Bio::DB::Das::BioSQL::Segment - DAS-style access to a BioSQL database
# Get a Bio::Das::SegmentI object from a Bio::DB::Das::BioSQL database... #Should be created through Bio::DB::Das::BioSQL. @features = $segment->overlapping_features(-type=>['type1','type2']); # each feature is a Bio::SeqFeatureI-compliant object @features = $segment->contained_features(-type=>['type1','type2']); @features = $segment->contained_in(-type=>['type1','type2']); $stream = $segment->get_feature_stream(-type=>['type1','type2','type3']; while (my $feature = $stream->next_seq) { # do something with feature }
Bio::DB::Das::BioSQL::Segment is a simplified alternative interface to sequence annotation databases used by the distributed annotation system. In this scheme, the genome is represented as a series of landmarks. Each Bio::DB::Das::BioSQL::Segment object ("segment") corresponds to a genomic region defined by a landmark and a start and end position relative to that landmark. A segment is created using the Bio::DB::Das::BioSQL segment() method.
The segment will load its features only when the features() method is called. If start and end are not specified and features are requested, all the features for the current segment will be retrieved, which may be slow.
Segment can be created as relative or absolute. If it's absolute ,all locations are given beginning from segment's start, that is, they are between [1 .. (end-start)]. Otherwise, they are given relative to the true start of the segment, irregardless of the start value.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : seq_id Usage : $ref = $s->seq_id Function: return the ID of the landmark Returns : a string Args : none Status : Public
Title : start Usage : $s->start Function: start of segment Returns : integer Args : none Status : Public
This is a read-only accessor for the start of the segment.
Title : end Usage : $s->end Function: end of segment Returns : integer Args : none Status : Public
This is a read-only accessor for the end of the segment.
Title : abs_start Usage : $s->abs_start Function: start of segment Returns : integer Args : none Status : Public
Return the absolute start of the segment
Title : abs_end Usage : $s->abs_end Function: end of segment Returns : integer Args : none Status : Public
Return the absolute end of the segment
Title : length Usage : $s->length Function: length of segment Returns : integer Args : none Status : Public
Returns the length of the segment. Always a positive number.
Title : absolute Usage : $s->absolute Function: whether the positions are counted from the true start of the segment or from the start value Returns : boolean Args : none Status : Public
This is a read-only accessor.
Title : features Usage : @features = $s->features(@args) Function: get features that overlap this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public
This method will find all features that intersect the segment in a variety of ways and return a list of Bio::SeqFeatureI objects. The feature locations will use coordinates relative to the reference sequence in effect at the time that features() was called.
The returned list can be limited to certain types, attributes or range intersection modes. Types of range intersection are one of:
"overlaps" the default "contains" return features completely contained within the segment "contained_in" return features that completely contain the segment
Two types of argument lists are accepted. In the positional argument form, the arguments are treated as a list of feature types. In the named parameter form, the arguments are a series of -name=>value pairs.
Argument Description -------- ------------ -types An array reference to type names in the format "method:source" -attributes A hashref containing a set of attributes to match -rangetype One of "overlaps", "contains", or "contained_in". -iterator Return an iterator across the features. -callback A callback to invoke on each feature
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. More complex filtering can be performed using the -callback option (see below).
If -iterator is true, then the method returns an object reference that implements the next_seq() method. Each call to next_seq() returns a new Bio::SeqFeatureI object.
If -callback is passed a code reference, the code reference will be invoked on each feature returned. The code will be passed two arguments consisting of the current feature and the segment object itself, and must return a true value. If the code returns a false value, feature retrieval will be aborted.
-callback and -iterator are mutually exclusive options. If -iterator is defined, then -callback is ignored.
NOTE: In his implementation, -attributes does exactly nothing, and features() is wildly inefficient because it works by calling top_SeqFeatures and then filters by position in the Perl layer, rather than filtering by position in the SQL layer.
Title : top_SeqFeatures Usage : $s->top_SeqFeatures Function: retrieve an array of features from the underlying BioDB object. Returns : an array Args : none Status : Private
First, make the adaptor retrieve the feature objects from the database. Then, get the actual objects and adjust the features' locations if necessary.
Title : get_seq_stream Usage : my $seqio = $self->get_seq_stream(@args) Function: Performs a query and returns an iterator over it Returns : a Bio::SeqIO stream capable of returning Bio::Das::SegmentI 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.
Title : seq Usage : $s->seq Function: get the sequence string for this segment Returns : a string Args : none Status : Public
Returns the sequence for this segment as a Bio::PrimarySeq object.
Title : factory Usage : $factory = $s->factory Function: return the segment factory Returns : a Bio::DasI object Args : see below Status : Public
This method returns a Bio::DasI object that can be used to fetch more segments. This is typically the Bio::DasI object from which the segment was originally generated.
Title : bioseq Usage : $bioseq = $s->bioseq Function: return the underlying Bio::Seq object Returns : a Bio::Seq object Args : none Status : Public
Title : asString Usage : $s->asString Function: human-readable representation of the segment Returns : a string Args : none Status : Public
This method will return a human-readable representation of the segment. It is the overloaded method call for the "" operator.
Currently the format is:
refseq:start,stop
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