mspire 0.8.6.1 → 0.8.6.2

data/Rakefile

@@ -13,19 +13,18 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems}
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince", "Simon Chiang"]
-  gem.add_dependency "nokogiri", "~> 1.5"
+  gem.add_dependency "nokogiri", "~> 1.5.9"
   gem.add_dependency "bsearch", ">= 1.5.0"
-  gem.add_dependency "andand", ">= 1.3.1"
-  gem.add_dependency "obo", ">= 0.1.0"
-  gem.add_dependency "builder", "~> 3.0.0"
-  gem.add_dependency "bio", "~> 1.4.2"
+  gem.add_dependency "andand", ">= 1.3.3"
+  gem.add_dependency "obo", ">= 0.1.3"
+  gem.add_dependency "builder", "~> 3.2.0"
+  gem.add_dependency "bio", "~> 1.4.3"
   gem.add_dependency "trollop", "~> 2.0.0"
-  gem.add_dependency "uuid", ">= 2.3.5"
   # this should be a real dependency, but need to document getting this
   # working on windows first!
   gem.add_development_dependency "fftw3", "~> 0.3"
-  gem.add_development_dependency "rspec", "~> 2.6"
-  gem.add_development_dependency "jeweler", "~> 1.5.2"
+  gem.add_development_dependency "rspec", "~> 2.13"
+  gem.add_development_dependency "jeweler", "~> 1.8.4"
   #gem.add_development_dependency "rcov", ">= 0"
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.8.6.1
+0.8.6.2

data/lib/mspire/ident/peptide/db/creator.rb

@@ -12,20 +12,19 @@ class Mspire::Ident::Peptide::Db::Creator
 
   DEFAULT_PEPTIDE_CENTRIC_DB = {
     missed_cleavages: 2, 
-    min_length: 4,
+    min_length: 5,
     enzyme: Mspire::Digester[:trypsin], 
     remove_digestion_file: true, 
     cleave_initiator_methionine: true, 
-    expand_aa: true, 
-    uniprot: true 
+    expand_aa: false, 
+    uniprot: true,
+    data_type: :hash,
   }
 
+  # sets defaults according to DEFAULT_PEPTIDE_CENTRIC_DB
   def self.cmdline(argv)
+    opt = DEFAULT_PEPTIDE_CENTRIC_DB.dup
 
-    opt = {
-      :remove_digestion_file => true,
-      :enzyme => Mspire::Digester[:trypsin]
-    }
     opts = OptionParser.new do |op|
       op.banner = "usage: #{File.basename($0)} <file>.fasta ..."
       op.separator "output: "
@@ -40,11 +39,12 @@ class Mspire::Ident::Peptide::Db::Creator
       op.on("--missed-cleavages <#{opt[:missed_cleavages]}>", Integer, "max num of missed cleavages") {|v| opt[:missed_cleavages] = v }
       op.on("--min-length <#{opt[:min_length]}>", Integer, "the minimum peptide aaseq length") {|v| opt[:min_length] = v }
       op.on("--no-cleaved-methionine", "does not cleave off initiator methionine") { opt[:cleave_initiator_methionine] = false }
-      op.on("--no-expand-x", "don't enumerate aa possibilities", "(removes these peptides)") { opt[:expand_aa] = false }
+      op.on("--expand-x", "enumerate all aa possibilities for 'X'", "(default is to remove these peptides)") {|v| opt[:expand_aa] = v }
       op.on("--no-uniprot", "use entire protid section of fasta header", "for non-uniprot fasta files") { opt[:uniprot] = false }
-      op.on("--trie", "use a trie (for very large uniprot files)", "must have fast_trie gem installed") {|v| opt[:trie] = v }
+      #op.on("--trie", "use a trie (for very large uniprot files)", "must have fast_trie gem installed") {|v| opt[:trie] = v }
+      op.on("--data-type <#{opt[:data_type]}>", "hash|google_hash|trie", "need google_hash or fast_trie gem installed") {|v| opt[:data_type] = v.to_sym }
 
