differential_expression_scripts/compare_fold_changes at develop · khayer/differential_expression_scripts · GitHub

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#!/usr/bin/env ruby
require 'csv'

usage =<<EOF

      #{$0} in.csv col1 col2 col3 col4 out.csv

      ------------------------------------------------------
      * in.csv   :: in_csv_file
      * col1     :: e.g. "log2_FC:MUTAS|MUTPS"
      * col2     :: e.g. "log2_FC:SIBAS|SIBPS"
      * col3     :: e.g. "UCount_MUTAS"
      * col4     :: e.g. "UCount_MUTPS"
      * col5     :: e.g. "UCount_SIBAS"
      * col6     :: e.g. "UCount_SIBPS"
      * out.csv  :: out_csv_file
      ------------------------------------------------------

      - VERSION 5/16/2013 ----------------------------------

      Note: only works with output of add_refseq_gen_names
      script (CVS_file)

      ------------------------------------------------------

                                                       by khayer

EOF

if ARGV.length != 8
  puts usage
  exit
end

in_csv_file = ARGV[0]
col1 = ARGV[1]
col2 = ARGV[2]
c_MUTAS = ARGV[3]
c_MUTPS = ARGV[4]
c_SIBAS = ARGV[5]
c_SIBPS = ARGV[6]
out_csv_file = ARGV[7]

i = 0
stddev = 1.5
CSV.open(out_csv_file, "wb") do |csv|
  csv << ["GeneID","GenName",
    "FC:MUTAS|MUTPS-FC:SIBAS|SIBPS","logRPKM_MUTAS",
    "logRPKM_MUTPS","logRPKM_SIBAS","logRPKM_SIBPS",
    "FC:MUTAS|SIBAS","log2_FC:MUTAS|SIBAS",
    "FC:MUTPS|SIBPS","log2_FC:MUTPS|SIBPS",
    "FC:MUTAS|MUTPS","log2_FC:MUTAS|MUTPS",
    "FC:SIBAS|SIBPS","log2_FC:SIBAS|SIBPS",
    "UCount_MUTAS","UCount_MUTPS","Ucount_SIBAS",
    "UCount_SIBPS"]
  CSV.foreach(in_csv_file, headers: true) do |row|

    next if (row[col1].to_f - row[col2].to_f).abs < 1.0
    #puts row[col1].to_f - row[col2].to_f
    #puts row["GeneID"]
    #puts row[col1]
    #puts row[col2]
    #STDIN.gets
    #if i == 100
    #  STDIN.gets
    #  i = 0
    #end
    #i += 1
    diff = (row[col1].to_f - row[col2].to_f).abs
    csv << [row["GeneID"],row["GenName"],diff,
      row["logRPKM_MUTAS"],
      row["logRPKM_MUTPS"],row["logRPKM_SIBAS"],
      row["logRPKM_SIBPS"],row["FC:MUTAS|SIBAS"],
      row["log2_FC:MUTAS|SIBAS"],row["FC:MUTPS|SIBPS"],
      row["log2_FC:MUTPS|SIBPS"],row["FC:MUTAS|MUTPS"],
      row["log2_FC:MUTAS|MUTPS"],row["FC:FC:SIBAS|SIBPS"],
      row["log2_FC:SIBAS|SIBPS"],row["UCount_MUTAS"],
      row["UCount_MUTPS"],row["Ucount_SIBAS"],
      row["UCount_SIBPS"]]
  end
end