Class: Bio::Locations
- Includes:
- Enumerable
- Defined in:
- lib/bio/location.rb
Overview
Description
The Bio::Locations class is a container for Bio::Location objects: creating a Bio::Locations object (based on a GenBank style position string) will spawn an array of Bio::Location objects.
Usage
locations = Bio::Locations.new('join(complement(500..550), 600..625)')
locations.each do |loc|
puts "class = " + loc.class.to_s
puts "range = #{loc.from}..#{loc.to} (strand = #{loc.strand})"
end
# Output would be:
# class = Bio::Location
# range = 500..550 (strand = -1)
# class = Bio::Location
# range = 600..625 (strand = 1)
# For the following three location strings, print the span and range
['one-of(898,900)..983',
'one-of(5971..6308,5971..6309)',
'8050..one-of(10731,10758,10905,11242)'].each do |loc|
location = Bio::Locations.new(loc)
puts location.span
puts location.range
end
GenBank location descriptor classification
Definition of the position notation of the GenBank location format
According to the GenBank manual ‘gbrel.txt’, position notations were classified into 10 patterns - (A) to (J).
3.4.12.2 Feature Location
The second column of the feature descriptor line designates the
location of the feature in the sequence. The location descriptor
begins at position 22. Several conventions are used to indicate
sequence location.
Base numbers in location descriptors refer to numbering in the entry,
which is not necessarily the same as the numbering scheme used in the
published report. The first base in the presented sequence is numbered
base 1. Sequences are presented in the 5 to 3 direction.
Location descriptors can be one of the following:
(A) 1. A single base;
(B) 2. A contiguous span of bases;
(C) 3. A site between two bases;
(D) 4. A single base chosen from a range of bases;
(E) 5. A single base chosen from among two or more specified bases;
(F) 6. A joining of sequence spans;
(G) 7. A reference to an entry other than the one to which the feature
belongs (i.e., a remote entry), followed by a location descriptor
referring to the remote sequence;
(H) 8. A literal sequence (a string of bases enclosed in quotation marks).
Description commented with pattern IDs.
(C) A site between two residues, such as an endonuclease cleavage site, is
indicated by listing the two bases separated by a carat (e.g., 23^24).
(D) A single residue chosen from a range of residues is indicated by the
number of the first and last bases in the range separated by a single
period (e.g., 23.79). The symbols < and > indicate that the end point
(I) of the range is beyond the specified base number.
(B) A contiguous span of bases is indicated by the number of the first and
last bases in the range separated by two periods (e.g., 23..79). The
(I) symbols < and > indicate that the end point of the range is beyond the
specified base number. Starting and ending positions can be indicated
by base number or by one of the operators described below.
Operators are prefixes that specify what must be done to the indicated
sequence to locate the feature. The following are the operators
available, along with their most common format and a description.
(J) complement (location): The feature is complementary to the location
indicated. Complementary strands are read 5 to 3.
(F) join (location, location, .. location): The indicated elements should
be placed end to end to form one contiguous sequence.
(F) order (location, location, .. location): The elements are found in the
specified order in the 5 to 3 direction, but nothing is implied about
the rationality of joining them.
(F) group (location, location, .. location): The elements are related and
should be grouped together, but no order is implied.
(E) one-of (location, location, .. location): The element can be any one,
but only one, of the items listed.
Reduction strategy of the position notations
-
(A) Location n
-
(B) Location n..m
-
© Location n^m
-
(D) (n.m) => Location n
-
(E)
-
one-of(n,m,..) => Location n
-
one-of(n..m,..) => Location n..m
-
-
(F)
-
order(loc,loc,..) => join(loc, loc,..)
-
group(loc,loc,..) => join(loc, loc,..)
-
join(loc,loc,..) => Sequence
-
-
(G) ID:loc => Location with ID
-
(H) “atgc” => Location only with Sequence
-
(I)
-
<n => Location n with lt flag
-
>n => Location n with gt flag
-
<n..m => Location n..m with lt flag
-
n..>m => Location n..m with gt flag
-
<n..>m => Location n..m with lt, gt flag
-
-
(J) complement(loc) => Sequence
-
(K) replace(loc, str) => Location with replacement Sequence
Instance Attribute Summary collapse
-
#locations ⇒ Object
An Array of Bio::Location objects.
Instance Method Summary collapse
-
#[](n) ⇒ Object
Returns nth Bio::Location object.
-
#absolute(n, type = nil) ⇒ Object
Converts relative position in the locus to position in the whole of the DNA sequence.
-
#each ⇒ Object
Iterates on each Bio::Location object.
-
#equals?(other) ⇒ Boolean
Evaluate equality of Bio::Locations object.
-
#first ⇒ Object
Returns first Bio::Location object.
