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#!/usr/bin/env ruby
require "set"
def getselectedseqnums(numofsequences,numtoselect)
if numofsequences < numtoselect
STDERR.puts "#{$0}: cannot select #{numotoselect} sequences from file " +
"#{inputfile}: this contains #{numofsequences} sequences"
exit 1
end
selectedseqnums = Set.new
loop do
idx = rand(numofsequences)
if not selectedseqnums.member?(idx)
selectedseqnums.add(idx)
if selectedseqnums.size == numtoselect
break
end
end
end
return selectedseqnums
end
def countnumofsequences(inputfile)
seqcount = 0
File.open(inputfile).each_line do |line|
if line.match(/^>/)
seqcount+=1
end
end
return seqcount
end
def outputselectedsequences(selectedseqnums,inputfile,fp=STDOUT)
currentseqnum = 0
dooutseq = false
File.open(inputfile).each_line do |line|
if line.match(/^\s*$/) # discard blank line
next
elsif line.match(/^\s*#/) # discard comment line
next
elsif line.match(/^>/)
if selectedseqnums.member?(currentseqnum)
dooutseq = true
else
dooutseq = false
end
currentseqnum += 1
end
if dooutseq
fp.print line
end
end
end
if ARGV.length != 2
STDERR.puts "Usage: #{$0} <num of seq to select> <fastafile>"
exit 1
end
numtoselect = ARGV[0].to_i
inputfile = ARGV[1]
numofsequences = countnumofsequences(inputfile)
srand(37739292920)
selectedseqnums = getselectedseqnums(numofsequences,numtoselect)
outputselectedsequences(selectedseqnums,inputfile)
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