar type to be deleted, or an
reference to an array of types.
-force Force operation to be performed even if it would delete
entire feature table.
-range_type Control the range type of the deletion. One of "overlaps" (default)
"contains" or "contained_in"
Examples:
$db->delete(-type=>['intron','repeat:repeatMasker']); # remove all introns & repeats
$db->delete(-name=>'chr3',-start=>1,-end=>1000); # remove annotations on chr3 from 1 to 1000
$db->delete(-name=>'chr3',-type=>'exon'); # remove all exons on chr3
The short form of this call, as described in segment() is also allowed:
$db->delete("chr3",1=>1000);
$db->delete("chr3");
IMPORTANT NOTE: This method only deletes features. It does *NOT*
delete the names of groups that contain the deleted features. Group
IDs will be reused if you later load a feature with the same group name
as one that was previously deleted.
NOTE ON FEATURE COUNTS: The DBI-based versions of this call return the
result code from the SQL DELETE operation. Some dbd drivers return the
count of rows deleted, while others return 0E0. Caveat emptor.
absolute
Title : absolute
Usage : $abs = $db->absolute([$abs]);
Function: gets/sets absolute mode
Returns : current setting of absolute mode boolean
Args : new setting for absolute mode boolean
Status : public
$db->absolute(1) will turn on absolute mode for the entire database.
All segments retrieved will use absolute coordinates by default, rather
than relative coordinates. You can still set them to use relative
coordinates by calling $segment->absolute(0).
Note that this is not the same as calling abs_segment(); it continues
to allow you to look up groups that are not used directly as reference
sequences.
strict_bounds_checking
Title : strict_bounds_checking
Usage : $flag = $db->strict_bounds_checking([$flag])
Function: gets/sets strict bounds checking
Returns : current setting of bounds checking flag
Args : new setting for bounds checking flag
Status : public
This flag enables extra checks for segment requests that go beyond the
ends of their reference sequences. If bounds checking is enabled, then
retrieved segments will be truncated to their physical length, and
their truncated() methods will return true.
If the flag is off (the default), then the module will return segments
that appear to extend beyond their physical boundaries. Requests for
features beyond the end of the segment will, however, return empty.
get_Seq_by_id
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
NOTE: Bio::DB::RandomAccessI compliant method
get_Seq_by_accession
Title : get_Seq_by_accession
Usage : $seq = $db->get_Seq_by_accession('AL12234')
Function: Gets a Bio::Seq object by its accession
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
NOTE: Bio::DB::RandomAccessI compliant method
get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
NOTE: Bio::DB::RandomAccessI compliant method
get_Stream_by_name
Title : get_Stream_by_name
Usage : $seq = $db->get_Stream_by_name(@ids);
Function: Retrieves a stream of Seq objects given their names
Returns : a Bio::SeqIO stream object
Args : an array of unique ids/accession numbers, or
an array reference
NOTE: This is also called get_Stream_by_batch()
get_Stream_by_id
Title : get_Stream_by_id
Usage : $seq = $db->get_Stream_by_id(@ids);
Function: Retrieves a stream of Seq objects given their ids
Returns : a Bio::SeqIO stream object
Args : an array of unique ids/accession numbers, or
an array reference
NOTE: This is also called get_Stream_by_batch()
get_Stream_by_batch ()
Title : get_Stream_by_batch
Usage : $seq = $db->get_Stream_by_batch(@ids);
Function: Retrieves a stream of Seq objects given their ids
Returns : a Bio::SeqIO stream object
Args : an array of unique ids/accession numbers, or
an array reference
NOTE: This is the same as get_Stream_by_id().
get_Stream_by_group ()
Bioperl compatibility.
all_seqfeatures
Title : all_seqfeatures
Usage : @features = $db->all_seqfeatures(@args)
Function: fetch all the features in the database
Returns : an array of features, or an iterator
Args : See below
Status : public
This is equivalent to calling $db->features() without any types, and
will return all the features in the database. The -merge and -iterator
arguments are recognized, and behave the same as described for
features().
