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#!/usr/bin/env ruby
require_relative "fasta"
require_relative "print_sequence"
def cutsinglesequence(sequence,header,maxnumber,minlength,
maxlength,linelength)
pos = 0
count = 0
remaininglength = sequence.length
while pos < sequence.length and remaininglength >= minlength do
puts ">#{header}"
print_sequence(sequence[pos..pos+maxlength-1],linelength)
pos += maxlength
remaininglength -= maxlength
count += 1
if count >= maxnumber
break
end
end
return count
end
def cutsequences(inputfile,maxnumber,minlength,maxlength)
count = 0
linelength = 70
count = 0
Fasta.read_multi_file(inputfile) do |curr_entry|
len = curr_entry.get_seqlength()
if len >= minlength
sequence = curr_entry.get_sequence()
header = curr_entry.get_header()
if len > maxlength
count += cutsinglesequence(sequence,header,maxnumber,minlength,
maxlength,linelength)
else
puts ">#{header}"
print_sequence(sequence,linelength)
end
if count >= maxnumber
break
end
end
end
end
if __FILE__ == "#{$0}"
if ARGV.length != 4
STDERR.puts "Usage: #{$0} <inputfile> <maxnumber|all> <minlength> <maxlength>"
exit 1
end
inputfile = ARGV[0]
if ARGV[1] == "all"
maxnumber = INT_MAX
else
maxnumber = ARGV[1].to_i
end
minlength = ARGV[2].to_i
maxlength = ARGV[3].to_i
cutsequences(inputfile,minlength,maxlength)
end
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