Provided by: libbio-perl-perl_1.6.923-1_all 
NAME
Bio::DB::GFF::RelSegment -- Sequence segment with relative coordinate support
SYNOPSIS
See Bio::DB::GFF.
DESCRIPTION
Bio::DB::GFF::RelSegment is a stretch of sequence that can handle relative coordinate
addressing. It inherits from Bio::DB::GFF::Segment, and is the base class for
Bio::DB::GFF::Feature.
In addition to the source sequence, a relative segment has a "reference sequence", which
is used as the basis for its coordinate system. The reference sequence can be changed at
will, allowing you freedom to change the "frame of reference" for features contained
within the segment. For example, by setting a segment's reference sequence to the
beginning of a gene, you can view all other features in gene-relative coordinates.
The reference sequence and the source sequence must be on the same physical stretch of
DNA, naturally. However, they do not have to be on the same strand. The strandedness of
the reference sequence determines whether coordinates increase to the right or the left.
Generally, you will not create or manipulate Bio::DB::GFF::RelSeg0ment objects directly,
but use those that are returned by the Bio::DB::GFF module.
An Example
To understand how relative coordinates work, consider the following example from the C.
elegans database. First we create the appropriate GFF accessor object (the factory):
my $db = Bio::DB::GFF->new(-dsn => 'dbi:mysql:elegans',
-adaptor=>'dbi:mysqlopt');
Now we fetch out a segment based on cosmid clone ZK909:
my $seg = $db->segment('ZK909');
If we call the segment's refseq() method, we see that the base of the coordinate system is
the sequence "ZK154", and that its start and stop positions are 1 and the length of the
cosmid:
print $seg->refseq;
=> ZK909
print $seg->start,' - ',$seg->stop;
=> 1 - 33782
As a convenience, the "" operator is overloaded in this class, to give the reference
sequence, and start and stop positions:
print $seg;
=> ZK909:1,33782
Internally, Bio::DB::GFF::RelSegment has looked up the absolute coordinates of this
segment and maintains the source sequence and the absolute coordinates relative to the
source sequence. We can see this information using sourceseq() (inherited from
Bio::DB::GFF::Segment) and the abs_start() and abs_end() methods:
print $seg->sourceseq;
=> CHROMOSOME_I
print $seg->abs_start,' - ',$seg->abs_end;
=> 14839545 - 14873326
We can also put the segment into absolute mode, so that it behaves like Bio::DB::Segment,
and always represents coordinates on the source sequence. This is done by passing a true
value to the absolute() method:
$seq->absolute(1);
print $seg;
=> CHROMOSOME_I:14839545,14873326
We can change the reference sequence at any time. One way is to call the segment's ref()
method, giving it the ID (and optionally the class) of another landmark on the genome.
For example, if we know that cosmid ZK337 is adjacent to ZK909, then we can view ZK909 in
ZK337-relative coordinates:
$seg->refseq('ZK337');
print $seg;
=> ZK337:-33670,111
We can call the segment's features() method in order to get the list of contigs that
overlap this segment (in the C. elegans database, contigs have feature type
"Sequence:Link"):
@links = $seg->features('Sequence:Link');
We can now set the reference sequence to the first of these contigs like so:
$seg->refseq($links[0]);
print $seg;
=> Sequence:Link(LINK_Y95D11A):3997326,4031107
API
The remainder of this document describes the API for Bio::DB::GFF::Segment.
new
Title : new
Usage : $s = Bio::DB::GFF::RelSegment->new(@args)
Function: create a new relative segment
Returns : a new Bio::DB::GFF::RelSegment object
Args : see below
Status : Public
This method creates a new Bio::DB::GFF::RelSegment object. Generally this is called
automatically by the Bio::DB::GFF module and derivatives.
This function uses a named-argument style:
-factory a Bio::DB::GFF::Adaptor to use for database access
-seq ID of the source sequence
-class class of the source sequence
-start start of the desired segment relative to source sequence
-stop stop of the desired segment relative to source sequence
-ref ID of the reference sequence
-refclass class of the reference sequence
-offset 0-based offset from source sequence to start of segment
-length length of desired segment
-absolute, -force_absolute
use absolute coordinates, rather than coordinates relative
to the start of self or the reference sequence
The -seq argument accepts the ID of any landmark in the database. The stored source
sequence becomes whatever the GFF file indicates is the proper sequence for this landmark.
A class of "Sequence" is assumed unless otherwise specified in the -class argument.
If the argument to -seq is a Bio::GFF::Featname object (such as returned by the group()
method), then the class is taken from that.
The optional -start and -stop arguments specify the end points for the retrieved segment.