-      op.on("-e", "--enzyme <name>", "enzyme for digestion") {|v| opt[:enzyme] = Mspire::Insilico::Digester.const_get(v.upcase) }
+      op.on("-e", "--enzyme <#{opt[:enzyme].name}>", "enzyme for digestion (Mspire::Digester[name])") {|v| opt[:enzyme] = Mspire::Digester[v] }
       op.on("-v", "--verbose", "talk about it") { $VERBOSE = 5 }
       op.on("--list-enzymes", "lists approved enzymes and exits") do
       op.on("-v", "--verbose", "talk about it") { $VERBOSE = 5 }
@@ -101,7 +101,7 @@ class Mspire::Ident::Peptide::Db::Creator
               peptides.select {|pep| pep !~ letters_to_expand_re }
             end
           header = prot.header
-          id = opts[:uniprot] ? Mspire::Fasta.uniprot_id(header) : header.split(/\s+/).first
+          id = opts[:uniprot] ? Mspire::Fasta.uniprot_id(header) : header.split(/\s/,2).first
           fh.puts( id + "\t" + peptides.join(" ") )
         end
       end
@@ -118,11 +118,11 @@ class Mspire::Ident::Peptide::Db::Creator
     puts "Organizing raw digestion #{digestion_file} ..." if $VERBOSE
 
     puts "#{Time.now - start_time} sec" if $VERBOSE
-    hash_like = hash_like_from_digestion_file(digestion_file, opts[:min_length], opts[:trie])
+    hash_like = hash_like_from_digestion_file(digestion_file, opts[:min_length], opts[:data_type])
 
     base = digestion_file.chomp(File.extname(digestion_file))
     final_outfile = 
-      if opts[:trie]
+      if opts[:data_type] == :trie
         base + ".min_aaseq#{opts[:min_length]}"
       else
         base + ".min_aaseq#{opts[:min_length]}" + ".yml"
@@ -131,7 +131,7 @@ class Mspire::Ident::Peptide::Db::Creator
     start_time = Time.now
     print "Writing #{hash_like.size} peptides to #{} ..." if $VERBOSE
 
-      if opts[:trie]
+      if opts[:data_type] == :trie
         trie = hash_like
         trie.save(final_outfile)
       else
@@ -159,8 +159,11 @@ class Mspire::Ident::Peptide::Db::Creator
     Trie.new
   end
 
-  def hash_like_from_digestion_file(digestion_file, min_length, use_trie=false)
-    if use_trie
+  # data_type can be :hash (default), :google_hash (better memory and speed),
+  # or :trie (experimental/broken)
+  def hash_like_from_digestion_file(digestion_file, min_length, data_type=:hash)
+    case data_type
+    when :trie
       trie = get_a_trie
       ::IO.foreach(digestion_file) do |line|
         line.chomp!
@@ -179,8 +182,20 @@ class Mspire::Ident::Peptide::Db::Creator
         end
       end
       trie
-    else
-      hash = Hash.new {|h,k| h[k] = [] }
+    when :hash, :google_hash
+      hash = 
+        case data_type
+        when :hash
+          Hash.new
+        when :google_hash
+          require 'google_hash'
+          # this guy is very slow compared to ruby hash (10X slower?) but more
+          # memory efficient (but only ~10% or so improvement with this
+          # application)
+          GoogleHashDenseRubyToRuby.new
+          # still need to try Sparse one out and compare performance
+          #GoogleHashSparseRubyToRuby.new
+        end
       ::IO.foreach(digestion_file) do |line|
         line.chomp!
         (prot, *peps) = line.split(/\s+/)
@@ -188,7 +203,11 @@ class Mspire::Ident::Peptide::Db::Creator
         peps.uniq!
         peps.each do |pep|
           if pep.size >= min_length
-            hash[pep] << prot
+            if hash.key?(pep)
+              hash[pep] << prot
+            else
+              hash[pep] = [prot]
+            end
           end
         end
       end

