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Versions: 16
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Contents
#!/usr/bin/env ruby
require 'mspire/mzml'
require 'optparse'
# returns '3+' for 3 or '2-' for -2
def mascot_charge(val)
"#{val}#{val > 0 ? '+' : '-'}"
end
opt = {
filter_zero_intensity: true,
retention_times: true,
}
opts = OptionParser.new do |op|
op.banner = "usage: #{File.basename($0)} <file>.mzML ..."
op.separator "outputs: <file>.mgf"
op.on("--no-filter-zeros", "won't remove values with zero intensity") {|v| opt[:filter_zero_intensity] = false }
# the default is set in ms/msrun/search.rb -> set_opts
op.on("--no-retention-times", "won't include RT even if available") {|v| opt[:retention_times] = false }
end
opts.parse!
if ARGV.size == 0
puts opts
exit
end
filter_zeros = opt[:filter_zero_intensity]
ARGV.each do |file|
basename = file.chomp(File.extname(file))
outfile = basename + ".mgf"
File.open(outfile, 'w') do |out|
Mspire::Mzml.foreach(file).with_index do |spectrum,i|
next unless spectrum.ms_level > 1
out.puts "BEGIN IONS"
# id, spectrumid,
rt = spectrum.retention_time
title_ar = [i, "id_#{spectrum.id}"]
title_ar.push("rt_#{rt.round}") if opt[:retention_times]
title = title_ar.join('.')
out.puts "TITLE=#{title}"
out.puts "RTINSECONDS=#{rt}" if opt[:retention_times]
out.puts "PEPMASS=#{spectrum.precursor_mz}"
if z=spectrum.precursor_charge
out.puts "CHARGE=#{mascot_charge(z)}"
end
spectrum.each do |mz,int|
unless filter_zeros && (int==0.0)
out.puts([mz, int].join(" "))
end
end
out.puts "END IONS"
out.puts ""
end
end
end
Version data entries
16 entries across 16 versions & 1 rubygems