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Contents
#!/usr/bin/env ruby
require 'optparse'
require 'bio'
require 'csv'
#$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
#$: << File.expand_path('.')
#path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polyploid-tools.rb')
#require path
options = {}
options[:identity] = 50
options[:min_bases] = 200
options[:blastx] = "-"
OptionParser.new do |opts|
opts.banner = "Usage: filter_blat.rb [options]"
opts.on("-p", "--blastx FILE", "BLAST XML file") do |o|
options[:blastx] = o
end
opts.on("-i", "--identity FLOAT", "Minimum percentage identity") do |o|
options[:identity] = o.to_f
end
opts.on("-c", "--min_bases int", "Minimum alignment length (default 200)") do |o|
options[:min_bases] = o.to_i
end
opts.on("-t", "--triads FILE", "CSV file with the gene triad names in the named columns 'A','B' and 'D' ") do |o|
options[:triads] = o
end
end.parse!
valid_pairs_A_B = Hash.new
valid_pairs_A_D = Hash.new
valid_pairs_B_D = Hash.new
CSV.foreach(options[:triads], headers:true ) do |row|
valid_pairs_A_B[row['A']] = row['B']
valid_pairs_A_D[row['A']] = row['D']
valid_pairs_B_D[row['B']] = row['D']
end
stream = ARGF
stream = IO.open(options[:blastx]) unless options[:blastx] == "-"
puts "Loaded #{valid_pairs_B_D.length} triads"
$stdout.flush
blast_report = Bio::FlatFile.new(Bio::Blast::Report, stream)
blast_report.each_entry do |report|
puts "Hits for " + report.query_def + " against " + report.db
$stdout.flush
report.each do |hit|
query = hit.query_id.split("-")[0]
target = hit.target_id.split("-")[0]
if valid_pairs_A_B[query] == target or valid_pairs_A_D[query] == target or valid_pairs_B_D[query] == target
puts hit.target_id, "\t", hit.evalue, "\n" if hit.evalue < 0.001
puts hit.inspect
end
end
end
stream.close unless options[:blat_file] == "-"
Version data entries
29 entries across 29 versions & 1 rubygems