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#
# = sample/demo_sequence.rb - demonstration of sequence manipulation
#
# Copyright:: Copyright (C) 2000-2006
# Toshiaki Katayama <k@bioruby.org>,
# Mitsuteru C. Nakao <n@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# == Description
#
# Demonstration of biological sequence manipulation.
#
# == Usage
#
# Simply run this script.
#
# $ ruby demo_sequence.rb
#
# == Development information
#
# The code was moved from lib/bio/sequence.rb.
#
require 'bio'
#if __FILE__ == $0
puts "== Test Bio::Sequence::NA.new"
p Bio::Sequence::NA.new('')
p na = Bio::Sequence::NA.new('atgcatgcATGCATGCAAAA')
p rna = Bio::Sequence::NA.new('augcaugcaugcaugcaaaa')
puts "\n== Test Bio::Sequence::AA.new"
p Bio::Sequence::AA.new('')
p aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
puts "\n== Test Bio::Sequence#to_s"
p na.to_s
p aa.to_s
puts "\n== Test Bio::Sequence#subseq(2,6)"
p na
p na.subseq(2,6)
puts "\n== Test Bio::Sequence#[2,6]"
p na
p na[2,6]
puts "\n== Test Bio::Sequence#to_fasta('hoge', 8)"
puts na.to_fasta('hoge', 8)
puts "\n== Test Bio::Sequence#window_search(15)"
p na
na.window_search(15) {|x| p x}
puts "\n== Test Bio::Sequence#total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})"
p na.total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})
puts "\n== Test Bio::Sequence#composition"
p na
p na.composition
p rna
p rna.composition
puts "\n== Test Bio::Sequence::NA#splicing('complement(join(1..5,16..20))')"
p na
p na.splicing("complement(join(1..5,16..20))")
p rna
p rna.splicing("complement(join(1..5,16..20))")
puts "\n== Test Bio::Sequence::NA#complement"
p na.complement
p rna.complement
p Bio::Sequence::NA.new('tacgyrkmhdbvswn').complement
p Bio::Sequence::NA.new('uacgyrkmhdbvswn').complement
puts "\n== Test Bio::Sequence::NA#translate"
p na
p na.translate
p rna
p rna.translate
puts "\n== Test Bio::Sequence::NA#gc_percent"
p na.gc_percent
p rna.gc_percent
puts "\n== Test Bio::Sequence::NA#illegal_bases"
p na.illegal_bases
p Bio::Sequence::NA.new('tacgyrkmhdbvswn').illegal_bases
p Bio::Sequence::NA.new('abcdefghijklmnopqrstuvwxyz-!%#$@').illegal_bases
puts "\n== Test Bio::Sequence::NA#molecular_weight"
p na
p na.molecular_weight
p rna
p rna.molecular_weight
puts "\n== Test Bio::Sequence::NA#to_re"
p Bio::Sequence::NA.new('atgcrymkdhvbswn')
p Bio::Sequence::NA.new('atgcrymkdhvbswn').to_re
p Bio::Sequence::NA.new('augcrymkdhvbswn')
p Bio::Sequence::NA.new('augcrymkdhvbswn').to_re
puts "\n== Test Bio::Sequence::NA#names"
p na.names
puts "\n== Test Bio::Sequence::NA#pikachu"
p na.pikachu
puts "\n== Test Bio::Sequence::NA#randomize"
print "Orig : "; p na
print "Rand : "; p na.randomize
print "Rand : "; p na.randomize
print "Rand : "; p na.randomize.randomize
print "Block : "; na.randomize do |x| print x end; puts
print "Orig : "; p rna
print "Rand : "; p rna.randomize
print "Rand : "; p rna.randomize
print "Rand : "; p rna.randomize.randomize
print "Block : "; rna.randomize do |x| print x end; puts
puts "\n== Test Bio::Sequence::NA.randomize(counts)"
print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'t'=>40}
print "Rand : "; p Bio::Sequence::NA.randomize(counts)
print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
print "Rand : "; p Bio::Sequence::NA.randomize(counts)
print "Block : "; Bio::Sequence::NA.randomize(counts) {|x| print x}; puts
puts "\n== Test Bio::Sequence::AA#codes"
p aa
p aa.codes
puts "\n== Test Bio::Sequence::AA#names"
p aa
p aa.names
puts "\n== Test Bio::Sequence::AA#molecular_weight"
p aa.subseq(1,20)
p aa.subseq(1,20).molecular_weight
puts "\n== Test Bio::Sequence::AA#randomize"
aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
s = Bio::Sequence::AA.new(aaseq)
print "Orig : "; p s
print "Rand : "; p s.randomize
print "Rand : "; p s.randomize
print "Rand : "; p s.randomize.randomize
print "Block : "; s.randomize {|x| print x}; puts
puts "\n== Test Bio::Sequence::AA.randomize(counts)"
print "Count : "; p counts = s.composition
print "Rand : "; puts Bio::Sequence::AA.randomize(counts)
print "Block : "; Bio::Sequence::AA.randomize(counts) {|x| print x}; puts
#end
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