ms-sequest 0.0.24 → 0.1.0

data/History

@@ -1,3 +1,7 @@
+== 0.1.0 / 2011-04-11
+
+* moved Arrayclass objects to Struct objects
+
 == 0.0.15 / 2010-08-25
 
 * Fixed another bug in the srf_to_sqt.rb commandline when called without an output file

data/Rakefile

@@ -1,12 +1,4 @@
 require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
 require 'rake'
 
 require 'jeweler'
@@ -19,7 +11,13 @@ Jeweler::Tasks.new do |gem|
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince"]
   gem.rubyforge_project = 'mspire'
-  # include dependencies in Gemfile
+  gem.add_runtime_dependency "ms-ident", ">= 0.0.20"
+  gem.add_runtime_dependency "ms-core", ">= 0.0.17"
+  #gem.add_runtime_dependency "ms-msrun", ">= 0.3.4"
+  gem.add_runtime_dependency "trollop", "~> 1.16"
+  gem.add_development_dependency "jeweler", "~> 1.5.2"
+  gem.add_development_dependency "ms-testdata", ">= 0.1.1"
+  gem.add_development_dependency "spec-more", ">= 0"
 end
 Jeweler::RubygemsDotOrgTasks.new
 
@@ -30,12 +28,12 @@ Rake::TestTask.new(:spec) do |spec|
   spec.verbose = true
 end
 
-require 'rcov/rcovtask'
-Rcov::RcovTask.new do |spec|
-  spec.libs << 'spec'
-  spec.pattern = 'spec/**/*_spec.rb'
-  spec.verbose = true
-end
+#require 'rcov/rcovtask'
+#Rcov::RcovTask.new do |spec|
+#  spec.libs << 'spec'
+#  spec.pattern = 'spec/**/*_spec.rb'
+#  spec.verbose = true
+#end
 
 task :default => :spec
 

data/VERSION

@@ -1 +1 @@
-0.0.24
+0.1.0

data/lib/ms/sequest/bioworks.rb

@@ -378,7 +378,7 @@ class Bioworks::Prot
   end
 end
 
-Bioworks::Pep = Arrayclass.new( %w(sequence mass deltamass charge xcorr deltacn sp rsp ions count tic prots base_name first_scan last_scan peptide_probability file _num_prots _first_prot aaseq) )
+Bioworks::Pep = Struct.new( *%w(sequence mass deltamass charge xcorr deltacn sp rsp ions count tic prots base_name first_scan last_scan peptide_probability file _num_prots _first_prot aaseq).map(&:to_sym) )
 # 0=sequence 1=mass 2=deltamass 3=charge 4=xcorr 5=deltacn 6=sp 7=rsp 8=ions 9=count 10=tic 11=prots 12=base_name 13=first_scan 14=last_scan 15=peptide_probability 16=file 17=_num_prots 18=_first_prot 19=aaseq
 
 class Bioworks::Pep

data/lib/ms/sequest/sqt.rb

@@ -5,7 +5,6 @@ require 'set'
 require 'ms/fasta'
 require 'digest/md5'
 
-
 require 'ms/ident/peptide'
 require 'ms/ident/search'
 
@@ -116,7 +115,7 @@ module Ms
       end
 
       NEW_PROT = lambda do |_prot, _peptides|
-        Ms::Sequest::Sqt::Locus.new([_prot.locus, _prot.description, _peptides])
+        Ms::Sequest::Sqt::Locus.new(_prot.locus, _prot.description, _peptides)
       end
 
       # if the file contains the header key '/$Percolator v/' then the results
@@ -229,7 +228,7 @@ end
 
 # all are cast as expected (total_intensity is a float)
 # mh = observed mh
-Ms::Sequest::Sqt::Spectrum = Arrayclass.new(%w[first_scan last_scan charge time_to_process node mh total_intensity lowest_sp num_matched_peptides matches])
+Ms::Sequest::Sqt::Spectrum = Struct.new(* %w(first_scan last_scan charge time_to_process node mh total_intensity lowest_sp num_matched_peptides matches).map(&:to_sym) )
 
 # 0=first_scan 1=last_scan 2=charge 3=time_to_process 4=node 5=mh 6=total_intensity 7=lowest_sp 8=num_matched_peptides 9=matches
 
