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#!/usr/bin/env ruby
require_relative "fasta"
def print_wildcard_replace(seq, linelength, fp=STDOUT)
pos = 0
while pos < seq.length do
fp.puts replacewildcards(seq[pos..pos+linelength-1])
pos += linelength
end
end
def convert2myersformat(header, length, id)
new_header = ">m000000_000000_00000_c1898213712391273/#{id}/0_#{length}"
return header.sub(/^\S+/, new_header)
end
# Replace all non-DNA characters by randomly chosen DNA characters (a,c,g,t).
def replacewildcards(seq)
bases = ['a', 'c', 'g', 't']
finished = seq.sub!(/[^acgtACGT]/, bases.sample).nil? until finished
return seq
end
# read all files and output them verbatim on lines of width 70
if __FILE__ == $0
ARGV.each do |filename|
id = 0
Fasta.read_multi_file(filename) do |entry|
puts "#{convert2myersformat(entry.get_header(), entry.get_seqlength(), id)}"
print_wildcard_replace(entry.get_sequence(),70)
id += 1
end
end
end
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