SYNOPSIS
# Get a Bio::Das::SegmentI object from a Bio::DasI database...
$segment = $das->segment(-name=>'Landmark',
-start=>$start,
-end => $end);
@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
}
$count = $segment->features_callback(-type=>['type1','type2','type3'],
-callback => sub { ... { }
);
DESCRIPTION
Bio::Das::SegmentI 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::Das::SegmentI 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::DasI segment() method.Features can be filtered by the following attributes:
1) their location relative to the segment (whether overlapping,
contained within, or completely containing)
2) their type
3) other attributes using tag/value semantics
Access to the feature list uses three distinct APIs:
1) fetching entire list of features at a time 2) fetching an iterator across features 3) a callback
FEEDBACK
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Support
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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 [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _seq_id
Title : seq_id Usage : $ref = $s->seq_id Function: return the ID of the landmark Returns : a string Args : none Status : Public
display_name
Title : seq_name Usage : $ref = $s->seq_name Function: return the human-readable name for the landmark Returns : a string Args : none Status : Public
This defaults to the same as seq_id.
start
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. Alias to low() for Gadfly compatibility.
end
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. Alias to high() for Gadfly compatibility.
length
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.
seq
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 simple string.
ref
Title : ref Usage : $ref = $s->ref([$newlandmark]) Function: get/set the reference landmark for addressing Returns : a string Args : none Status : Public
This method is used to examine/change the reference landmark used to establish the coordinate system. By default, the landmark cannot be changed and therefore this has the same effect as seq_id(). The new landmark might be an ID, or another Das::SegmentI object.
absolute
Title : absolute Usage : $s->absolute([$new_value]) Function: get/set absolute addressing mode Returns : flag Args : new flag (optional) Status : Public
Turn on and off absolute-addressing mode. In absolute addressing mode, coordinates are relative to some underlying ``top level'' coordinate system (such as a chromosome). ref() returns the identity of the top level landmark, and start() and end() return locations relative to that landmark. In relative addressing mode, coordinates are relative to the landmark sequence specified at the time of segment creation or later modified by the ref() method.
The default is to return false and to do nothing in response to attempts to set absolute addressing mode.
features
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: the following methods all build on top of features(), and do not need to be explicitly implemented.
overlapping_features()
contained_features()
contained_in()
get_feature_stream()
overlapping_features
Title : overlapping_features Usage : @features = $s->overlapping_features(@args) Function: get features that overlap this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public
This method is identical to features() except that it defaults to finding overlapping features.
contained_features
Title : contained_features Usage : @features = $s->contained_features(@args) Function: get features that are contained in this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public
This method is identical to features() except that it defaults to a range type of 'contained'.
contained_in
Title : contained_in Usage : @features = $s->contained_in(@args) Function: get features that contain this segment Returns : a list of Bio::SeqFeatureI objects Args : see below Status : Public
This method is identical to features() except that it defaults to a range type of 'contained_in'.
get_feature_stream
Title : get_feature_stream Usage : $iterator = $s->get_feature_stream(@args) Function: get an iterator across the segment Returns : an object that implements next_seq() Args : see below Status : Public
This method is identical to features() except that it always generates an iterator.
NOTE: This is defined in the interface in terms of features(). You do not have to implement it.
factory
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.
primary_tag
Title : primary_tag Usage : $tag = $s->primary_tag Function: identifies the segment as type "DasSegment" Returns : a string named "DasSegment" Args : none Status : Public, but see below
This method provides Bio::Das::Segment objects with a primary_tag() field that identifies them as being of type ``DasSegment''. This allows the Bio::Graphics engine to render segments just like a feature in order nis way useful.
This does not need to be implemented. It is defined by the interface.
strand
Title : strand Usage : $strand = $s->strand Function: identifies the segment strand as 0 Returns : the number 0 Args : none Status : Public, but see below
This method provides Bio::Das::Segment objects with a strand() field that identifies it as being strandless. This allows the Bio::Graphics engine to render segments just like a feature in order nis way useful.
This does not need to be implemented. It is defined by the interface.