Bio::DB::SeqFeature::Segment man page on Pidora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Pidora logo
[printable version]

Bio::DB::SeqFeature::SUsernContributed Perl DocBio::DB::SeqFeature::Segment(3)

NAME
       Bio::DB::SeqFeature::Segment -- Location-based access to genome
       annotation data

SYNOPSIS
	use Bio::DB::SeqFeature::Store;
	# Open the sequence database
	my $db	    = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
						       -dsn	=> 'dbi:mysql:test');
	my $segment  = $db->segment('Chr1',5000=>6000);
	my @features = $segment->features('mRNA','match');

DESCRIPTION
       The segment object simplifies access to Bio::DB::SeqFeature store by
       acting as a placeholder for a region of the genome. You can replace
       this statement:

	@features = $db->features(-seq_id=>'Chr1',
				  -start=>5000,
				  -end=>6000,
				  -types=>['mRNA','match','repeat_region']);

       with these statements:

	$segment = $db->segment('Chr1',5000=>6000);
	@features = $segment->features('mRNA','match','repeat_region');

       You can also initialize a segment from an existing SeqFeature object.
       The range will be picked up from the SeqFeature boundaries:

	$segment = Bio::DB::SeqFeature::Segment->new($feature);	       # for Bio::DB::SeqFeature
	$segment = Bio::DB::SeqFeature::Segment->new($feature,$store); # for other Bio::SeqFeatureI objects

       The segment object implements the full Bio::SeqFeature::CollectionI
       interface, thereby allowing you to iterate over all features in the
       range.

PUBLIC METHODS
       The following are public methods intended for external use.

   new
	Title	: new
	Usage	: $segment = Bio::DB::SeqFeature::Segment->new(@options)
	Function: create a new Segment object
	Returns : A Bio::DB::SeqFeature::Segment object
	Args	: several - see below
	Status	: public

       This class method creates a Bio::DB::SeqFeature::Segment object. You
       must provide a Bio::DB::SeqFeature::Store as well as the coordinates of
       the segment. These arguments can be provided explicitly or indirectly.

       First form:

	$segment = Bio::DB::SeqFeature::Segment->new($store,$seqid,$start,$end,$strand)

       In this form a segment is defined by a Bio::DB::SeqFeature::Store, the
       sequence ID, the start, end and strand. This is the form that is
       invoked internally by Bio::DB::SeqFeature::Store when you call its
       segment() method.

       Second form:

	$segment = Bio::DB::SeqFeature::Segment->new($seqfeature [,$store]);

       In this form, you pass new() a Bio::SeqFeatureI object. The segment is
       constructed from the seq_id and coordinates are taken from the object.
       If you pass a store-aware seqfeature object (e.g. Bio::DB::SeqFeature)
       then the store database is also derived from the feature. Otherwise you
       will have to pass the store as a second argument.

   features
	Title	: features
	Usage	: @features = $segment->features(@args)
	Function: fetch seqfeatures that overlap the segment
	Returns : list of features
	Args	: see below
	Status	: Public

       This is the workhorse for feature query and retrieval. It takes a
       series of -name=>$value arguments filter arguments. Features that match
       all the filters are returned.

	 Argument	Value
	 --------	-----

	Location filters:
	 -strand	Strand
	 -range_type	Type of range match ('overlaps','contains','contained_in')

	Name filters:
	 -name		Name of feature (may be a glob expression)
	 -aliases	If true, match aliases as well as display names
	 -class		Archaic argument for backward compatibility.
			 (-class=>'Clone',-name=>'ABC123') is equivalent
			 to (-name=>'Clone:ABC123')

	Type filters:
	 -types		List of feature types (array reference) or one type (scalar)
	 -type		Synonym for the above
	 -primary_tag	Synonym for the above

	 -attributes	Hashref of attribute=>value pairs as per
			   get_features_by_attribute(). Multiple alternative values
			   can be matched by providing an array reference.
	 -attribute	synonym for -attributes

       This is identical to the Bio::DB::SeqFeature::Store->features() method,
       except that the -seq_id, -start, and -end arguments are provided by the
       segment object. If a simple list of arguments is provided, then the
       list is taken to be the set of feature types (primary tags) to filter
       on.

