Provided by: libbio-perl-perl_1.7.2-2_all 
NAME
Bio::DasI - DAS-style access to a feature database
SYNOPSIS
# Open up a feature database somehow...
$db = Bio::DasI->new(@args);
@segments = $db->segment(-name => 'NT_29921.4',
-start => 1,
-end => 1000000);
# segments are Bio::Das::SegmentI - compliant objects
# fetch a list of features
@features = $db->features(-type=>['type1','type2','type3']);
# invoke a callback over features
$db->features(-type=>['type1','type2','type3'],
-callback => sub { ... }
);
$stream = $db->get_seq_stream(-type=>['type1','type2','type3']);
while (my $feature = $stream->next_seq) {
# each feature is a Bio::SeqFeatureI-compliant object
}
# get all feature types
@types = $db->types;
# count types
%types = $db->types(-enumerate=>1);
@feature = $db->get_feature_by_name($class=>$name);
@feature = $db->get_feature_by_target($target_name);
@feature = $db->get_feature_by_attribute($att1=>$value1,$att2=>$value2);
$feature = $db->get_feature_by_id($id);
$error = $db->error;
DESCRIPTION
Bio::DasI is a simplified alternative interface to sequence annotation databases used by
the distributed annotation system (see Bio::Das). In this scheme, the genome is
represented as a series of features, a subset of which are named. Named features can be
used as reference points for retrieving "segments" (see Bio::Das::SegmentI), and these
can, in turn, be used as the basis for exploring the genome further.
In addition to a name, each feature has a "class", which is essentially a namespace
qualifier and a "type", which describes what type of feature it is. Das uses the GO
consortium's ontology of feature types, and so the type is actually an object of class
Bio::Das::FeatureTypeI (see Bio::Das::FeatureTypeI). Bio::DasI provides methods for
interrogating the database for the types it contains and the counts of each type.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one of the Bioperl mailing lists. Your
participation is much appreciated.
bioperl-l@bioperl.org
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will
be able look at the problem and quickly address it. Please include a thorough description
of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Lincoln Stein
Email lstein@cshl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are
usually preceded with a _
new
Title : new
Usage : Bio::DasI->new(@args)
Function: Create new Bio::DasI object
Returns : a Bio::DasI object
Args : see below
The new() method creates a new object. The argument list is either a single argument
consisting of a connection string, or the following list of -name=>value arguments:
Argument Description
-------- -----------
-dsn Connection string for database
-adaptor Name of an adaptor class to use when connecting
-aggregator Array ref containing list of aggregators
"semantic mappers" to apply to database
-user Authentication username
-pass Authentication password
Implementors of DasI may add other arguments.
types
Title : types
Usage : $db->types(@args)
Function: return list of feature types in database
Returns : a list of Bio::Das::FeatureTypeI objects
Args : see below
This routine returns a list of feature types known to the database. It is also possible to
find out how many times each feature occurs.
Arguments are -option=>value pairs as follows:
-enumerate if true, count the features
The returned value will be a list of Bio::Das::FeatureTypeI objects (see
Bio::Das::FeatureTypeI.
If -enumerate is true, then the function returns a hash (not a hash reference) in which
the keys are the stringified versions of Bio::Das::FeatureTypeI and the values are the
number of times each feature appears in the database.
parse_types
Title : parse_types
Usage : $db->parse_types(@args)
Function: parses list of types
Returns : an array ref containing ['method','source'] pairs
Args : a list of types in 'method:source' form
Status : internal
This method takes an array of type names in the format "method:source" and returns an
array reference of ['method','source'] pairs. It will also accept a single argument
consisting of an array reference with the list of type names.
segment
Title : segment
Usage : $db->segment(@args);
Function: create a segment object
Returns : segment object(s)
Args : see below
This method generates a Bio::Das::SegmentI object (see Bio::Das::SegmentI). The segment
can be used to find overlapping features and the raw sequence.
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 region spanned by the landmark is used to generate
the segment.
Arguments are -option=>value pairs as follows:
-name ID of the landmark sequence.
-class A namespace qualifier. It is not necessary for the
database to honor namespace qualifiers, but if it
does, this is where the qualifier is indicated.