@@ -255,7 +254,11 @@ class Ms::Sequest::Sqt::Spectrum
                         Ms::Sequest::Sqt::Match
                       end
         match = match_klass.new.from_line( line )
-        match[10,3] = spectrum[0,3]
+        #match[10,3] = spectrum[0,3]
+        # structs cannot set multiple values at a time :(
+        match[10] = spectrum[0]
+        match[11] = spectrum[1]
+        match[12] = spectrum[2]
         match[15] = base_name
         matches << match
         peptides << match
@@ -265,7 +268,7 @@ class Ms::Sequest::Sqt::Spectrum
       when Ms::Sequest::Sqt::Locus::Leader
         line.chomp!
         key = line.split(Ms::Sequest::Sqt::Delimiter)[1]
-        locus = Ms::Sequest::Sqt::Locus.new.from_line( line )
+        locus = Ms::Sequest::Sqt::Locus.from_line( line )
         loci << locus
       end
     end
@@ -308,7 +311,7 @@ class Ms::Sequest::Sqt::Spectrum
 end
 
 # Sqt format uses only indices 0 - 9
-Ms::Sequest::Sqt::Match = Arrayclass.new(%w[rxcorr rsp mh deltacn_orig xcorr sp ions_matched ions_total sequence manual_validation_status first_scan last_scan charge deltacn aaseq base_name loci])
+Ms::Sequest::Sqt::Match = Struct.new( *%w[rxcorr rsp mh deltacn_orig xcorr sp ions_matched ions_total sequence manual_validation_status first_scan last_scan charge deltacn aaseq base_name loci].map(&:to_sym) )
 
 # 0=rxcorr 1=rsp 2=mh 3=deltacn_orig 4=xcorr 5=sp 6=ions_matched 7=ions_total 8=sequence 9=manual_validation_status 10=first_scan 11=last_scan 12=charge 13=deltacn 14=aaseq 15=base_name 16=loci
 
@@ -374,7 +377,7 @@ class Ms::Sequest::Sqt::Match::Percolator < Ms::Sequest::Sqt::Match
   end
 end
 
-Ms::Sequest::Sqt::Locus = Arrayclass.new(%w[locus description peptides])
+Ms::Sequest::Sqt::Locus = Struct.new( :locus, :description, :peptides )
 
 class Ms::Sequest::Sqt::Locus
   Leader = 'L'
@@ -382,12 +385,14 @@ class Ms::Sequest::Sqt::Locus
   def first_entry ; self[0] end
   def reference ; self[0] end
 
-  def from_line(line)
+  def initialize(locus=nil, description=nil, peptides=[])
+    super(locus, description, peptides)
+  end
+
+  # returns a new Locus object
+  def self.from_line(line)
     line.chomp!
-    ar = line.split(Ms::Sequest::Sqt::Delimiter)
-    self[0] = ar[1]
-    self[1] = ar[2]
-    self
+    self.new( *line.split(Ms::Sequest::Sqt::Delimiter) )  # fills in the first two values 
   end
 
 end

data/lib/ms/sequest/srf.rb

@@ -4,9 +4,6 @@ require 'set'
 require 'fileutils'
 require 'scanf'
 
-# other gems
-require 'arrayclass'
-
 # in library
 require 'ms/ident/search'
 require 'ms/ident/peptide'
@@ -169,9 +166,9 @@ class Ms::Sequest::Srf
     fh.pos = start
 
     num_files.times do |i|
-      dta_files[i] = Ms::Sequest::Srf::Dta.new.from_io(fh, unpack_35) 
+      dta_files[i] = Ms::Sequest::Srf::Dta.from_io(fh, unpack_35) 
       #p dta_files[i]
-      out_files[i] = Ms::Sequest::Srf::Out.new.from_io(fh, unpack_35, dup_refs_gt_0)
+      out_files[i] = Ms::Sequest::Srf::Out.from_io(fh, unpack_35, dup_refs_gt_0)
       #p out_files[i]
     end
     [dta_files, out_files]
@@ -208,7 +205,7 @@ class Ms::Sequest::Srf
     end
 
