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| #!/usr/bin/env ruby | |
| require 'rubygems' | |
| require 'active_support/core_ext/hash/conversions' | |
| require 'open-uri' | |
| require 'json' | |
| require 'yaml' | |
| require 'pp' | |
| infile = ARGV[0] | |
| outfmt = (ARGV[1] || 'simple') | |
| def print_usage | |
| puts "Usage: " | |
| puts "" | |
| puts " #{$0} runParameters.xml [outfmt]" | |
| puts "" | |
| puts " runParameters.xml: file or URL(http://~)" | |
| puts " outfmt: json, json_pretty, yaml, ruby, or simple" | |
| puts " (default = simple)" | |
| puts "" | |
| exit | |
| end | |
| def convert(h, format) | |
| case format | |
| when 'json' | |
| json = h.to_json | |
| puts json | |
| when 'json_pretty' | |
| puts JSON.pretty_generate(h) | |
| when 'yaml' | |
| yaml = h['RunParameters']['Setup'].to_yaml | |
| puts yaml | |
| when 'simple' | |
| hh = h['RunParameters']['Setup'] | |
| h2 = Hash.new | |
| h2['RunID'] = hh['RunID'] | |
| date = Date.parse(hh['RunStartDate']).to_s | |
| h2['RunStartDate'] = date | |
| h2['RunMode'] = hh['RunMode'] | |
| h2['SeqType'] = (hh['PairEndFC'] == 'true' ? "Paired-end" : "Single-read") | |
| h2['ReadPattern'] = "Read1:#{hh['Read1']} + Index1:#{hh['IndexRead1']}" | |
| h2['ReadPattern'] += " + Index2:#{hh['IndexRead2']}" unless hh['IndexRead2'] == '0' | |
| h2['ReadPattern'] += " + Read2:#{hh['Read2']}" unless hh['Read2'] == '0' | |
| h2['ClusteringChoice'] = hh['ClusteringChoice'] | |
| h2['Flowcell'] = hh['Flowcell'] | |
| h2['Sbs'] = hh['Sbs'] | |
| h2['Index'] = hh['Index'] | |
| puts h2.to_yaml | |
| when 'ruby' | |
| pp h['RunParameters']['Setup'] | |
| else | |
| raise "No outfmt option" | |
| end | |
| end | |
| unless infile | |
| print_usage | |
| end | |
| xml = nil | |
| if /^http:.+\.xml/.match(infile) | |
| uri = infile | |
| xml = open(uri).read | |
| else | |
| xml = File.open(infile).read | |
| end | |
| h = Hash.from_xml(xml) | |
| puts "# source: #{infile}" | |
| puts "" | |
| convert(h, outfmt) |
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