Creating and Loading GFF Databases
initialize
Title : initialize
Usage : $db->initialize(-erase=>$erase,-option1=>value1,-option2=>value2);
Function: initialize a GFF database
Returns : true if initialization successful
Args : a set of named parameters
Status : Public
This method can be used to initialize an empty database. It takes the
following named arguments:
-erase A boolean value. If true the database will be wiped clean if it
already contains data.
Other named arguments may be recognized by subclasses. They become
database meta values that control various settable options.
As a shortcut (and for backward compatibility) a single true argument
is the same as initialize(-erase=>1).
load_gff
Title : load_gff
Usage : $db->load_gff($file|$directory|$filehandle [,$verbose]);
Function: load GFF data into database
Returns : count of records loaded
Args : a directory, a file, a list of files,
or a filehandle
Status : Public
This method takes a single overloaded argument, which can be any of:
· a scalar corresponding to a GFF file on the system
A pathname to a local GFF file. Any files ending with the .gz, .Z,
or .bz2 suffixes will be transparently decompressed with the
appropriate command-line utility.
· an array reference containing a list of GFF files on the system
For example ['/home/gff/gff1.gz','/home/gff/gff2.gz']
· directory path
The indicated directory will be searched for all files ending in
the suffixes .gff, .gff.gz, .gff.Z or .gff.bz2.
· filehandle
An open filehandle from which to read the GFF data. Tied
filehandles now work as well.
· a pipe expression
A pipe expression will also work. For example, a GFF file on a
remote web server can be loaded with an expression like this:
$db->load_gff("lynx -dump -source http://stein.cshl.org/gff_test |");
The optional second argument, if true, will turn on verbose status
reports that indicate the progress.
If successful, the method will return the number of GFF lines
successfully loaded.
NOTE:this method used to be called load(), but has been changed. The
old method name is also recognized.
load_gff_file
Title : load_gff_file
Usage : $db->load_gff_file($file [,$verbose]);
Function: load GFF data into database
Returns : count of records loaded
Args : a path to a file
Status : Public
This is provided as an alternative to load_gff_file. It doesn't munge
STDIN or play tricks with ARGV.
load_fasta
Title : load_fasta
Usage : $db->load_fasta($file|$directory|$filehandle);
Function: load FASTA data into database
Returns : count of records loaded
Args : a directory, a file, a list of files,
or a filehandle
Status : Public
This method takes a single overloaded argument, which can be any of:
· scalar corresponding to a FASTA file on the system
A pathname to a local FASTA file. Any files ending with the .gz,
.Z, or .bz2 suffixes will be transparently decompressed with the
appropriate command-line utility.
· array reference containing a list of FASTA files on the system
For example
['/home/fasta/genomic.fa.gz','/home/fasta/genomic.fa.gz']
· path to a directory
The indicated directory will be searched for all files ending in
the suffixes .fa, .fa.gz, .fa.Z or .fa.bz2.
· filehandle
An open filehandle from which to read the FASTA data.
· pipe expression
A pipe expression will also work. For example, a FASTA file on a
remote web server can be loaded with an expression like this:
$db->load_gff("lynx -dump -source http://stein.cshl.org/fasta_test.fa |");
load_fasta_file
Title : load_fasta_file
Usage : $db->load_fasta_file($file [,$verbose]);
Function: load FASTA data into database
Returns : count of records loaded
Args : a path to a file
Status : Public
This is provided as an alternative to load_fasta. It doesn't munge
STDIN or play tricks with ARGV.
load_sequence_string
Title : load_sequence_string
Usage : $db->load_sequence_string($id,$dna)
Function: load a single DNA entry
Returns : true if successfully loaded
Args : a raw sequence string (DNA, RNA, protein)
Status : Public
lock_on_load
Title : lock_on_load
Usage : $lock = $db->lock_on_load([$lock])
Function: set write locking during load
Returns : current value of lock-on-load flag
Args : new value of lock-on-load-flag
Status : Public
This method is honored by some of the adaptors. If the value is true,
the tables used by the GFF modules will be locked for writing during
loads and inaccessible to other processes.
meta
Title : meta
Usage : $value = $db->meta($name [,$newval])
Function: get or set a meta variable
Returns : a string
Args : meta variable name and optionally value
Status : abstract
Get or set a named metavalues for the database. Metavalues can be used
for database-specific settings.