     File.open(filename, 'rb') do |fh|
-      @header = Ms::Sequest::Srf::Header.new.from_io(fh)
+      @header = Ms::Sequest::Srf::Header.from_io(fh)
       @version = @header.version
 
       unpack_35 = case @version
@@ -267,11 +264,18 @@ class Ms::Sequest::Srf
     if opts[:read_pephits] && !@header.combined
       @index.each_with_index do |ind,i|
         mass_measured = @dta_files[i][0]
-        @out_files[i][0,3] = *ind
-        pep_hits = @out_files[i][6]
+        outfile = @out_files[i]
+        outfile.first_scan = ind[0]
+        outfile.last_scan = ind[1]
+        outfile.charge = ind[2]
+
+        pep_hits = @out_files[i].hits
         @peptides.push( *pep_hits )
         pep_hits.each do |pep_hit|
-          pep_hit[15,4] = @base_name, *ind
+          pep_hit[15] = @base_name
+          pep_hit[16] = ind[0]
+          pep_hit[17] = ind[1]
+          pep_hit[18] = ind[2]
           # add the deltamass
           pep_hit[12] = pep_hit[0] - mass_measured  # real - measured (deltamass)
           pep_hit[13] = 1.0e6 * pep_hit[12].abs / mass_measured ## ppm
@@ -320,7 +324,7 @@ class Ms::Sequest::Srf
     fh.pos = start
 
     header.num_dta_files.times do |i|
-      dta_files[i] = Ms::Sequest::Srf::Dta.new.from_io(fh, unpack_35) 
+      dta_files[i] = Ms::Sequest::Srf::Dta.from_io(fh, unpack_35) 
     end
     dta_files
   end
@@ -330,7 +334,7 @@ class Ms::Sequest::Srf
   def read_out_files(fh,number_files, unpack_35, dup_refs_gt_0)
     out_files = Array.new(number_files)
     header.num_dta_files.times do |i|
-      out_files[i] = Ms::Sequest::Srf::Out.new.from_io(fh, unpack_35, dup_refs_gt_0)
+      out_files[i] = Ms::Sequest::Srf::Out.from_io(fh, unpack_35, dup_refs_gt_0)
     end
     out_files
   end
@@ -390,11 +394,15 @@ class Ms::Sequest::Srf::Header
     @dta_gen.num_dta_files
   end
 
+  def self.from_io(fh)
+    self.new.from_io(fh)
+  end
+
   # sets fh to 0 and grabs the information it wants
   def from_io(fh)
     st = fh.read(4) 
     @version = '3.' + st.unpack('I').first.to_s
-    @dta_gen = Ms::Sequest::Srf::DtaGen.new.from_io(fh)
+    @dta_gen = Ms::Sequest::Srf::DtaGen.from_io(fh)
     # if the start_mass end_mass start_scan and end_scan are all zero, its a
     # combined srf file:
     @combined = [0.0, 0.0, 0, 0].zip(%w(start_mass end_mass start_scan end_scan)).all? do |one,two|
@@ -456,10 +464,14 @@ class Ms::Sequest::Srf::DtaGen
   # Integer
   attr_accessor :end_scan
 
-  # 
-  def from_io(fh)
-    fh.pos = 0 if fh.pos != 0  
-    st = fh.read(148)
+  def self.from_io(io)
+    self.new.from_io(io)
+  end
+
+  # sets self based on the io object and returns self
+  def from_io(io)
+    io.pos = 0 if io.pos != 0  
+    st = io.read(148)
     (@start_time, @start_mass, @end_mass, @num_dta_files, @group_scan, @min_group_count, @min_ion_threshold, @start_scan, @end_scan) = st.unpack('x36ex12ex4ex48Ix12IIIII')
     self
   end
@@ -468,7 +480,7 @@ end
 # total_num_possible_charge_states is not correct under 3.5 (Bioworks 3.3.1)
 # unknown is, well unknown...
 
-Ms::Sequest::Srf::Dta = Arrayclass.new( %w(mh dta_tic num_peaks charge ms_level unknown total_num_possible_charge_states peaks) )
+Ms::Sequest::Srf::Dta = Struct.new( *%w(mh dta_tic num_peaks charge ms_level unknown total_num_possible_charge_states peaks).map(&:to_sym) )
 
 class Ms::Sequest::Srf::Dta 
   # original
@@ -488,28 +500,23 @@ class Ms::Sequest::Srf::Dta
     "<Ms::Sequest::Srf::Dta @mh=#{mh} @dta_tic=#{dta_tic} @num_peaks=#{num_peaks} @charge=#{charge} @ms_level=#{ms_level} @total_num_possible_charge_states=#{total_num_possible_charge_states} @peaks=#{peaks_st} >"
   end
 
-  def from_io(fh, unpack_35)
-    if unpack_35
-      @unpack = Unpack_35
-      @read_header = 34
-      @read_spacer = 22
-    else
-      @unpack = Unpack_32
-      @read_header = 24
-      @read_spacer = 24
-    end
+  def self.from_io(fh, unpack_35)
+    (unpack, read_header, read_spacer) = 
+      if unpack_35
+        [Unpack_35, 34, 22]
+      else
+        [Unpack_32, 24, 24]
+      end
 
