Contents

#!/usr/bin/env ruby

require 'rbbt-util'
require 'rbbt/util/simpleopt'

$0 = "rbbt #{$previous_commands*" "} #{ File.basename(__FILE__) }" if $previous_commands

options = SOPT.setup <<EOF

View TSV nicer

$ #{$0} [options] <filename.tsv|->

Use - to read from STDIN

-h--help Print this help

EOF
if options[:help]
  if defined? rbbt_usage
    rbbt_usage 
  else
    puts SOPT.doc
  end
  exit 0
end


file = ARGV.shift

file = STDIN if file == '-' || file.nil?

case
when options[:tokyocabinet]
  tsv = Persist.open_tokyocabinet(file, false)
when options[:tokyocabinet_bd]
  tsv = Persist.open_tokyocabinet(file, false, nil, TokyoCabinet::BDB)
else
  if String === file
    file = file.dup
    Path.setup(File.expand_path(file))
  end
  tsv = file
end

tsv = TSV.open(tsv) if IO === tsv


begin
  require 'rbbt/workflow'
  Workflow.require_workflow "Genomics"
  tsv = Genomics.job(:names, nil, :tsv => tsv).run
rescue
end

puts [Log.highlight(Log.color(:magenta, tsv.key_field)), Log.color(:yellow, tsv.fields * "\t")] * "\t"
TSV.traverse tsv do |k,values,fields|
  fvalues = values.zip(fields).collect do |v,field|
    if String === v
      v = v.to_f.round(2) if v =~ /^-?\d+\.\d+$/
      v = v.to_i if v =~ /^-?\d+$/
    end

    if Numeric === v
      if field =~ /p.?value/i
        v = v.round(4)
        v < 0.05 ? Log.color(:cyan, v.to_s) : v
      else
        v = v.round(2)
        v < 0 ? Log.color(:red, v.to_s) : Log.color(:green, v.to_s)
      end
    else
      v
    end
  end
  puts [Log.color(:magenta, k), fvalues] * "\t"
end

Version data entries

1 entries across 1 versions & 1 rubygems

Version	Path
rbbt-util-5.34.8	share/rbbt_commands/tsv/view