For those who do not like 1-based indexing, -offset and -length are provided. If both
-start/-stop and -offset/-length are provided, the latter overrides the former. Generally
it is not a good idea to mix metaphors.
-ref and -refclass together indicate a sequence to be used for relative coordinates. If
not provided, the source sequence indicated by -seq is used as the reference sequence. If
the argument to -ref is a Bio::GFF::Featname object (such as returned by the group()
method), then the class is taken from that.
-force_absolute should be used if you wish to skip the lookup of the absolute position of
the source sequence that ordinarily occurs when you create a relative segment. In this
case, the source sequence must be a sequence that has been specified as the "source" in
the GFF file.
refseq
Title : refseq
Usage : $ref = $s->refseq([$newseq] [,$newseqclass])
Function: get/set reference sequence
Returns : current reference sequence
Args : new reference sequence and class (optional)
Status : Public
This method will get or set the reference sequence. Called with no arguments, it returns
the current reference sequence. Called with either a sequence ID and class, a
Bio::DB::GFF::Segment object (or subclass) or a Bio::DB::GFF::Featname object, it will set
the current reference sequence and return the previous one.
The method will generate an exception if you attempt to set the reference sequence to a
sequence that isn't contained in the database, or one that has a different source sequence
from the segment.
abs_low
Title : abs_low
Usage : $s->abs_low
Function: the absolute lowest coordinate of the segment
Returns : an integer
Args : none
Status : Public
This is for GadFly compatibility, and returns the low coordinate in absolute coordinates;
abs_high
Title : abs_high
Usage : $s->abs_high
Function: the absolute highest coordinate of the segment
Returns : an integer
Args : none
Status : Public
This is for GadFly compatibility, and returns the high coordinate in absolute coordinates;
asString
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
name
Title : name
Usage : Alias for asString()
absolute
Title : absolute
Usage : $abs = $s->absolute([$abs])
Function: get/set absolute coordinates
Returns : a boolean flag
Args : new setting for flag (optional)
Status : Public
Called with a boolean flag, this method controls whether to display relative coordinates
(relative to the reference sequence) or absolute coordinates (relative to the source
sequence). It will return the previous value of the setting.
features
Title : features
Usage : @features = $s->features(@args)
Function: get features that overlap this segment
Returns : a list of Bio::DB::GFF::Feature objects
Args : see below
Status : Public
This method will find all features that overlap the segment and return a list of
Bio::DB::GFF::Feature objects. The features 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 of feature by filtering on their method
and/or source. In addition, it is possible to obtain an iterator that will step through a
large number of features sequentially.
Arguments can be provided positionally or using the named arguments format. In the former
case, the arguments are a list of feature types in the format "method:source". Either
method or source can be omitted, in which case the missing component is treated as a
wildcard. If no colon is present, then the type is treated as a method name. Multiple
arguments are ORed together.
Examples:
@f = $s->features('exon:curated'); # all curated exons
@f = $s->features('exon:curated','intron'); # curated exons and all introns
@f = $s->features('similarity:.*EST.*'); # all similarities
# having something to do
# with ESTs
The named parameter form gives you control over a few options:
-types an array reference to type names in the format
"method:source"
-merge Whether to apply aggregators to the generated features (default yes)
-rare Turn on an optimization suitable for a relatively rare feature type,
where it will be faster to filter by feature type first
and then by position, rather than vice versa.
-attributes a hashref containing a set of attributes to match
-range_type One of 'overlapping', 'contains', or 'contained_in'
-iterator Whether to return an iterator across the features.
-binsize A true value will create a set of artificial features whose
start and stop positions indicate bins of the given size, and
whose scores are the number of features in the bin. The
class and method of the feature will be set to "bin",
its source to "method:source", and its group to "bin:method:source".
This is a handy way of generating histograms of feature density.
-merge is a boolean flag that controls whether the adaptor's aggregators wll be applied to
the features returned by this method.
If -iterator is true, then the method returns a single scalar value consisting of a
Bio::SeqIO object. You can call next_seq() repeatedly on this object to fetch each of the
features in turn. If iterator is false or absent, then all the features are returned as a
list.
