Created
August 9, 2012 12:56
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Reading BLAST result table (fmt6,7) and add description of target seq referring blastdb
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| $infile = ARGV[0] | |
| $blastdb = ARGV[1] | |
| $keypos = (ARGV[2] || 1).to_i | |
| =begin | |
| counter = Hash.new(0) | |
| File.open($infile).each do |l| | |
| next if /^\#/.match(l) | |
| a = l.chomp.split(/\t/) | |
| tophit = a[2] | |
| counter[tophit] += 1 | |
| end | |
| =end | |
| class DeflineParser | |
| def initialize | |
| # @entry_id = nil | |
| # @desc = nil | |
| # @species = nil | |
| end | |
| attr_accessor :entry_id, :desc, :species | |
| def parse(line, opt={}) | |
| comment = line.sub(/^>/, "") | |
| m = /^(\S+?)\s+(.+)$/.match(comment) | |
| entry_id = m[1] | |
| desc = m[2] | |
| entry_id.sub!(/^lcl\|/, "") | |
| h = { | |
| 'entry_id' => entry_id, | |
| 'comment' => comment, | |
| 'desc' => desc} | |
| end | |
| end | |
| class DPSilva < DeflineParser | |
| def parse(line) | |
| h = super | |
| tmp = h['desc'].split(/;/).last | |
| if m = /(.+)\s*\((.+)\)/.match(tmp) | |
| species = m[1] | |
| common_name = m[2] | |
| else | |
| species = tmp.strip | |
| common_name = nil | |
| end | |
| h.update({'species' => species, 'common_name' => common_name}) | |
| h | |
| end | |
| end | |
| dp = DeflineParser.new | |
| cache = Hash.new | |
| File.open($infile).each do |l| | |
| # p l | |
| next if /^#/.match(l) | |
| a = l.chomp.split(/\t/) | |
| target_id = a[$keypos] | |
| # p target_id | |
| unless cache[target_id] | |
| cmd = "fastacmd -d #{$blastdb} -s \"#{target_id}\" | head -1" | |
| res = nil | |
| IO.popen(cmd){|io| res = io.read} | |
| # p res | |
| h = dp.parse(res) | |
| cache[target_id] = h | |
| end | |
| data = cache[target_id] | |
| outdat = a | |
| # p outdat | |
| outdat += [data['entry_id'], data['desc']] | |
| puts outdat.flatten.join("\t") | |
| end |
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