-    st = fh.read(@read_header)
     # get the bulk of the data in single unpack
-    self[0,7] = st.unpack(@unpack)
+    # sets the first 7 attributes
+    dta = self.new(*fh.read(read_header).unpack(unpack))
 
     # Scan numbers are given at the end in an index!
-    st2 = fh.read(@read_spacer)
+    fh.read(read_spacer) # throwaway the spacer
 
-    num_bytes_to_read = num_peaks * 8  
-    st3 = fh.read(num_bytes_to_read)
-    self[7] = st3
-    self
+    dta[7] = fh.read(dta.num_peaks * 8)  # (num_peaks * 8) is the number of bytes to read
+    dta
   end
 
   def to_dta_file_data
@@ -537,7 +544,8 @@ class Ms::Sequest::Srf::Dta
 end
 
 
-Ms::Sequest::Srf::Out = Arrayclass.new( %w(first_scan last_scan charge num_hits computer date_time hits total_inten lowest_sp num_matched_peptides db_locus_count) )
+#Ms::Sequest::Srf::Out = Struct.new( *%w(first_scan last_scan charge num_hits computer date_time hits total_inten lowest_sp num_matched_peptides db_locus_count).map(&:to_sym) )
+Ms::Sequest::Srf::Out = Struct.new( *%w(num_hits computer date_time total_inten lowest_sp num_matched_peptides db_locus_count hits first_scan last_scan charge).map(&:to_sym) )
 
 # 0=first_scan, 1=last_scan, 2=charge, 3=num_hits, 4=computer, 5=date_time, 6=hits, 7=total_inten, 8=lowest_sp, 9=num_matched_peptides, 10=db_locus_count
 
@@ -548,7 +556,7 @@ class Ms::Sequest::Srf::Out
   undef_method :inspect
   def inspect
     hits_s = 
-      if self[6]
+      if self.hits
         ", @hits(#)=#{hits.size}"
       else
         ''
@@ -556,21 +564,26 @@ class Ms::Sequest::Srf::Out
     "<Ms::Sequest::Srf::Out  first_scan=#{first_scan}, last_scan=#{last_scan}, charge=#{charge}, num_hits=#{num_hits}, computer=#{computer}, date_time=#{date_time}#{hits_s}>"
   end
 
-  def from_io(fh, unpack_35, dup_refs_gt_0)
+  # returns an Ms::Sequest::Srf::Out object
+  def self.from_io(fh, unpack_35, dup_refs_gt_0)
     ## EMPTY out file is 96 bytes
     ## each hit is 320 bytes
     ## num_hits and charge:
     st = fh.read(96)
 
-    self[3,3] = st.unpack( (unpack_35 ? Unpack_35 : Unpack_32) )
-    self[7,4] = st.unpack('@8eex4Ix4I')
-    num_hits = self[3]
+    # num_hits computer date_time
+    initial_vals = st.unpack( (unpack_35 ? Unpack_35 : Unpack_32) )
+    # total_inten lowest_sp num_matched_peptides db_locus_count
+    initial_vals.push( *st.unpack('@8eex4Ix4I') )
+    out_obj = self.new( *initial_vals )
+
+    _num_hits = out_obj.num_hits
 
-    ar = Array.new(num_hits)
+    ar = Array.new(_num_hits)
     if ar.size > 0
       num_extra_references = 0
-      num_hits.times do |i|
-        ar[i] = Ms::Sequest::Srf::Out::Peptide.new.from_io(fh, unpack_35)
+      _num_hits.times do |i|
+        ar[i] = Ms::Sequest::Srf::Out::Peptide.from_io(fh, unpack_35)
         num_extra_references += ar[i].num_other_loci
       end
       if dup_refs_gt_0
@@ -581,13 +594,11 @@ class Ms::Sequest::Srf::Out
       ## (the same as bioworks and prophet)
       Ms::Sequest::Srf::Out::Peptide.set_deltacn_from_deltacn_orig(ar)
     end
-    self[6] = ar
-    self[4].chomp!
-    self
+    out_obj.hits = ar
+    out_obj[1].chomp! # computer
+    out_obj
   end
 