By default, this method does nothing!
default_meta_values
Title : default_meta_values
Usage : %values = $db->default_meta_values
Function: empty the database
Returns : a list of tag=>value pairs
Args : none
Status : protected
This method returns a list of tag=>value pairs that contain default
meta information about the database. It is invoked by initialize() to
write out the default meta values. The base class version returns an
empty list.
For things to work properly, meta value names must be UPPERCASE.
error
Title : error
Usage : $db->error( [$new error] );
Function: read or set error message
Returns : error message
Args : an optional argument to set the error message
Status : Public
This method can be used to retrieve the last error message. Errors are
not reset to empty by successful calls, so contents are only valid
immediately after an error condition has been detected.
debug
Title : debug
Usage : $db->debug( [$flag] );
Function: read or set debug flag
Returns : current value of debug flag
Args : new debug flag (optional)
Status : Public
This method can be used to turn on debug messages. The exact nature of
those messages depends on the adaptor in use.
automerge
Title : automerge
Usage : $db->automerge( [$new automerge] );
Function: get or set automerge value
Returns : current value (boolean)
Args : an optional argument to set the automerge value
Status : Public
By default, this module will use the aggregators to merge groups into
single composite objects. This default can be changed to false by
calling automerge(0).
attributes
Title : attributes
Usage : @attributes = $db->attributes($id,$name)
Function: get the "attributes" on a particular feature
Returns : an array of string
Args : feature ID
Status : public
Some GFF version 2 files use the groups column to store a series of
attribute/value pairs. In this interpretation of GFF, the first such
pair is treated as the primary group for the feature; subsequent pairs
are treated as attributes. Two attributes have special meaning: "Note"
is for backward compatibility and is used for unstructured text
remarks. "Alias" is considered as a synonym for the feature name.
If no name is provided, then attributes() returns a flattened hash, of
attribute=>value pairs. This lets you do:
%attributes = $db->attributes($id);
If no arguments are provided, attributes() will return the list of all
attribute names:
@attribute_names = $db->attributes();
Normally, however, attributes() will be called by the feature:
@notes = $feature->attributes('Note');
In a scalar context, attributes() returns the first value of the
attribute if a tag is present, otherwise a hash reference in which the
keys are attribute names and the values are anonymous arrays containing
the values.
fast_queries
Title : fast_queries
Usage : $flag = $db->fast_queries([$flag])
Function: turn on and off the "fast queries" option
Returns : a boolean
Args : a boolean flag (optional)
Status : public
The mysql database driver (and possibly others) support a "fast" query
mode that caches results on the server side. This makes queries come
back faster, particularly when creating iterators. The downside is
that while iterating, new queries will die with a "command synch"
error. This method turns the feature on and off.
For databases that do not support a fast query, this method has no
effect.
add_aggregator
Title : add_aggregator
Usage : $db->add_aggregator($aggregator)
Function: add an aggregator to the list
Returns : nothing
Args : an aggregator
Status : public
This method will append an aggregator to the end of the list of
registered aggregators. Three different argument types are accepted:
1) a Bio::DB::GFF::Aggregator object -- will be added
2) a string in the form "aggregator_name{subpart1,subpart2,subpart3/main_method}"
-- will be turned into a Bio::DB::GFF::Aggregator object (the /main_method
part is optional).
