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#!/usr/bin/env ruby
require 'optparse'
require 'ostruct'
Sortinfo = Struct.new("Sortinfo",:len,:seqnum,:startfwdstrand)
def line2sortinfo(line)
arr = line.split(/\s/)
return Sortinfo.new(arr[4].to_i,arr[5].to_i,arr[6].to_i)
end
def compare_matches(line0,line1)
sortinfo0 = line2sortinfo(line0)
sortinfo1 = line2sortinfo(line1)
if sortinfo0.seqnum < sortinfo1.seqnum or
(sortinfo0.seqnum == sortinfo1.seqnum and
sortinfo0.startfwdstrand + sortinfo0.len <=
sortinfo1.startfwdstrand + sortinfo1.len)
return -1
end
return 1
end
def parseargs(argv)
options = OpenStruct.new
options.inputfile = nil
opts = OptionParser.new()
opts.on("-c","--check","check order") do |x|
options.check = true
end
opts.on( '-h', '--help', 'Display this screen' ) do
puts "Usage: #{$0} [options] [inputfile]"
puts "read matches from file or STDIN and sort them in ascending order of\nquery numbers. Matches on the same query are sorted in ascending order of the end position in query"
exit 0
end
rest = opts.parse(argv)
if rest.length == 1
options.inputfile = rest[0]
elsif rest.length > 1
STDERR.puts options.banner
exit 1
end
return options
end
def matches_checkorder(fpin)
previousline = nil
fpin.each_line do |line|
if line.match(/^[0-9]/)
if not previousline.nil? and compare_matches(previousline,line) > 0
STDERR.puts "#{previousline.chomp} >\n#{line}"
exit 1
end
previousline = line
end
end
end
def matches_orderedoutput(fpin)
header = Array.new()
headercomplete = false
footer = Array.new()
matchlines = Array.new()
fpin.each_line do |line|
if line.match(/^#/)
if not line.match(/^# seed/)
if headercomplete
footer.push(line)
else
header.push(line)
end
end
elsif line.match(/^[0-9]/)
headercomplete = true
matchlines.push(line)
end
end
matchlines.sort! {|a,b| compare_matches(a,b)}
puts header
puts matchlines
puts footer
end
options = parseargs(ARGV)
if options.inputfile.nil?
fpin = STDIN
else
begin
fpin = File.new(options.inputfile,"r")
rescue => err
STDERR.puts "#{$0}: cannot open #{options.inputfile}: #{err}"
exit 1
end
end
if options.check
matches_checkorder(fpin)
else
matches_orderedoutput(fpin)
end
if not options.inputfile.nil?
fpin.close_read
end
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