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An mspire library for working with SEQUEST related data (.srf files, .sqt files, etc).
Ruby
Branch: master

README.rdoc

mspire-sequest

An mspire library supporting SEQUEST, Bioworks, SQT and associated formats.

Current API

Cite

Prince JT, Marcotte EM. mspire: mass spectrometry proteomics in Ruby. Bioinformatics. 2008 Dec 1;24(23):2796-7. (pubmed)

Examples

Provides three executables for extracting information from an Srf file (run without file for usage):

srf_to_sqt.rb file.srf     # => file.sqt
srf_to_search.rb file.srf  # => file.mgf  (also can make .dta files)
srf_to_pepxml.rb file.srf  # => file.xml  (pepxml file)

Mspire::Sequest::Srf

Can read and convert Bioworks Sequest Results Files (SRF).

require 'mspire/sequest/srf'
srf = Mspire::Sequest::Srf.new("file.srf")

Conversions (see api for options):

require 'mspire/sequest/srf/sqt'  # require this in addition to 'mspire/sequest/srf'
srf.to_sqt            # (outputs a file) -> file.sqt

require 'mspire/sequest/srf/search' # require this in addition to 'mspire/sequest/srf'
srf.to_mgf            # (outputs a file) -> file.mgf
srf.to_dta            # (outputs a dir)  -> file
srf.to_dta("file.tgz", :tgz)  # on the fly tgz (requires archive-tar-minitar)

require 'mspire/sequest/srf/pepxml' # require this in addition to 'mspire/sequest/srf'
srf.to_pepxml # (outputs a file) -> file.xml

Object access (see Mspire::Sequest::Srf for much more):

srf.header         # Mspire::Sequest::Srf::Header object
srf.params         # Mspire::Sequest::Params object
srf.dta_files      # Mspire::Sequest::Srf::Dta objects
srf.out_files      # Mspire::Sequest::Srf::Out objects
srf.peptide_hits   # Mspire::Sequest::Srf::Out::Peptide objects

Mspire::Sequest::Params

Object or hash access to any parameter in the file. Also provides a unified interface across several versions (3.1 - 3.3)

require 'mspire/sequest/params'
params = Mspire::Sequest::Params.new("sequest.params")
params.any_existing_param    # -> some value or empty string if no value
params['any_existing_param'] # -> some value or empty string if no value
params.non_existent_param    # -> nil

# some unified interace methods:
params.enzyme              # -> enzyme name with no parentheses
params.database            # -> first_database_name
params.enzyme_specificity  # -> [offset, cleave_at, expect_if_after]
params.precursor_mass_type  # => "average" | "monoisotopic"
params.fragment_mass_type   # => "average" | "monoisotopic"

Mspire::Sequest::Sqt

sqt = Mspire::Sequest::Sqt.new("file.sqt")
sqt.header
sqt.spectra.each do |spectrum|      # an Mspire::Sequest::Sqt::Spectrum object
  spectrum.matches.each do |match|    # an Mspire::Sequest::Sqt::Match object
    match.loci.each do |locus|          # an Mspire::Sequest::Sqt::Locus object
    end
  end
end

# or more direct access to Match objects:
sqt.peptide_hits

Also reads Percolator SQT output files

psqt = Mspire::Sequest::Sqt.new("percolator_output.sqt")
psqt.peptide_hits.each do |pmatch|
  pmatch.percolator_score  ==  pmatch.xcorr
  pmatch.negative_q_value  ==  pmatch.sp
  pmatch.q_value           ==  -pmatch.negative_q_value 
end

Installation

gem install mspire-sequest

Copyright

See LICENSE (MIT)

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