3) a valid Perl token -- will be turned into a Bio::DB::GFF::Aggregator
subclass, where the token corresponds to the subclass name.
aggregators
Title : aggregators
Usage : $db->aggregators([@new_aggregators]);
Function: retrieve list of aggregators
Returns : list of aggregators
Args : a list of aggregators to set (optional)
Status : public
This method will get or set the list of aggregators assigned to the
database. If 1 or more arguments are passed, the existing set will be
cleared.
clear_aggregators
Title : clear_aggregators
Usage : $db->clear_aggregators
Function: clears list of aggregators
Returns : nothing
Args : none
Status : public
This method will clear the aggregators stored in the database object.
Use aggregators() or add_aggregator() to add some back.
preferred_groups
Title : preferred_groups
Usage : $db->preferred_groups([$group_name_or_arrayref])
Function: get/set list of groups for altering GFF2 parsing
Returns : a list of classes
Args : new list (scalar or array ref)
Status : public
Methods for use by Subclasses
The following methods are chiefly of interest to subclasses and are not
intended for use by end programmers.
abscoords
Title : abscoords
Usage : $db->abscoords($name,$class,$refseq)
Function: finds position of a landmark in reference coordinates
Returns : ($ref,$class,$start,$stop,$strand)
Args : name and class of landmark
Status : public
This method is called by Bio::DB::GFF::RelSegment to obtain the
absolute coordinates of a sequence landmark. The arguments are the
name and class of the landmark. If successful, abscoords() returns the
ID of the reference sequence, its class, its start and stop positions,
and the orientation of the reference sequence's coordinate system ("+"
for forward strand, "-" for reverse strand).
If $refseq is present in the argument list, it forces the query to
search for the landmark in a particular reference sequence.
Protected API
The following methods are not intended for public consumption, but are
intended to be overridden/implemented by adaptors.
default_aggregators
Title : default_aggregators
Usage : $db->default_aggregators;
Function: retrieve list of aggregators
Returns : array reference containing list of aggregator names
Args : none
Status : protected
This method (which is intended to be overridden by adaptors) returns a
list of standard aggregators to be applied when no aggregators are
specified in the constructor.
do_load_gff
Title : do_load_gff
Usage : $db->do_load_gff($handle)
Function: load a GFF input stream
Returns : number of features loaded
Args : A filehandle.
Status : protected
This method is called to load a GFF data stream. The method will read
GFF features from <> and load them into the database. On exit the
method must return the number of features loaded.
Note that the method is responsible for parsing the GFF lines. This is
to allow for differences in the interpretation of the "group" field,
which are legion.
You probably want to use load_gff() instead. It is more flexible about
the arguments it accepts.
load_sequence
Title : load_sequence
Usage : $db->load_sequence($handle)
Function: load a FASTA data stream
Returns : number of sequences
Args : a filehandle to the FASTA file
Status : protected
You probably want to use load_fasta() instead.
setup_load
Title : setup_load
Usage : $db->setup_load
Function: called before load_gff_line()
Returns : void
Args : none
Status : abstract
This abstract method gives subclasses a chance to do any schema-
specific initialization prior to loading a set of GFF records. It must
be implemented by a subclass.
finish_load
Title : finish_load
Usage : $db->finish_load
Function: called after load_gff_line()
Returns : number of records loaded
Args : none
Status :abstract
This method gives subclasses a chance to do any schema-specific cleanup
after loading a set of GFF records.
load_gff_line
Title : load_gff_line
Usage : $db->load_gff_line(@args)
Function: called to load one parsed line of GFF
Returns : true if successfully inserted
Args : see below
Status : abstract
This abstract method is called once per line of the GFF and passed a
hashref containing parsed GFF fields. The fields are:
{ref => $ref,
class => $class,
source => $source,
method => $method,
start => $start,
stop => $stop,
score => $score,
strand => $strand,
phase => $phase,
gclass => $gclass,
gname => $gname,
tstart => $tstart,
tstop => $tstop,
attributes => $attributes}
do_initialize
Title : do_initialize
Usage : $db->do_initialize([$erase])
Function: initialize and possibly erase database
Returns : true if successful
Args : optional erase flag
Status : protected
This method implements the initialize() method described above, and
takes the same arguments.
dna
Title : dna
Usage : $db->dna($id,$start,$stop,$class)
Function: return the raw DNA string for a segment
Returns : a raw DNA string
Args : id of the sequence, its class, start and stop positions
Status : public
This method is invoked by Bio::DB::GFF::Segment to fetch the raw DNA
sequence.
