Bio::DB::Das::Chado::Segment - DAS-style access to a chado database
# Get a Bio::Das::SegmentI object from a Bio::DB::Das::Chado database... $segment = $das->segment(-name => 'Landmark', -start=> $start, -stop => $stop); @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 { ... { } );
Bio::DB::Das::Chado::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::Chado::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::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
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : name Usage : $segname = $seg->name(); Function: Returns the name of the segment Returns : see above Args : none Status : public
Title : feature_id Usage : $obj->feature_id($newval) Function: holds feature.feature_id Returns : value of feature_id (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : strand Usage : $obj->strand() Function: Returns the strand of the feature. Unlike the other methods, the strand cannot be changed once the object is created (due to coordinate considerations). corresponds to featureloc.strand Returns : -1, 0, or 1 Args : on set, new value (a scalar or undef, optional)
Title : attributes Usage : @attributes = $obj->attributes; Function: get the "attributes" of this segment Returns : An array of strings Args : None
This is a object-specific wrapper on the more generic attributes method in Bio::DB::Das::Chado.
Title : _search_by_name Usage : _search_by_name($name); Function: Searches for segments based on a name Returns : Either a scalar (a feature_id) or an arrary ref (containing feature_ids) Args : A string (name) Status : private (used by new)
Title : class Usage : $obj->class($newval) Function: Returns the segment class (synonymous with type) Returns : value of class (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : type Usage : $obj->type($newval) Function: used to be alias of class() for backward compatibility, now behaves the same as Bio::DB::Das::Chado::Segment::Feature->type Returns : A Bio::DB::GFF::Typename object Args : on set, new value: Bio::DB::GFF::Typename object
Title : seq_id Usage : $ref = $s->seq_id Function: return the ID of the landmark, aliased to name() for backward compatibility Returns : a string Args : none Status : Public
Title : start Usage : $s->start Function: start of segment Returns : integer Args : none Status : Public
Title : low Usage : $s->low Function: start of segment Returns : integer Args : none Status : Public
Alias of start for backward compatibility
Title : end Usage : $s->end Function: end of segment Returns : integer Args : none Status : Public
Title : high Usage : $s->high Function: end of segment Returns : integer Args : none Status : Public
Alias of end for backward compatiblity
Title : stop Usage : $s->stop Function: end of segment Returns : integer Args : none Status : Public
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 : 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.
See: features
Its a crude copy past from feature + additionnal code to handle prefetching of 2 levels features. The generated query is ~ as performant as the one generated by features, and the calls to Bio::DB::Das::Chado::Segment->sub_SeqFeatures are avoided, but this doesn't lead to a huge performace boost.
If a further development increases the performances provided by this 2 level prefetch, we will need to refactor features and _features2level to avoid code duplication
Title : get_all_SeqFeature, get_SeqFeatures, top_SeqFeatures, all_SeqFeatures Usage : $s->get_all_SeqFeature() Function: get the sequence string for this segment Returns : a string Args : none Status : Public
Several aliases of features() for backward compatibility
Title : dna Usage : $s->dna Function: get the dna string this segment Returns : a string Args : none Status : Public
Returns the sequence for this segment as a string.
Title : seq Usage : $s->seq Function: get a Bio::Seq object for this segment Returns : a Bio::Seq object Args : none Status : Public
Returns the sequence for this segment as a Bio::Seq 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 : srcfeature_id Usage : $obj->srcfeature_id($newval) Function: undocumented method by Scott Cain Returns : value of srcfeature_id (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : source Usage : $obj->source($newval) Function: Returns the source; sets with an argument Returns : A string that is the source Args : A string to set the source
Title : source_tag Function: aliased to source() for Bio::SeqFeatureI compatibility
Title : alphabet Usage : $obj->alphabet($newval) Function: Returns the sequence "type", ie, dna Returns : scalar 'dna' Args : None
Title : display_id, display_name, accession_number, desc Usage : $s->display_name() Function: Alias of name() Returns : string Args : none
Several aliases for name; it may be that these could do something better than just giving back the name.
Title : get_feature_stream Usage : $db->get_feature_stream(@args) Function: creates a feature iterator Returns : A Bio::DB::Das::ChadoIterator object Args : The same arguments as the feature method
get_feature_stream has an alias called get_seq_stream for backward compatability.
Title : clone Usage : $copy = $s->clone Function: make a copy of this segment Returns : a Bio::DB::GFF::Segment object Args : none Status : Public
Title : sourceseq Usage : $obj->sourceseq($newval) Function: undocumented method by Scott Cain Returns : value of sourceseq (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : refseq Usage : $s->refseq Function: get or set the reference sequence Returns : a string Args : none Status : Public
Examine or change the reference sequence. This is an alias to sourceseq(), provided here for API compatibility with Bio::DB::GFF::RelSegment.
Title : abs_ref Usage : $obj->abs_ref() Function: Alias of sourceseq Returns : value of sourceseq (a scalar) Args : none
Alias of sourceseq for backward compatibility
Title : abs_start Usage : $obj->abs_start() Function: Alias of start Returns : value of start (a scalar) Args : none
Title : abs_end Usage : $obj->abs_end() Function: Alias of end Returns : value of end (a scalar) Args : none
Title : asString Usage : $s->asString Function: human-readable string for segment Returns : a string Args : none Status : Public
Returns a human-readable string representing this sequence. Format is:
sourceseq:start,stop
To install Bio::DB::Das::Chado, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::DB::Das::Chado
CPAN shell
perl -MCPAN -e shell install Bio::DB::Das::Chado
For more information on module installation, please visit the detailed CPAN module installation guide.