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#
# = sample/demo_bl2seq_report.rb - demo of bl2seq (BLAST 2 sequences) parser
#
# Copyright:: Copyright (C) 2005 Naohisa Goto <ng@bioruby.org>
# License:: The Ruby License
#
# == Description
#
# Demonstration of Bio::Blast::Bl2seq::Report, bl2seq (BLAST 2 sequences)
# parser class.
#
# == Usage
#
# Run this script with specifying filename(s) containing bl2seq result(s).
#
# $ ruby demo_bl2seq_report.rb files...
#
# Example usage using test data:
#
# $ ruby -I lib sample/demo_bl2seq_report.rb test/data/bl2seq/cd8a_cd8b_blastp.bl2seq
#
# == Development information
#
# The code was moved from lib/bio/appl/bl2seq/report.rb
#
require 'bio'
if ARGV.empty? then
puts "Demonstration of bl2seq (BLAST 2 sequences) parser."
puts "Usage: #{$0} files..."
exit(0)
end
Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, ARGF) do |ff|
ff.each do |rep|
print "# === Bio::Blast::Bl2seq::Report\n"
puts
#@#print " rep.program #=> "; p rep.program
#@#print " rep.version #=> "; p rep.version
#@#print " rep.reference #=> "; p rep.reference
#@#print " rep.db #=> "; p rep.db
#print " rep.query_id #=> "; p rep.query_id
print " rep.query_def #=> "; p rep.query_def
print " rep.query_len #=> "; p rep.query_len
#puts
#@#print " rep.version_number #=> "; p rep.version_number
#@#print " rep.version_date #=> "; p rep.version_date
puts
print "# === Parameters\n"
#puts
#print " rep.parameters #=> "; p rep.parameters
puts
print " rep.matrix #=> "; p rep.matrix
print " rep.expect #=> "; p rep.expect
#print " rep.inclusion #=> "; p rep.inclusion
print " rep.sc_match #=> "; p rep.sc_match
print " rep.sc_mismatch #=> "; p rep.sc_mismatch
print " rep.gap_open #=> "; p rep.gap_open
print " rep.gap_extend #=> "; p rep.gap_extend
#print " rep.filter #=> "; p rep.filter
#@#print " rep.pattern #=> "; p rep.pattern
#print " rep.entrez_query #=> "; p rep.entrez_query
#puts
#@#print " rep.pattern_positions #=> "; p rep.pattern_positions
puts
print "# === Statistics (last iteration's)\n"
#puts
#print " rep.statistics #=> "; p rep.statistics
puts
print " rep.db_num #=> "; p rep.db_num
print " rep.db_len #=> "; p rep.db_len
#print " rep.hsp_len #=> "; p rep.hsp_len
print " rep.eff_space #=> "; p rep.eff_space
print " rep.kappa #=> "; p rep.kappa
print " rep.lambda #=> "; p rep.lambda
print " rep.entropy #=> "; p rep.entropy
puts
print " rep.num_hits #=> "; p rep.num_hits
print " rep.gapped_kappa #=> "; p rep.gapped_kappa
print " rep.gapped_lambda #=> "; p rep.gapped_lambda
print " rep.gapped_entropy #=> "; p rep.gapped_entropy
print " rep.posted_date #=> "; p rep.posted_date
puts
#@#print "# === Message (last iteration's)\n"
#@#puts
#@#print " rep.message #=> "; p rep.message
#puts
#@#print " rep.converged? #=> "; p rep.converged?
#@#puts
print "# === Iterations\n"
puts
print " rep.itrerations.each do |itr|\n"
puts
rep.iterations.each do |itr|
print "# --- Bio::Blast::Bl2seq::Report::Iteration\n"
puts
print " itr.num #=> "; p itr.num
#print " itr.statistics #=> "; p itr.statistics
#@#print " itr.message #=> "; p itr.message
print " itr.hits.size #=> "; p itr.hits.size
#puts
#@#print " itr.hits_newly_found.size #=> "; p itr.hits_newly_found.size;
#@#print " itr.hits_found_again.size #=> "; p itr.hits_found_again.size;
#@#if itr.hits_for_pattern then
#@#itr.hits_for_pattern.each_with_index do |hp, hpi|
#@#print " itr.hits_for_pattern[#{hpi}].size #=> "; p hp.size;
#@#end
#@#end
#@#print " itr.converged? #=> "; p itr.converged?