data/lib/mspire/imzml/writer.rb

@@ -1,6 +1,6 @@
 
 require 'nokogiri'
-require 'uuid'
+require 'securerandom'
 require 'cv'
 require 'mspire/mzml'
 require 'mspire/mzml/spectrum'
@@ -311,7 +311,7 @@ module Mspire::Imzml
       config[:imzml_filename] = base + ".imzML"
       config[:ibd_filename] = base + ".ibd"
 
-      uuid_with_hyphens = UUID.new.generate
+      uuid_with_hyphens = SecureRandom.uuid
       config[:uuid_hyphenated] = uuid_with_hyphens
       config[:uuid] = uuid_with_hyphens.gsub('-','')
 
@@ -375,7 +375,7 @@ module Mspire::Imzml
       sourcefile_id_to_sourcefile = Hash[ source_files.group_by(&:id).map {|k,v| [k,v.first] } ]
 
       imzml_obj = Mspire::Mzml.new do |imzml|
-        imzml.id = UUID.new.generate.gsub('-','')
+        imzml.id = SecureRandom.uuid.gsub('-','')
         imzml.cvs = Mspire::Mzml::CV::DEFAULT_CVS
 
         imzml.file_description = create_file_description(source_files, config)

data/lib/mspire/mzml/io_index.rb

@@ -39,7 +39,7 @@ module Mspire
       end
 
       def each(&block)
-        return enum_for(__method__) unless block
+        return to_enum(__method__) unless block
         (0...byte_index.size).each do |int|
           block.call(self[int])
         end

data/lib/mspire/mzml/io_indexable_list.rb

@@ -37,7 +37,6 @@ module Mspire
         base.to_sym
       end
 
-
       # method to generate the id_to_index hash from the underlying delegated
       # object.
       def create_id_to_index!

data/lib/mspire/mzml.rb

@@ -119,7 +119,7 @@ module Mspire
       end
 
       def foreach(filename, &block)
-        block or return enum_for(__method__, filename)
+        return to_enum(__method__, filename) unless block
         open(filename) do |mzml|
           mzml.each(&block)
         end

data/script/accession_quantifier.rb

@@ -1,8 +1,10 @@
 #!/usr/bin/env ruby
 
+require 'gnuplot'
 require 'optparse'
 require 'ostruct'
 require 'set'
+require 'array_stats'
 
 require 'mspire/mzml'
 require 'mspire/digester'
@@ -11,8 +13,10 @@ require 'mspire/mascot/dat'
 
 class Array
 
-  def sum
-    inject( nil ) { |sum,x| sum ? sum + x.to_f : x.to_f }
+  alias_method :sum, :total_sum
+
+  def avg
+    sum / array.size
   end
 
   def weighted_mean(weights_array)
@@ -29,6 +33,7 @@ opt = OpenStruct.new( {
   max_rt_after: 60,
   mz_window: 0.01,
   scan_id_regex: Regexp.new("(.*)"),
+  ions_score_cutoff: 15.0,
   # the regex I use:
   #scan_id_regex: Regexp.new("id_([^\\.]+)"),
 } )
@@ -44,6 +49,7 @@ opts = OptionParser.new do |op|
   op.on("--mz_window <#{opt.mz_window}>", Float, "(Th) window around m/z value") {|v| opt.mz_window = v }
   op.on("--scan_id_regex <#{opt.scan_id_regex.source}>", "scan") {|v| opt.scan_id_regex = Regexp.new(v) } 
   op.on("--add-filename", "adds the filename to output files") {|v| opt.add_filename = v }
+  op.on("--ions-score_cutoff <#{opt.ions_score_cutoff}", Float, "minimum ions score") {|v| opt.ions_score_cutoff = v }
 end
 opts.parse!
 
