Sort a list of genetic variants by chromosomal position

sort_variants.rb

# Sorts a file by chromosomal position
# 
# Input file must have the following format:
# - Column 1: chromosome (e.g. chr1, chr10 *OR* 1, 10)
# - Column 2: start position (e.g. 4325484)
# - All other columns can be ordered in any way
#
# Input file sample:
#   chr17:5432542:G>A     .........
#   17:5432542:G>A        .........
#   chr17  5432542  G  A  .........
#   17  5432542  G  A     .........
#   17,5432542,G,A        .........
# DO NOT USE SPACES! TABS ARE THE ONLY WHITESPACE-DELIMITER ALLOWED!
#
# Example usage (INPUT FILE HAS A HEADER):
#   ruby sort_variants.rb input.txt > output.txt
#   
# Example usage (INPUT FILE HAS *NO* HEADER):
#   ruby sort_variants.rb --no-header input.txt > output.txt
#   ruby sort_variants.rb -n input.txt > output.txt

if ARGV.include?("--no-header") || ARGV.include?("-n")
  # This file does NOT include a header...
  ARGV.delete("--no-header")
  ARGV.delete("-n")
  HEADER = false
else
  # This file includes a header...
  HEADER = true
end

F_IN = ARGV[0]

# Get proper dilimiters from 2nd line
line = `tail -n+2 #{F_IN} | head -n1`.chomp
delim1,delim2,delim3,delim4 = line.scan(/[:>,\t]/)

# If delim2/delim3/delim4 don't exist, just use a space
delim2 = ' ' if delim2.nil?
delim3 = ' ' if delim3.nil?
delim4 = ' ' if delim4.nil?

# Set input
if HEADER
  # Print header
  puts `head -1 #{F_IN}`
  # Input all file contents except header
  INPUT = "tail -n+2 #{F_IN}"
else
  # Input all file contents
  INPUT = "cat #{F_IN}"
end

# To sort:
# 1.) Replace all delimiters with spaces so that
#     Linux sort works reliably
# 2.) Sort on 1st, then 2nd, then 3rd, then 4th,
#     then 5th-and-so-on fields
# 3.) Replace all spaces with original delimiters
puts `
  #{INPUT} \
  | sed 's/#{delim1}/ /' \
  | sed 's/#{delim2}/ /' \
  | sed 's/#{delim3}/ /' \
  | sed 's/#{delim4}/ /' \
  | sort -k1,1d -k2,2n -k3,3d -k4,4d -k5d \
  | sed 's/ /#{delim1}/' \
  | sed 's/ /#{delim2}/' \
  | sed 's/ /#{delim3}/' \
  | sed 's/ /#{delim4}/'
`