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Contents
#!/usr/bin/env ruby
require 'rbbt-util'
require 'rbbt/util/simpleopt'
options = SOPT.setup <<EOF
Change the ID format of a column in a tsv file
$ rbbt command command [options] -f file
Use - to read from STDIN. The `field` is the tsv column to change.
the `target` is the target format, as appearing in the `identifiers`
file or in `Organism.identifiers(Organism.default_code("Hsa"))`.
-f--file* File to process
-f--field* Field to change
-t--target* Target format
-i--identifiers* Identifier file to use
-h--help Help
EOF
rbbt_usage and exit 0 if options[:help]
SOPT.require options, :file, :field, :target
require 'rbbt/sources/organism'
identifiers = options[:identifiers] || Organism.identifiers(Organism.default_code("Hsa")).find
begin
index = TSV.index(identifiers, :persist => true, :target => target, :merge => true)
rescue
raise ParameterException, "Could not build index for '#{target}': #{ identifiers }"
end
tsv = TSV.open file
tsv.process field do |value|
if Array === value
index.values_at *value
else
index[value]
end
end
tsv.fields = tsv.fields.collect{|f| f == field ? target : f}
puts tsv
Version data entries
710 entries across 710 versions & 1 rubygems