@@ -93,9 +99,9 @@ def create_chromatogram(mzml, index_enum, mz, mz_window, ms_level=1, &block)
   chromatogram
 end
 
-Pephit = Struct.new(:spectrum_id, :exp_mz, :charge, :seq, :accessions, :var_mods_string, :chromatogram)
+Pephit = Struct.new(:spectrum_id, :exp_mz, :charge, :seq, :accessions, :var_mods_string, :chromatogram, :mean_mz, :rt, :rt_start, :rt_end, :num_hits, :file_tic, :ions_score)
 
-pephits = []
+all_pephits = []
 Mspire::Mascot::Dat.open(dat_file) do |dat|
   dat.each_peptide(1) do |pephit|     
     intersecting_accessions = accessions & pephit.protein_hits_info.map(&:accession)
@@ -108,69 +114,122 @@ Mspire::Mascot::Dat.open(dat_file) do |dat|
       if md
         spectrum_id = md[1]
       end
-      pephits << Pephit.new(spectrum_id, exp_mz, z, pephit.seq, intersecting_accessions.to_a, pephit.var_mods_string)
+      if pephit.ions_score > opt.ions_score_cutoff
+        mypephit = Pephit.new(spectrum_id, exp_mz, z, pephit.seq, intersecting_accessions.to_a, pephit.var_mods_string)
+        mypephit.ions_score = pephit.ions_score
+        all_pephits << mypephit
+      end
     end
   end
 end
 
-puts "Found: #{pephits.size} pephits"
-exit unless pephits.size > 0
+# group all_pephits here, then combine if they aren't outliers
+# not a sophisticated algorithm:
+# combine everything that is within the windows specified and with same
+# sequence, charge, or var_mods_string
+pephit_groups = all_pephits.group_by {|pephit| [pephit.seq, pephit.charge, pephit.var_mods_string] }.map do |grouping, pephits|
+  # throw out any peptides that are more than the window edges away from the
+  # mean of the group
+  median_mz = pephits.map(&:exp_mz).median
+  same_mz_pephits = pephits.select {|pephit| (pephit.exp_mz - median_mz).abs <= (opt.mz_window / 2.0) }
+  mean_mz = same_mz_pephits.map(&:exp_mz).mean
+  same_mz_pephits.each {|pephit| pephit.mean_mz = mean_mz }
+  same_mz_pephits.size > 0 ? same_mz_pephits : nil
+end.compact
+
+puts "Found: #{pephit_groups.size} pephit groupings"
+p pephit_groups.first
+
+pephits = Mspire::Mzml.open(mzml_file) do |mzml|
 
-Mspire::Mzml.open(mzml_file) do |mzml|
   spec_index = mzml.index_list[:spectrum]
 
   tic = mzml.map {|spec| spec.fetch_by_acc('MS:1000285').to_f }.reduce(:+)
-  divisor = tic.to_f/1e7
   
   id_to_index = {}
   spec_index.ids.each_with_index {|id,index| id_to_index[id] = index }
 
+  print "." ; $stdout.flush
+  pephit_groups.map do |pephit_group|
+
+    pephit_group.each {|pephit| pephit.rt = mzml[pephit.spectrum_id].retention_time }
+
+    pephit_group.sort_by!(&:rt)
+
+    median_pephit = pephit_group[ pephit_group.size / 2 ]
+    median_rt = median_pephit.rt
+    valid_pephits = pephit_group.select do |pephit| 
+      if pephit.rt <= median_rt
+        (median_rt - pephit.rt) <= opt.max_rt_before
+      else
+        pephit.rt - median_rt <= opt.max_rt_after
+      end
+    end
+
+    valid_rts = valid_pephits.map(&:rt)
+    rep_pephit = median_pephit.dup
+
+    rep_pephit.ions_score = valid_pephits.map(&:ions_score)
+    rep_pephit.file_tic = tic
 