Arguments: -name sequence name
-start start position
-stop stop position
-class sequence class
If start and stop are both undef, then the entire DNA is retrieved. So
to fetch the whole dna, call like this:
$db->dna($name_of_sequence);
or like this:
$db->dna(-name=>$name_of_sequence,-class=>$class_of_sequence);
NOTE: you will probably prefer to create a Segment and then invoke its
dna() method.
get_dna
Title : get_dna
Usage : $db->get_dna($id,$start,$stop,$class)
Function: get DNA for indicated segment
Returns : the dna string
Args : sequence ID, start, stop and class
Status : protected
If start > stop and the sequence is nucleotide, then this method should
return the reverse complement. The sequence class may be ignored by
those databases that do not recognize different object types.
get_features
Title : get_features
Usage : $db->get_features($search,$options,$callback)
Function: get list of features for a region
Returns : count of number of features retrieved
Args : see below
Status : protected
The first argument is a hash reference containing search criteria for
retrieving features. It contains the following keys:
rangetype One of "overlaps", "contains" or "contained_in". Indicates
the type of range query requested.
refseq ID of the landmark that establishes the absolute
coordinate system.
refclass Class of this landmark. Can be ignored by implementations
that don't recognize such distinctions.
start Start of the range, inclusive.
stop Stop of the range, inclusive.
types Array reference containing the list of annotation types
to fetch from the database. Each annotation type is an
array reference consisting of [source,method].
The second argument is a hash reference containing certain options that
affect the way information is retrieved:
sort_by_group
A flag. If true, means that the returned features should be
sorted by the group that they're in.
sparse A flag. If true, means that the expected density of the
features is such that it will be more efficient to search
by type rather than by range. If it is taking a long
time to fetch features, give this a try.
binsize A true value will create a set of artificial features whose
start and stop positions indicate bins of the given size, and
whose scores are the number of features in the bin. The
class of the feature will be set to "bin", and its name to
"method:source". This is a handy way of generating histograms
of feature density.
The third argument, the $callback, is a code reference to which
retrieved features are passed. It is described in more detail below.
This routine is responsible for getting arrays of GFF data out of the
database and passing them to the callback subroutine. The callback
does the work of constructing a Bio::DB::GFF::Feature object out of
that data. The callback expects a list of 13 fields:
$refseq The reference sequence
$start feature start
$stop feature stop
$source feature source
$method feature method
$score feature score
$strand feature strand
$phase feature phase
$groupclass group class (may be undef)
$groupname group ID (may be undef)
$tstart target start for similarity hits (may be undef)
$tstop target stop for similarity hits (may be undef)
$feature_id A unique feature ID (may be undef)
These fields are in the same order as the raw GFF file, with the
exception that the group column has been parsed into group class and
group name fields.
The feature ID, if provided, is a unique identifier of the feature
line. The module does not depend on this ID in any way, but it is
available via Bio::DB::GFF->id() if wanted. In the dbi::mysql and
dbi::mysqlopt adaptor, the ID is a unique row ID. In the acedb adaptor
it is not used.
_feature_by_name
Title : _feature_by_name
Usage : $db->_feature_by_name($class,$name,$location,$callback)
Function: get a list of features by name and class
Returns : count of number of features retrieved
Args : name of feature, class of feature, and a callback
Status : abstract
This method is used internally. The callback arguments are the same as
those used by make_feature(). This method must be overidden by
subclasses.
