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|
#
# = sample/demo_prosite.rb - demonstration of Bio::PROSITE
#
# Copyright:: Copyright (C) 2001 Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
#
# == Description
#
# Demonstration of Bio::PROSITE, parser class for PROSITE database entry.
#
# == Usage
#
# Specify files containing PROSITE data.
#
# $ ruby demo_prosite.rb files...
#
# Example usage using test data:
#
# $ ruby -Ilib sample/demo_prosite.rb test/data/prosite/prosite.dat
#
# == Development information
#
# The code was moved from lib/bio/db/prosite.rb.
#
require 'bio'
begin
require 'pp'
alias p pp
rescue LoadError
end
Bio::FlatFile.foreach(Bio::PROSITE, ARGF) do |ps|
puts "### ps = Bio::PROSITE.new(str)"
list = %w(
name
division
ac
entry_id
dt
date
de
definition
pa
pattern
ma
profile
ru
rule
nr
statistics
release
swissprot_release_number
swissprot_release_sequences
total
total_hits
total_sequences
positive
positive_hits
positive_sequences
unknown
unknown_hits
unknown_sequences
false_pos
false_positive_hits
false_positive_sequences
false_neg
false_negative_hits
partial
cc
comment
max_repeat
site
skip_flag
dr
sp_xref
pdb_xref
pdoc_xref
)
list.each do |method|
puts ">>> #{method}"
p ps.__send__(method)
end
puts ">>> taxon_range"
p ps.taxon_range
puts ">>> taxon_range(expand)"
p ps.taxon_range(true)
puts ">>> list_truepositive"
p ps.list_truepositive
puts ">>> list_truepositive(by_name)"
p ps.list_truepositive(true)
puts ">>> list_falsenegative"
p ps.list_falsenegative
puts ">>> list_falsenegative(by_name)"
p ps.list_falsenegative(true)
puts ">>> list_falsepositive"
p ps.list_falsepositive
puts ">>> list_falsepositive(by_name)"
p ps.list_falsepositive(true)
puts ">>> list_potentialhit"
p ps.list_potentialhit
puts ">>> list_potentialhit(by_name)"
p ps.list_potentialhit(true)
puts ">>> list_unknown"
p ps.list_unknown
puts ">>> list_unknown(by_name)"
p ps.list_unknown(true)
puts "=" * 78
end
|
