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#!/usr/bin/env ruby
#
# Copyright (c) 2009 Sascha Steinbiss <steinbiss@zbh.uni-hamburg.de>
# Copyright (c) 2009 Center for Bioinformatics, University of Hamburg
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
#
def each_seq(filename)
File.open(filename) do |file|
(farr = file.read.split(">")).each do |fitem|
seq = fitem.split("\n")
fline = seq.shift
next if fline.nil?
sequence = seq.collect{|l| l.chomp}.join
yield fline, sequence
end
end
end
if ARGV.length != 1 then
STDERR.puts "Usage: #{$0} <FASTA file>"
exit 1
end
j=0
begin
each_seq(ARGV[0]) do |header, seq|
# break up headers into words and create description lines not longer than
# 70 characters of length
hlines = [[]]
llen = 0
lineno = 0
header.chomp.split(/\s+/).each do |word|
if llen + word.length + 1 > 70
hlines.push([])
lineno += 1
llen = 0
end
hlines[lineno].push(word)
llen += word.length + 1
end
i=1
puts "ID sequence#{j}"
puts "XX"
hlines.each do |hline|
puts "DE #{hline.join(" ")}"
end
puts "XX"
puts "SQ"
print " "
seq.each_byte do |c|
putc c
if i % 10 == 0 then
print " "
end
if i % 60 == 0 then
printf("%9s\n ", i)
end
i += 1
end
printf(' '*(80-i%60-(i%60)/10-13) + "%9d\n", i-1)
puts "//\n\n"
j+=1
end
rescue StandardError => msg
STDERR.puts "Error: #{msg}"
exit 1
end
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