_feature_by_id
Title : _feature_by_id
Usage : $db->_feature_by_id($ids,$type,$callback)
Function: get a feature based
Returns : count of number of features retrieved
Args : arrayref to feature IDs to fetch
Status : abstract
This method is used internally to fetch features either by their ID or
their group ID. $ids is a arrayref containing a list of IDs, $type is
one of "feature" or "group", and $callback is a callback. The callback
arguments are the same as those used by make_feature(). This method
must be overidden by subclasses.
overlapping_features
Title : overlapping_features
Usage : $db->overlapping_features(@args)
Function: get features that overlap the indicated range
Returns : a list of Bio::DB::GFF::Feature objects
Args : see below
Status : public
This method is invoked by Bio::DB::GFF::Segment->features() to find the
list of features that overlap a given range. It is generally
preferable to create the Segment first, and then fetch the features.
This method takes set of named arguments:
-refseq ID of the reference sequence
-class Class of the reference sequence
-start Start of the desired range in refseq coordinates
-stop Stop of the desired range in refseq coordinates
-types List of feature types to return. Argument is an array
reference containing strings of the format "method:source"
-parent A parent Bio::DB::GFF::Segment object, used to create
relative coordinates in the generated features.
-rare Turn on an optimization suitable for a relatively rare feature type,
where it will be faster to filter by feature type first
and then by position, rather than vice versa.
-merge Whether to apply aggregators to the generated features.
-iterator Whether to return an iterator across the features.
If -iterator is true, then the method returns a single scalar value
consisting of a Bio::SeqIO object. You can call next_seq() repeatedly
on this object to fetch each of the features in turn. If iterator is
false or absent, then all the features are returned as a list.
Currently aggregation is disabled when iterating over a series of
features.
Types are indicated using the nomenclature "method:source". Either of
these fields can be omitted, in which case a wildcard is used for the
missing field. Type names without the colon (e.g. "exon") are
interpreted as the method name and a source wild card. Regular
expressions are allowed in either field, as in: "similarity:BLAST.*".
contained_features
Title : contained_features
Usage : $db->contained_features(@args)
Function: get features that are contained within the indicated range
Returns : a list of Bio::DB::GFF::Feature objects
Args : see overlapping_features()
Status : public
This call is similar to overlapping_features(), except that it only
retrieves features whose end points are completely contained within the
specified range.
Generally you will want to fetch a Bio::DB::GFF::Segment object and
call its contained_features() method rather than call this directly.
contained_in
Title : contained_in
Usage : @features = $s->contained_in(@args)
Function: get features that contain this segment
Returns : a list of Bio::DB::GFF::Feature objects
Args : see features()
Status : Public
This is identical in behavior to features() except that it returns only
those features that completely contain the segment.
get_abscoords
Title : get_abscoords
Usage : $db->get_abscoords($name,$class,$refseq)
Function: get the absolute coordinates of sequence with name & class
Returns : ($absref,$absstart,$absstop,$absstrand)
Args : name and class of the landmark
Status : protected
Given the name and class of a genomic landmark, this function returns a
four-element array consisting of:
$absref the ID of the reference sequence that contains this landmark
$absstart the position at which the landmark starts
$absstop the position at which the landmark stops
$absstrand the strand of the landmark, relative to the reference sequence
If $refseq is provided, the function searches only within the specified
reference sequence.
get_types
Title : get_types
Usage : $db->get_types($absref,$class,$start,$stop,$count)
Function: get list of all feature types on the indicated segment
Returns : list or hash of Bio::DB::GFF::Typename objects
Args : see below
Status : protected
Arguments are:
$absref the ID of the reference sequence
$class the class of the reference sequence
$start the position to start counting
$stop the position to end counting
$count a boolean indicating whether to count the number
of occurrences of each feature type
If $count is true, then a hash is returned. The keys of the hash are
feature type names in the format "method:source" and the values are the
number of times a feature of this type overlaps the indicated segment.