-
#initialize(position) ⇒ Locations
constructor
Parses a GenBank style position string and returns a Bio::Locations object, which contains a list of Bio::Location objects.
-
#last ⇒ Object
Returns last Bio::Location object.
-
#length ⇒ Object
(also: #size)
Returns a length of the spliced RNA.
-
#range ⇒ Object
Similar to span, but returns a Range object min..max.
-
#relative(n, type = nil) ⇒ Object
Converts absolute position in the whole of the DNA sequence to relative position in the locus.
-
#span ⇒ Object
Returns an Array containing overall min and max position [min, max] of this Bio::Locations object.
Constructor Details
#initialize(position) ⇒ Locations
295 296 297 298 299 300 301 302 |
# File 'lib/bio/location.rb', line 295 def initialize(position) if position.is_a? Array @locations = position else position = gbl_cleanup(position) # preprocessing @locations = gbl_pos2loc(position) # create an Array of Bio::Location objects end end |
Instance Attribute Details
#locations ⇒ Object
An Array of Bio::Location objects
305 306 307 |
# File 'lib/bio/location.rb', line 305 def locations @locations end |
Instance Method Details
#[](n) ⇒ Object
Returns nth Bio::Location object.
327 328 329 |
# File 'lib/bio/location.rb', line 327 def [](n) @locations[n] end |
#absolute(n, type = nil) ⇒ Object
Converts relative position in the locus to position in the whole of the DNA sequence.
This method can for example be used to relate positions in a DNA-sequence with those in RNA. In this use, the optional ‘:aa’-flag returns the position of the associated amino-acid rather than the nucleotide.
loc = Bio::Locations.new('complement(12838..13533)')
puts loc.absolute(10) # => 13524
puts loc.absolute(10, :aa) # => 13506
Arguments:
-
(required) position: nucleotide position within locus
-
:aa: flag to be used if position is a aminoacid position rather than a nucleotide position
- Returns
-
position within the whole of the sequence
417 418 419 420 421 422 423 424 425 426 427 |
# File 'lib/bio/location.rb', line 417 def absolute(n, type = nil) case type when :location ; when :aa n = (n - 1) * 3 + 1 rel2abs(n) else rel2abs(n) end end |
#each ⇒ Object
Iterates on each Bio::Location object.
320 321 322 323 324 |
# File 'lib/bio/location.rb', line 320 def each @locations.each do |x| yield(x) end end |
#equals?(other) ⇒ Boolean
Evaluate equality of Bio::Locations object.
308 309 310 311 312 313 314 315 316 317 |
# File 'lib/bio/location.rb', line 308 def equals?(other) if ! other.kind_of?(Bio::Locations) return nil end if self.sort == other.sort return true else return false end end |
#first ⇒ Object
Returns first Bio::Location object.
332 333 334 |
# File 'lib/bio/location.rb', line 332 def first @locations.first end |
#last ⇒ Object
Returns last Bio::Location object.
337 338 339 |
# File 'lib/bio/location.rb', line 337 def last @locations.last end |
#length ⇒ Object Also known as: size
Returns a length of the spliced RNA.
356 357 358 359 360 361 362 363 364 365 366 |
# File 'lib/bio/location.rb', line 356 def length len = 0 @locations.each do |x| if x.sequence len += x.sequence.size else len += (x.to - x.from + 1) end end len end |
#range ⇒ Object
Similar to span, but returns a Range object min..max
350 351 352 353 |
# File 'lib/bio/location.rb', line 350 def range min, max = span min..max end |
#relative(n, type = nil) ⇒ Object
Converts absolute position in the whole of the DNA sequence to relative position in the locus.
This method can for example be used to relate positions in a DNA-sequence with those in RNA. In this use, the optional ‘:aa’-flag returns the position of the associated amino-acid rather than the nucleotide.
loc = Bio::Locations.new('complement(12838..13533)')
puts loc.relative(13524) # => 10
puts loc.relative(13506, :aa) # => 3
Arguments:
-
(required) position: nucleotide position within whole of the sequence
-
:aa: flag that lets method return position in aminoacid coordinates
- Returns
-
position within the location
385 386 387 388 389 390 391 392 393 394 395 396 397 398 |
# File 'lib/bio/location.rb', line 385 def relative(n, type = nil) case type when :location ; when :aa if n = abs2rel(n) (n - 1) / 3 + 1 else nil end else abs2rel(n) end end |
#span ⇒ Object
Returns an Array containing overall min and max position [min, max] of this Bio::Locations object.
343 344 345 346 347 |
# File 'lib/bio/location.rb', line 343 def span span_min = @locations.min { |a,b| a.from <=> b.from } span_max = @locations.max { |a,b| a.to <=> b.to } return span_min.from, span_max.to end |