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.
get_SeqFeatures
Title : get_SeqFeatures
Usage :
Function: returns the top level sequence features
Returns : L<Bio::SeqFeatureI> objects
Args : none
Segments do not ordinarily return any subfeatures.
feature_count
Title : feature_count
Usage : $seq->feature_count()
Function: Return the number of SeqFeatures attached to a sequence
Returns : integer representing the number of SeqFeatures
Args : none
This method comes through extension of Bio::FeatureHolderI. See Bio::FeatureHolderI for
more information.
get_feature_stream
Title : features
Usage : $stream = $s->get_feature_stream(@args)
Function: get a stream of features that overlap this segment
Returns : a Bio::SeqIO::Stream-compliant stream
Args : see below
Status : Public
This is the same as features(), but returns a stream. Use like this:
$stream = $s->get_feature_stream('exon');
while (my $exon = $stream->next_seq) {
print $exon->start,"\n";
}
get_seq_stream
Title : get_seq_stream
Usage : $stream = $s->get_seq_stream(@args)
Function: get a stream of features that overlap this segment
Returns : a Bio::SeqIO::Stream-compliant stream
Args : see below
Status : Public
This is the same as feature_stream(), and is provided for Bioperl compatibility. Use like
this:
$stream = $s->get_seq_stream('exon');
while (my $exon = $stream->next_seq) {
print $exon->start,"\n";
}
overlapping_features
Title : overlapping_features
Usage : @features = $s->overlapping_features(@args)
Function: get features that overlap this segment
Returns : a list of Bio::DB::GFF::Feature objects
Args : see features()
Status : Public
This is an alias for the features() method, and takes the same arguments.
contained_features
Title : contained_features
Usage : @features = $s->contained_features(@args)
Function: get features that are contained by this segment
Returns : a list of Bio::DB::GFF::Feature objects
Args : see features()
Status : Public
This is identical in behavior to features() except that it returns only those features
that are completely contained within the segment, rather than any that overlap.
contained_in
Title : contained_in
Usage : @features = $s->contained_in(@args)
Function: get features that contain this segment
Returns : a list of Bio::DB::GFF::Feature objects
Args : see features()
Status : Public
This is identical in behavior to features() except that it returns only those features
that completely contain the segment.
delete
Title : delete
Usage : $db->delete(@args)
Function: delete features
Returns : count of features deleted -- if available
Args : numerous, see below
Status : public
This method deletes all features that overlap the specified region or are of a particular
type. If no arguments are provided and the -force argument is true, then deletes ALL
features.
Arguments:
-type,-types Either a single scalar type to be deleted, or an
reference to an array of types.
-range_type Control the range type of the deletion. One of "overlaps" (default)
"contains" or "contained_in"
Examples:
$segment->delete(-type=>['intron','repeat:repeatMasker']); # remove all introns & repeats
$segment->delete(-type=>['intron','repeat:repeatMasker']
-range_type => 'contains'); # remove all introns & repeats
# strictly contained in segment
IMPORTANT NOTE: This method only deletes features. It does *NOT* delete the names of
groups that contain the deleted features. Group IDs will be reused if you later load a
feature with the same group name as one that was previously deleted.
NOTE ON FEATURE COUNTS: The DBI-based versions of this call return the result code from
the SQL DELETE operation. Some dbd drivers return the count of rows deleted, while others
return 0E0. Caveat emptor.
_process_feature_args
Title : _process_feature_args
Usage : @args = $s->_process_feature_args(@args)
Function: preprocess arguments passed to features,
contained_features, and overlapping_features
Returns : a list of parsed arguents
Args : see feature()
Status : Internal
This is an internal method that is used to check and format the arguments to features()
before passing them on to the adaptor.
types
Title : types
Usage : @types = $s->types([-enumerate=>1])
Function: list feature types that overlap this segment
Returns : a list of Bio::DB::GFF::Typename objects or a hash
Args : see below
Status : Public
The types() method will return a list of Bio::DB::GFF::Typename objects, each
corresponding to a feature that overlaps the segment. If the optional -enumerate
parameter is set to a true value, then the method will return a hash in which the keys are
the type names and the values are the number of times a feature of that type is present on
the segment. For example:
%count = $s->types(-enumerate=>1);
Internal Methods
The following are internal methods and should not be called directly.
new_from_segment
Title : new_from_segment
Usage : $s = $segment->new_from_segment(@args)
Function: create a new relative segment
Returns : a new Bio::DB::GFF::RelSegment object
Args : see below
Status : Internal
This constructor is used internally by the subseq() method. It forces the new segment
into the Bio::DB::GFF::RelSegment package, regardless of the package that it is called
from. This causes subclass-specfic information, such as feature types, to be dropped when
a subsequence is created.
_abs2rel
Title : _abs2rel
Usage : @coords = $s->_abs2rel(@coords)
Function: convert absolute coordinates into relative coordinates
Returns : a list of relative coordinates
Args : a list of absolute coordinates
Status : Internal
This is used internally to map from absolute to relative coordinates. It does not take the
offset of the reference sequence into account, so please use abs2rel() instead.
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::RangeI Methods
The following Bio::RangeI methods are supported:
overlaps(), contains(), equals(),intersection(),union(),overlap_extent()
BUGS
Schemas need some work.
SEE ALSO
bioperl
AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it under the same
terms as Perl itself.