Otherwise, the call returns a set of Bio::DB::GFF::Typename objects.
If $start or $stop are undef, then all features on the indicated
segment are enumerated. If $absref is undef, then the call returns all
feature types in the database.
make_feature
Title : make_feature
Usage : $db->make_feature(@args)
Function: Create a Bio::DB::GFF::Feature object from string data
Returns : a Bio::DB::GFF::Feature object
Args : see below
Status : internal
This takes 14 arguments (really!):
$parent A Bio::DB::GFF::RelSegment object
$group_hash A hashref containing unique list of GFF groups
$refname The name of the reference sequence for this feature
$refclass The class of the reference sequence for this feature
$start Start of feature
$stop Stop of feature
$source Feature source field
$method Feature method field
$score Feature score field
$strand Feature strand
$phase Feature phase
$group_class Class of feature group
$group_name Name of feature group
$tstart For homologies, start of hit on target
$tstop Stop of hit on target
The $parent argument, if present, is used to establish relative
coordinates in the resulting Bio::DB::Feature object. This allows one
feature to generate a list of other features that are relative to its
coordinate system (for example, finding the coordinates of the second
exon relative to the coordinates of the first).
The $group_hash allows the group_class/group_name strings to be turned
into rich database objects via the make_obect() method (see above).
Because these objects may be expensive to create, $group_hash is used
to uniquefy them. The index of this hash is the composite key
{$group_class,$group_name,$tstart,$tstop}. Values are whatever object
is returned by the make_object() method.
The remainder of the fields are taken from the GFF line, with the
exception that "Target" features, which contain information about the
target of a homology search, are parsed into their components.
make_match_sub
Title : make_match_sub
Usage : $db->make_match_sub($types)
Function: creates a subroutine used for filtering features
Returns : a code reference
Args : a list of parsed type names
Status : protected
This method is used internally to generate a code subroutine that will
accept or reject a feature based on its method and source. It takes an
array of parsed type names in the format returned by parse_types(), and
generates an anonymous subroutine. The subroutine takes a single
Bio::DB::GFF::Feature object and returns true if the feature matches
one of the desired feature types, and false otherwise.
make_object
Title : make_object
Usage : $db->make_object($class,$name,$start,$stop)
Function: creates a feature object
Returns : a feature object
Args : see below
Status : protected
This method is called to make an object from the GFF "group" field. By
default, all Target groups are turned into Bio::DB::GFF::Homol objects,
and everything else becomes a Bio::DB::GFF::Featname. However,
adaptors are free to override this method to generate more interesting
objects, such as true BioPerl objects, or Acedb objects.
Arguments are:
$name database ID for object
$class class of object
$start for similarities, start of match inside object
$stop for similarities, stop of match inside object
do_attributes
Title : do_attributes
Usage : $db->do_attributes($id [,$tag]);
Function: internal method to retrieve attributes given an id and tag
Returns : a list of Bio::DB::GFF::Feature objects
Args : a feature id and a attribute tag (optional)
Status : protected
This method is overridden by subclasses in order to return a list of
attributes. If called with a tag, returns the value of attributes of
that tag type. If called without a tag, returns a flattened array of
(tag=>value) pairs. A particular tag can be present multiple times.
clone
The clone() method should be used when you want to pass the
Bio::DB::GFF object to a child process across a fork(). The child must
call clone() before making any queries.
The default behavior is to do nothing, but adaptors that use the DBI
interface may need to implement this in order to avoid database handle
errors. See the dbi adaptor for an example.
Internal Methods
The following methods are internal to Bio::DB::GFF and are not
guaranteed to remain the same.
_features
Title : _features
Usage : $db->_features($search,$options,$parent)
Function: internal method
Returns : a list of Bio::DB::GFF::Feature objects
Args : see below
Status : internal
This is an internal method that is called by overlapping_features(),
contained_features() and features() to create features based on a
parent segment's coordinate system. It takes three arguments, a search
options hashref, an options hashref, and a parent segment.