-  pephits.each do |pephit|
-    print "." ; $stdout.flush
+    rep_pephit.rt_start = valid_rts.min - opt.max_rt_before
+    rep_pephit.rt_end = valid_rts.max + opt.max_rt_after
+
+    ms1_spec_id = mzml[rep_pephit.spectrum_id].precursors.first.spectrum_id
 
-    ms1_spec_id = mzml[pephit.spectrum_id].precursors.first.spectrum_id
     index = id_to_index[ms1_spec_id]
     spectrum = mzml[index]
 
-    orig_rt = spectrum.retention_time
-    lo_rt = orig_rt - opt.max_rt_before
-    hi_rt = orig_rt + opt.max_rt_after
+    lo_rt = rep_pephit.rt_start
+    hi_rt = rep_pephit.rt_end
 
-    first_chunk = create_chromatogram(mzml, index.downto(0), pephit.exp_mz, opt.mz_window) {|rt| rt >= lo_rt }
-    last_chunk = create_chromatogram(mzml, (index+1).upto(Float::INFINITY), pephit.exp_mz, opt.mz_window) {|rt| rt <= hi_rt }
+    first_chunk = create_chromatogram(mzml, index.downto(0), rep_pephit.mean_mz, opt.mz_window) {|rt| rt >= lo_rt }
+    last_chunk = create_chromatogram(mzml, (index+1).upto(Float::INFINITY), rep_pephit.mean_mz, opt.mz_window) {|rt| rt <= hi_rt }
 
     chromatogram = (first_chunk + last_chunk).sort
-    chromatogram.each {|pair| pair[1] /= divisor }
 
-    pephit.chromatogram = chromatogram
+    rep_pephit.chromatogram = chromatogram
+    rep_pephit
   end
 end
 puts "finished with mzml"
 
-pephits.group_by {|pephit| [pephit.seq, pephit.charge, pephit.var_mods_string] }.map do |group, sub_pephits|
-  puts "grouping: #{group.join(', ')}"
-  avg_exp_mz = sub_pephits.map(&:exp_mz).reduce(:+) / sub_pephits.size
-  new_chrom = sub_pephits.flat_map(&:chromatogram).uniq.sort
-  cpephit = Pephit.new("(#{sub_pephits.size})", avg_exp_mz, *[:charge, :seq, :accessions, :var_mods_string].map {|key| sub_pephits.first.send(key) }, new_chrom)
-
-  fileparts = [cpephit.seq, cpephit.charge, cpephit.var_mods_string]
+pephits.each do |pephit|
+  fileparts = [:seq, :charge, :var_mods_string].map {|key| pephit.send(key) }
   if opt.add_filename
     fileparts.unshift(dat_file.chomp(File.extname(dat_file)))
   end
-  filename = fileparts.join(".") + ".tsv"
+  base = fileparts.join('.')
+  filename = base + ".tsv"
 
   puts "writing: #{filename}"
   File.open(filename, 'w') do |out|
-    cpephit.each_pair do |k,v|
+    pephit.each_pair do |k,v|
       out.puts "# #{k}: #{v}" unless k.to_sym == :chromatogram
     end
     out.puts
-    out.puts "rt(sec)\tnorm_intensity"
-    cpephit.chromatogram.each do |row|
+    out.puts "rt(sec)\tintensity"
+    pephit.chromatogram.each do |row|
       out.puts row.join("\t")
     end
   end
-end
 
