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#
# = sample/demo_fastaformat.rb - demonstration of the FASTA format parser
#
# Copyright:: Copyright (C) 2001, 2002
# Naohisa Goto <ng@bioruby.org>,
# Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# == Description
#
# Demonstration of FASTA format parser.
#
# == Usage
#
# Simply run the script.
#
# $ ruby demo_fastaformat.rb
#
# == Development information
#
# The code was moved from lib/bio/db/fasta.rb.
#
require 'bio'
f_str = <<END
>sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
>sce:YBR274W CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
KTGDPLEWRRLFKKISTICRDIILIPN
END
f = Bio::FastaFormat.new(f_str)
puts "### FastaFormat"
puts "# entry"
puts f.entry
puts "# entry_id"
p f.entry_id
puts "# definition"
p f.definition
puts "# data"
p f.data
puts "# seq"
p f.seq
puts "# seq.type"
p f.seq.type
puts "# length"
p f.length
puts "# aaseq"
p f.aaseq
puts "# aaseq.type"
p f.aaseq.type
puts "# aaseq.composition"
p f.aaseq.composition
puts "# aalen"
p f.aalen
puts
n_str = <<END
>CRA3575282.F
24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26
32 29 29 25
END
n = Bio::FastaNumericFormat.new(n_str)
puts "### FastaNumericFormat"
puts "# entry"
puts n.entry
puts "# entry_id"
p n.entry_id
puts "# definition"
p n.definition
puts "# data"
p n.data
puts "# length"
p n.length
#puts "# percent to ratio by yield"
#n.each do |x|
# p x/100.0
#end
puts "# first three"
p n[0]
p n[1]
p n[2]
puts "# last one"
p n[-1]
|
