mzid

ruby parser library for mzIdentML files

gem install mzid

A command line utility is provided to convert from mzid to csv, an example:

$ convert_mzid_to_csv.rb test.mzid -v -m 
DBSeq:         100% |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooo| Time:   0:00:01
Peptides:      100% |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooo| Time:   0:00:01
PepEv:         100% |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooo| Time:   0:00:01
Spectra:       100% |oooooooooooooooooooooooooooooooooooooooooooooooooooooooooo| Time:   0:00:02

this results in a file named test.csv since one was not explicitly provided.

parsing the output of an mzid file can be done in a simple block:

require 'mzid'

parser = MzID::Parser.new("output.mzid")
parser.each_psm do |spec_id|
  puts [spec_id.get_id, spec_id.get_pep, spec_id.get_spec_prob].join("\t")
end

alternatively, one can also specify a more memory-efficient parser for large files, reformatting their output into an easily parsable csv file:

parser = MzID::ParserSax.new("output.mzid")
parser.write_to_csv("output.csv")

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