The search hashref contains the following keys:
rangetype One of "overlaps", "contains" or "contained_in". Indicates
the type of range query requested.
refseq reference sequence ID
refclass reference sequence class
start start of range
stop stop of range
types arrayref containing list of types in "method:source" form
The options hashref contains zero or more of the following keys:
sparse turn on optimizations for a rare feature
automerge if true, invoke aggregators to merge features
iterator if true, return an iterator
The $parent argument is a scalar object containing a
Bio::DB::GFF::RelSegment object or descendent.
get_features_iterator
Title : get_features_iterator
Usage : $db->get_features_iterator($search,$options,$callback)
Function: get an iterator on a features query
Returns : a Bio::SeqIO object
Args : as per get_features()
Status : Public
This method takes the same arguments as get_features(), but returns an
iterator that can be used to fetch features sequentially, as per
Bio::SeqIO.
Internally, this method is simply a front end to range_query(). The
latter method constructs and executes the query, returning a statement
handle. This routine passes the statement handle to the constructor for
the iterator, along with the callback.
split_group
Title : split_group
Usage : $db->split_group($group_field,$gff3_flag)
Function: parse GFF group field
Returns : ($gclass,$gname,$tstart,$tstop,$attributes)
Args : the gff group column and a flag indicating gff3 compatibility
Status : internal
This is a method that is called by load_gff_line to parse out the
contents of one or more group fields. It returns the class of the
group, its name, the start and stop of the target, if any, and an array
reference containing any attributes that were stuck into the group
field, in [attribute_name,attribute_value] format.
_split_gff2_group
This is an internal method called by split_group().
gff3_name_munging
Title : gff3_name_munging
Usage : $db->gff3_name_munging($boolean)
Function: get/set gff3_name_munging flag
Returns : $current value of flag
Args : new value of flag (optional)
Status : utility
If this is set to true (default false), then features identified in
gff3 files with an ID in the format foo:bar will be parsed so that
"foo" is the class and "bar" is the name. This is mostly for backward
compatibility with GFF2.
_split_gff3_group
This is called internally from split_group().
_delete_features(),
_delete_groups(),_delete(),_delete_fattribute_to_features()
Title : _delete_features(), _delete_groups(),_delete(),_delete_fattribute_to_features()
Usage : $count = $db->_delete_features(@feature_ids)
$count = $db->_delete_groups(@group_ids)
$count = $db->_delete(\%delete_spec)
$count = $db->_delete_fattribute_to_features(@feature_ids)
Function: low-level feature/group deleter
Returns : count of groups removed
Args : list of feature or group ids removed
Status : for implementation by subclasses
These methods need to be implemented in adaptors. For
_delete_features, _delete_groups and _delete_fattribute_to_features,
the arguments are a list of feature or group IDs to remove. For
_delete(), the argument is a hashref with the three keys 'segments',
'types' and 'force'. The first contains an arrayref of
Bio::DB::GFF::RelSegment objects to delete (all FEATURES within the
segment are deleted). The second contains an arrayref of
[method,source] feature types to delete. The two are ANDed together.
If 'force' has a true value, this forces the operation to continue even
if it would delete all features.
BUGS
Features can only belong to a single group at a time. This must be
addressed soon.
Start coordinate can be greater than stop coordinate for relative
addressing. This breaks strict BioPerl compatibility and must be
fixed.
SEE ALSO
Bio::DB::GFF::RelSegment, Bio::DB::GFF::Aggregator,
Bio::DB::GFF::Feature, Bio::DB::GFF::Adaptor::dbi::mysqlopt,
Bio::DB::GFF::Adaptor::dbi::oracle, Bio::DB::GFF::Adaptor::memory
Bio::DB::GFF::Adaptor::berkeleydb
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
perl v5.14.1 2011-07-22 Bio::DB::GFF(3)
