Sha256: 9bf2a5935b42939fe04b914f1928d3ae608f2f99174cc4b88a3116158e2ed31a
Contents?: true
Size: 873 Bytes
Versions: 19
Compression:
Stored size: 873 Bytes
Contents
#!/usr/bin/ruby
if ARGV.size == 0
puts "usage: #{File.basename(__FILE__)} <file>.fasta ..."
puts "outputs: <file>_NCBI.fasta ..."
puts ""
puts "(Bioworks 3.3.1 [maybe others] does not seem to read an IPI"
puts "formatted fasta database header lines. This will change an"
puts "IPI format to an NCBI style format that Bioworks can read."
exit
end
ARGV.each do |file|
base = file.chomp(File.extname(file))
outfile = base + '_NCBI' + ".fasta"
File.open(outfile, 'w') do |out|
IO.foreach(file) do |line|
if line =~ /^>/
(codes, *description) = line[1..-1].split(" ")
description = description.join(" ")
code_section = codes.split('|').map {|code| (key, val) = code.split(':') ; "#{key}|#{val}|" }.join
out.puts ">#{code_section} #{description}"
else
out.print line
end
end
end
end
Version data entries
19 entries across 19 versions & 2 rubygems