+  xs = pephit.chromatogram.map(&:first)
+  ys = pephit.chromatogram.map(&:last)
+
+  Gnuplot.open do |gp|
+    Gnuplot::Plot.new( gp ) do |plot|
+      plot.title  base
+      plot.xlabel "rt(sec)"
+      plot.ylabel "intensity"
+      plot.terminal "svg"
+      plot.output( base + ".svg" )
+
+      plot.data << Gnuplot::DataSet.new( [xs, ys] ) do |ds|
+        ds.with = "linespoints"
+        ds.notitle
+      end
+    end
+  end
+end
 

data/script/peptide_hit_qvalues_to_spectral_counts_table.rb

@@ -147,6 +147,7 @@ if opt[:qspec] || opt[:descriptions]
   id_to_length = {}
   id_to_desc = {}
   Mspire::Fasta.foreach(opt[:fasta]) do |entry|
+    #acc = Mspire::Fasta.uniprot_id(entry.header)
     acc = entry.accession
     id_to_length[acc] = entry.length
     id_to_desc[acc] = entry.definition[/^\S+\s(.*)/,1]

data/spec/mspire/ident/peptide/db/creator_spec.rb

@@ -34,7 +34,7 @@ describe 'creating a peptide centric database' do
     end
 
     it 'converts a fasta file into peptide centric db' do
-      output_files = Mspire::Ident::Peptide::Db::Creator.cmdline([@fasta_file])
+      output_files = Mspire::Ident::Peptide::Db::Creator.cmdline([@fasta_file, "--min-length", "4"])
       output_files.first.should == File.expand_path(@output_file)
       File.exist?(@output_file).should == true
       hash = {}
@@ -49,7 +49,7 @@ describe 'creating a peptide centric database' do
       #File.unlink(@output_file)
     end
 
-    it 'can use a trie' do
+    xit 'can use a trie' do
       Mspire::Ident::Peptide::Db::Creator.cmdline([@fasta_file, '--trie'])
       triefile = TESTFILES + '/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4'
       %w(.trie .tail .da).each do |ext|

data/spec/mspire/mzml_spec.rb

@@ -326,7 +326,9 @@ describe Mspire::Mzml do
       it 'iterates with foreach' do
         mz_sizes = [20168, 315, 634]
         iter = Mspire::Mzml.foreach(@file)
-        3.times { iter.next.mzs.size.should == mz_sizes.shift }
+        3.times { 
+          iter.next.mzs.size.should == mz_sizes.shift 
+        }
         lambda {iter.next}.should raise_error
       end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.8.6.1
+  version: 0.8.6.2
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-16 00:00:00.000000000 Z
+date: 2013-05-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -19,7 +19,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: 1.5.9
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -27,7 +27,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '1.5'
+        version: 1.5.9
 - !ruby/object:Gem::Dependency
   name: bsearch
   requirement: !ruby/object:Gem::Requirement
@@ -51,7 +51,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.3.1
+        version: 1.3.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -59,7 +59,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.3.1
+        version: 1.3.3
 - !ruby/object:Gem::Dependency
   name: obo
   requirement: !ruby/object:Gem::Requirement
@@ -67,7 +67,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -75,7 +75,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.1.3
 - !ruby/object:Gem::Dependency
   name: builder
   requirement: !ruby/object:Gem::Requirement
@@ -83,7 +83,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 3.0.0
+        version: 3.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -91,7 +91,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 3.0.0
+        version: 3.2.0
 - !ruby/object:Gem::Dependency
   name: bio
   requirement: !ruby/object:Gem::Requirement
@@ -99,7 +99,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.4.2
+        version: 1.4.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -107,7 +107,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.4.2
+        version: 1.4.3
 - !ruby/object:Gem::Dependency
   name: trollop
   requirement: !ruby/object:Gem::Requirement
@@ -124,22 +124,6 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: 2.0.0
-- !ruby/object:Gem::Dependency
-  name: uuid
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 2.3.5
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 2.3.5
 - !ruby/object:Gem::Dependency
   name: fftw3
   requirement: !ruby/object:Gem::Requirement
@@ -163,7 +147,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.6'
+        version: '2.13'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -171,7 +155,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '2.6'
+        version: '2.13'
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
@@ -179,7 +163,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.5.2
+        version: 1.8.4
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -187,7 +171,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.5.2
+        version: 1.8.4
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com