       Examples:

       All features that overlap the current segment:

	@features = $segment->features;

       All features of type mRNA that overlap the current segment:

	@features = $segment->features('mRNA');

       All features that are completely contained within the current segment:

	@features = $segment->features(-range_type=>'contains');

       All "confirmed" mRNAs that overlap the current segment:

	@features = $segment->features(-attributes=>{confirmed=>1},-type=>'mRNA');

   get_seq_stream
	Title	: get_seq_stream
	Usage	: $iterator = $segment->get_seq_stream(@args)
	Function: return an iterator across all features in the database
	Returns : a Bio::DB::SeqFeature::Store::Iterator object
	Args	: (optional) the feature() method
	Status	: public

       This is identical to Bio::DB::SeqFeature::Store->get_seq_stream()
       except that the location filter is always automatically applied so that
       the iterator you receive returns features that overlap the segment's
       region.

       When called without any arguments this method will return an iterator
       object that will traverse all indexed features in the database that
       overlap the segment's region. Call the iterator's next_seq() method to
       step through them (in no particular order):

	 my $iterator = $db->get_seq_stream;
	 while (my $feature = $iterator->next_seq) {
	   print $feature->primary_tag,' ',$feature->display_name,"\n";
	 }

       You can select a subset of features by passing a series of filter
       arguments. The arguments are identical to those accepted by
       $segment->features().

       get_feature_stream() ican be used as a synonym for this method.

   store
	Title	: store
	Usage	: $store = $segment->store
	Function: return the Bio::DB::SeqFeature::Store object associated with the segment
	Returns : a Bio::DB::SeqFeature::Store: object
	Args	: none
	Status	: public

   primary_tag, type,
	Title	: primary_tag,type
	Usage	: $primary_tag = $segment->primary_tag
	Function: returns the string "region"
	Returns : "region"
	Args	: none
	Status	: public

       The primary_tag method returns the constant tag "region". type() is a
       synonym for this method.

   as_string
	Title	: as_string
	Usage	: $name = $segment->as_string
	Function: expands the object into a human-readable string
	Returns : "seq_id:start..end"
	Args	: none
	Status	: public

       The as_string() method is overloaded into the "" operator so that the
       object is represented as a human readable string in the form
       "seq_id:start..end" when used in a string context.

   rel2abs
	Title	: rel2abs
	Usage	: @coords = $s->rel2abs(@coords)
	Function: convert relative coordinates into absolute coordinates
	Returns : a list of absolute coordinates
	Args	: a list of relative coordinates
	Status	: Public

       This function takes a list of positions in relative coordinates to the
       segment, and converts them into absolute coordinates.

   abs2rel
	Title	: abs2rel
	Usage	: @rel_coords = $s->abs2rel(@abs_coords)
	Function: convert absolute coordinates into relative coordinates
	Returns : a list of relative coordinates
	Args	: a list of absolute coordinates
	Status	: Public

       This function takes a list of positions in absolute coordinates and
       returns a list expressed in relative coordinates.

   Bio::SeqFeatureI compatibility methods
       For convenience, segments are interchangeable with Bio::SeqFeature
       objects in many cases. This means that segments can be passed to
       BioPerl modules that expect Bio::SeqFeature objects and they should
       work as expected. The primary tag of segment objects is "region"
       (SO:0000001 "Continous sequence >=1 base pair").

       All these methods are read-only except for the primary_id, which can be
       get or set.

       The following Bio::SeqFeatureI methods are supported:

       start
       end
       seq_id
       strand
       length
       display_name
       primary_id
       primary_tag (always returns "region")
       source_tag (always returns "Bio::DB::SeqFeature::Segment")
       get_SeqFeatures (always returns an empty list)
       seq
       entire_seq
       location
       All Bio::RangeI methods

BUGS
       This is an early version, so there are certainly some bugs. Please use
       the BioPerl bug tracking system to report bugs.

SEE ALSO
       bioperl, Bio::DB::SeqFeature::Store, Bio::DB::SeqFeature::GFF3Loader,
       Bio::DB::SeqFeature::Store::DBI::mysql, Bio::DB::SeqFeature::Store::bdb

AUTHOR
       Lincoln Stein <lstein@cshl.org>.

       Copyright (c) 2006 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::SeqFeature::Segment(3)
[top]

List of man pages available for Pidora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net