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#
# = sample/demo_locations.rb - demonstration of Bio::Locations
#
# Copyright:: Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org>
# 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk>
# 2008 Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# == Description
#
# Demonstration of Bio::Locations, a parser class for the location string
# used in the INSDC Feature Table.
#
# == Usage
#
# Simply run this script.
#
# $ ruby demo_locations.rb
#
# == Development information
#
# The code was moved from lib/bio/location.rb.
#
require 'bio'
#if __FILE__ == $0
puts "Test new & span methods"
[
'450',
'500..600',
'join(500..550, 600..625)',
'complement(join(500..550, 600..625))',
'join(complement(500..550), 600..625)',
'754^755',
'complement(53^54)',
'replace(4792^4793,"a")',
'replace(1905^1906,"acaaagacaccgccctacgcc")',
'157..(800.806)',
'(67.68)..(699.703)',
'(45934.45974)..46135',
'<180..(731.761)',
'(88.89)..>1122',
'complement((1700.1708)..(1715.1721))',
'complement(<22..(255.275))',
'complement((64.74)..1525)',
'join((8298.8300)..10206,1..855)',
'replace((651.655)..(651.655),"")',
'one-of(898,900)..983',
'one-of(5971..6308,5971..6309)',
'8050..one-of(10731,10758,10905,11242)',
'one-of(623,627,632)..one-of(628,633,637)',
'one-of(845,953,963,1078,1104)..1354',
'join(2035..2050,complement(1775..1818),13..345,414..992,1232..1253,1024..1157)',
'join(complement(1..61),complement(AP000007.1:252907..253505))',
'complement(join(71606..71829,75327..75446,76039..76203))',
'order(3..26,complement(964..987))',
'order(L44135.1:(454.445)..>538,<1..181)',
'<200001..<318389',
].each do |pos|
p pos
# p Bio::Locations.new(pos)
# p Bio::Locations.new(pos).span
# p Bio::Locations.new(pos).range
Bio::Locations.new(pos).each do |location|
puts "class=" + location.class.to_s
puts "start=" + location.from.to_s + "\tend=" + location.to.to_s + "\tstrand=" + location.strand.to_s
end
end
puts "Test rel2abs/abs2rel method"
[
'6..15',
'join(6..10,16..30)',
'complement(join(6..10,16..30))',
'join(complement(6..10),complement(16..30))',
'join(6..10,complement(16..30))',
].each do |pos|
loc = Bio::Locations.new(pos)
p pos
# p loc
(1..21).each do |x|
print "absolute(#{x}) #=> ", y = loc.absolute(x), "\n"
print "relative(#{y}) #=> ", y ? loc.relative(y) : y, "\n"
print "absolute(#{x}, :aa) #=> ", y = loc.absolute(x, :aa), "\n"
print "relative(#{y}, :aa) #=> ", y ? loc.relative(y, :aa) : y, "\n"
end
end
pos = 'join(complement(6..10),complement(16..30))'
loc = Bio::Locations.new(pos)
print "pos : "; p pos
print "`- loc[1] : "; p loc[1]
print " `- range : "; p loc[1].range
puts Bio::Location.new('5').<=>(Bio::Location.new('3'))
#end
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