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Contents
#
# = bio/appl/blast/format8.rb - BLAST tab-delimited output (-m 8) parser
#
# Copyright:: Copyright (C) 2002, 2003, 2007 Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
# $Id:$
#
# == Note
#
# This file is automatically loaded by bio/appl/blast/report.rb
#
module Bio
class Blast
class Report
private
def tab_parse(data)
iteration = Iteration.new
@iterations.push(iteration)
@query_id = @query_def = data[/\S+/]
query_prev = ''
target_prev = ''
hit_num = 1
hsp_num = 1
hit = ''
data.each_line do |line|
ary = line.chomp.split("\t")
query_id, target_id, hsp = tab_parse_hsp(ary)
if query_prev != query_id or target_prev != target_id
hit = Hit.new
hit.num = hit_num
hit_num += 1
hit.query_id = hit.query_def = query_id
hit.accession = hit.definition = target_id
iteration.hits.push(hit)
hsp_num = 1
end
hsp.num = hsp_num
hsp_num += 1
hit.hsps.push(hsp)
query_prev = query_id
target_prev = target_id
end
end
def tab_parse_hsp(ary)
query_id, target_id,
percent_identity,
align_len,
mismatch_count,
gaps,
query_from,
query_to,
hit_from,
hit_to,
evalue,
bit_score = *ary
hsp = Hsp.new
hsp.align_len = align_len.to_i
hsp.gaps = gaps.to_i
hsp.query_from = query_from.to_i
hsp.query_to = query_to.to_i
hsp.hit_from = hit_from.to_i
hsp.hit_to = hit_to.to_i
hsp.evalue = evalue.strip.to_f
hsp.bit_score = bit_score.to_f
hsp.percent_identity = percent_identity.to_f
hsp.mismatch_count = mismatch_count.to_i
return query_id, target_id, hsp
end
end
end
end
Version data entries
29 entries across 29 versions & 4 rubygems