NAME

Bio::DB::GFF::RelSegment -- Sequence segment with relative coordinate support

SYNOPSIS

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

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.

AUTHOR

Lincoln Stein <lstein@cshl.org>.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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