puts
print " itr.hits.each do |hit|\n"
puts
itr.hits.each_with_index do |hit, i|
print "# --- Bio::Blast::Bl2seq::Default::Report::Hit"
print " ([#{i}])\n"
puts
#print " hit.num #=> "; p hit.num
#print " hit.hit_id #=> "; p hit.hit_id
print " hit.len #=> "; p hit.len
print " hit.definition #=> "; p hit.definition
#print " hit.accession #=> "; p hit.accession
#puts
print " hit.found_again? #=> "; p hit.found_again?
print " --- compatible/shortcut ---\n"
#print " hit.query_id #=> "; p hit.query_id
#print " hit.query_def #=> "; p hit.query_def
#print " hit.query_len #=> "; p hit.query_len
#print " hit.target_id #=> "; p hit.target_id
print " hit.target_def #=> "; p hit.target_def
print " hit.target_len #=> "; p hit.target_len
print " --- first HSP's values (shortcut) ---\n"
print " hit.evalue #=> "; p hit.evalue
print " hit.bit_score #=> "; p hit.bit_score
print " hit.identity #=> "; p hit.identity
#print " hit.overlap #=> "; p hit.overlap
print " hit.query_seq #=> "; p hit.query_seq
print " hit.midline #=> "; p hit.midline
print " hit.target_seq #=> "; p hit.target_seq
print " hit.query_start #=> "; p hit.query_start
print " hit.query_end #=> "; p hit.query_end
print " hit.target_start #=> "; p hit.target_start
print " hit.target_end #=> "; p hit.target_end
print " hit.lap_at #=> "; p hit.lap_at
print " --- first HSP's vaules (shortcut) ---\n"
print " --- compatible/shortcut ---\n"
puts
print " hit.hsps.size #=> "; p hit.hsps.size
if hit.hsps.size == 0 then
puts " (HSP not found: please see blastall's -b and -v options)"
puts
else
puts
print " hit.hsps.each do |hsp|\n"
puts
hit.hsps.each_with_index do |hsp, j|
print "# --- Bio::Blast::Default::Report::HSP (Bio::Blast::Bl2seq::Report::HSP)"
print " ([#{j}])\n"
puts
#print " hsp.num #=> "; p hsp.num
print " hsp.bit_score #=> "; p hsp.bit_score
print " hsp.score #=> "; p hsp.score
print " hsp.evalue #=> "; p hsp.evalue
print " hsp.identity #=> "; p hsp.identity
print " hsp.gaps #=> "; p hsp.gaps
print " hsp.positive #=> "; p hsp.positive
print " hsp.align_len #=> "; p hsp.align_len
#print " hsp.density #=> "; p hsp.density
print " hsp.query_frame #=> "; p hsp.query_frame
print " hsp.query_from #=> "; p hsp.query_from
print " hsp.query_to #=> "; p hsp.query_to
print " hsp.hit_frame #=> "; p hsp.hit_frame
print " hsp.hit_from #=> "; p hsp.hit_from
print " hsp.hit_to #=> "; p hsp.hit_to
#print " hsp.pattern_from#=> "; p hsp.pattern_from
#print " hsp.pattern_to #=> "; p hsp.pattern_to
print " hsp.qseq #=> "; p hsp.qseq
print " hsp.midline #=> "; p hsp.midline
print " hsp.hseq #=> "; p hsp.hseq
puts
print " hsp.percent_identity #=> "; p hsp.percent_identity
#print " hsp.mismatch_count #=> "; p hsp.mismatch_count
#
print " hsp.query_strand #=> "; p hsp.query_strand
print " hsp.hit_strand #=> "; p hsp.hit_strand
print " hsp.percent_positive #=> "; p hsp.percent_positive
print " hsp.percent_gaps #=> "; p hsp.percent_gaps
puts
end #each
end #if hit.hsps.size == 0
end
end
end #ff.each
end #FlatFile.open
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