Sha256: 9321b1e7fa79e9e5ce4620d0165ac41c2bbcbde5240a50dbf1d0edcd26540e79
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Size: 1.17 KB
Versions: 238
Compression:
Stored size: 1.17 KB
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
Description
$ rbbt tsv attach <file1> <file2> [<file3> ...] [options]
Use - to read from STDIN
-f--fields* Fields to attach (all if not specified)
-i--identifiers* Identifier file
-c--complete Complete TSV with keys new in other files
-h--help Print this help
EOF
if options[:help]
if defined? rbbt_usage
rbbt_usage
else
puts SOPT.usage
end
exit 0
end
file1, *rest = ARGV
fields = options[:fields]
identifiers = options[:identifiers]
complete = options[:complete]
if identifiers.nil?
require 'rbbt/sources/organism'
Organism.identifiers(Organism.default_code("Hsa"))
end
fields = fields ? fields.split(/[,|]/).collect{|f| f.strip} : nil
tsv = TSV.open(file1, :unnamed => true)
tsv = tsv.to_double if tsv.type == :flat
rest.each do |file2|
file_fields = TSV.parse_header(file2).all_fields - tsv.all_fields
these_fields = fields ? fields & file_fields : nil
tsv = tsv.attach file2, :fields => these_fields, :identifiers => identifiers, :complete => complete
end
puts tsv.to_s
Version data entries
238 entries across 238 versions & 1 rubygems