-version Version number of the landmark. It is not necessary for
the database to honor versions, but if it does, this is
where the version is indicated.
-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 End of the segment relative to the landmark. If not specified,
defaults to the end of the landmark.
The return value is a list of Bio::Das::SegmentI objects. If the method is called in a
scalar context and there are no more than one segments that satisfy the request, then it
is allowed to return the segment. Otherwise, the method must throw a "multiple segment
exception".
features
Title : features
Usage : $db->features(@args)
Function: get all features, possibly filtered by type
Returns : a list of Bio::SeqFeatureI 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 type
Arguments are -option=>value pairs as follows:
-types List of feature types to return. Argument is an array
of Bio::Das::FeatureTypeI objects or a set of strings
that can be converted into FeatureTypeI objects.
-callback A callback to invoke on each feature. The subroutine
will be passed each Bio::SeqFeatureI object in turn.
-attributes A hash reference containing attributes to match.
The -attributes argument is a hashref containing one or more attributes to match against:
-attributes => { Gene => 'abc-1',
Note => 'confirmed' }
Attribute matching is simple exact string matching, and multiple attributes are ANDed
together. See Bio::DB::ConstraintsI for a more sophisticated take on this.
If one provides a callback, it will be invoked on each feature in turn. If the callback
returns a false value, iteration will be interrupted. When a callback is provided, the
method returns undef.
get_feature_by_name
Title : get_feature_by_name
Usage : $db->get_feature_by_name(-class=>$class,-name=>$name)
Function: fetch features by their name
Returns : a list of Bio::SeqFeatureI objects
Args : the class and name of the desired feature
Status : public
This method can be used to fetch named feature(s) from the database. The -class and -name
arguments have the same meaning as in segment(), and the method also accepts the following
short-cut forms:
1) one argument: the argument is treated as the feature name
2) two arguments: the arguments are treated as the class and name
(note: this uses _rearrange() so the first argument must not
begin with a hyphen or it will be interpreted as a named
argument).
This method may return zero, one, or several Bio::SeqFeatureI objects. The implementor
may allow the name to contain wildcards, in which case standard C-shell glob semantics are
expected.
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::SeqFeatureI 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. The arguments are the same as get_feature_by_name(). If this is not implemented,
the interface defaults to using get_feature_by_name().
get_feature_by_id
Title : get_feature_by_id
Usage : $db->get_feature_by_target($id)
Function: fetch a feature by its ID
Returns : a Bio::SeqFeatureI objects
Args : the ID of the feature
Status : public
If the database provides unique feature IDs, this can be used to retrieve a single feature
from the database. If not overridden, this interface calls get_feature_by_name() and
returns the first element.
get_feature_by_attribute
Title : get_feature_by_attribute
Usage : $db->get_feature_by_attribute(attribute1=>value1,attribute2=>value2)
Function: fetch features by combinations of attribute values
Returns : a list of Bio::SeqFeatureI 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. If an attribute value
is an array reference, the list of values in the array is treated as an alternative set of
values to be ORed together.
search_notes
Title : search_notes
Usage : $db->search_notes($search_term,$max_results)
Function: full-text search on features, ENSEMBL-style
Returns : an array of [$name,$description,$score]
Args : see below
Status : public
This routine performs a full-text search on feature attributes (which attributes depend on
implementation) and returns a list of [$name,$description,$score], where $name is the
feature ID, $description is a human-readable description such as a locus line, and $score
is the match strength.
Since this is a decidedly non-standard thing to do (but the generic genome browser uses
it), the default method returns an empty list. You do not have to implement it.
get_seq_stream
Title : get_seq_stream
Usage : $seqio = $db->get_seq_stream(@args)
Function: Performs a query and returns an iterator over it
Returns : a Bio::SeqIO stream capable of returning Bio::SeqFeatureI objects
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: In the interface this method is aliased to get_feature_stream(), as the name is more
descriptive.
refclass
Title : refclass
Usage : $class = $db->refclass
Function: returns the default class to use for segment() calls
Returns : a string
Args : none
Status : public
For data sources which use namespaces to distinguish reference sequence accessions, this
returns the default namespace (or "class") to use. This interface defines a default of
"Accession".