-
-
 end
 
 
@@ -610,7 +621,7 @@ end
 # num_other_loci is the number of other loci that the peptide matches beyond
 # the first one listed
 # srf = the srf object this scan came from
-Ms::Sequest::Srf::Out::Peptide = Arrayclass.new( %w(mh deltacn_orig sf sp xcorr id num_other_loci rsp ions_matched ions_total sequence proteins deltamass ppm aaseq base_name first_scan last_scan charge srf deltacn deltacn_orig_updated) )
+Ms::Sequest::Srf::Out::Peptide = Struct.new( *%w(mh deltacn_orig sf sp xcorr id num_other_loci rsp ions_matched ions_total sequence proteins deltamass ppm aaseq base_name first_scan last_scan charge srf deltacn deltacn_orig_updated).map(&:to_sym) )
 # 0=mh 1=deltacn_orig 2=sp 3=xcorr 4=id 5=num_other_loci 6=rsp 7=ions_matched 8=ions_total 9=sequence 10=proteins 11=deltamass 12=ppm 13=aaseq 14=base_name 15=first_scan 16=last_scan 17=charge 18=srf 19=deltacn 20=deltacn_orig_updated
 
 class Ms::Sequest::Srf::Out::Peptide
@@ -689,36 +700,32 @@ class Ms::Sequest::Srf::Out::Peptide
   end
   # extra_references_array is an array that grows with peptides as extra
   # references are discovered.
-  def from_io(fh, unpack_35)
-    unpack = 
-      if unpack_35 ; Unpack_35
-      else ; Unpack_32
-      end
-
+  def self.from_io(fh, unpack_35)
     ## get the first part of the info
-    st = fh.read(( unpack_35 ? Read_35 : Read_32) ) ## read all the hit data
-
-    self[0,11] = st.unpack(unpack)
+    st = fh.read( unpack_35 ? Read_35 : Read_32 ) ## read all the hit data
 
+    
+    # sets the the first 11 attributes
+    peptide = self.new( *st.unpack( unpack_35 ? Unpack_35 : Unpack_32 ) )
 
     # set deltacn_orig_updated 
-    self[21] = self[1]
+    peptide[21] = peptide[1]
 
     # we are slicing the reference to 38 chars to be the same length as
     # duplicate references
-    self[11] = [Ms::Sequest::Srf::Out::Protein.new(self[11][0,38])]
+    peptide[11] = [Ms::Sequest::Srf::Out::Protein.new(peptide[11][0,38])]
 
-    self[14] = Ms::Ident::Peptide.sequence_to_aaseq(self[10])
+    peptide[14] = Ms::Ident::Peptide.sequence_to_aaseq(peptide[10])
 
     fh.read(6) if unpack_35
 
-    self
+    peptide
   end
 
 end
 
 
-Ms::Sequest::Srf::Out::Protein = Arrayclass.new( %w(reference peptides) )
+Ms::Sequest::Srf::Out::Protein = Struct.new( *%w(reference peptides).map(&:to_sym) )
 
 class Ms::Sequest::Srf::Out::Protein
   include Ms::Ident::Protein
@@ -729,11 +736,8 @@ class Ms::Sequest::Srf::Out::Protein
 
   tmp = $VERBOSE ; $VERBOSE = nil
   def initialize(reference=nil, peptides=[])
-    #super(@@arr_size)
-    super(self.class.size)
-    #@reference = reference
-    #@peptides = peptides
-    self[0,2] = reference, peptides
+    self[0] = reference
+    self[1] = peptides
   end
   $VERBOSE = tmp
 

data/spec/spec_helper.rb

@@ -1,20 +1,10 @@
 require 'rubygems'
-require 'bundler'
-
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
 require 'ms/testdata'
 require 'spec/more'
 
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 
-
 def capture_stderr
   begin
     $stderr = StringIO.new

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
+  - 1
   - 0
-  - 24
-  version: 0.0.24
+  version: 0.1.0
 platform: ruby
 authors: 
 - John T. Prince
@@ -14,11 +14,12 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-03-10 00:00:00 -07:00
+date: 2011-04-11 00:00:00 -06:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: ms-ident
+  prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -27,13 +28,13 @@ dependencies:
         segments: 
         - 0
         - 0
-        - 17
-        version: 0.0.17
+        - 20
+        version: 0.0.20
   type: :runtime
-  prerelease: false
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
   name: ms-core
+  prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -45,25 +46,24 @@ dependencies:
         - 17
         version: 0.0.17
   type: :runtime
-  prerelease: false
   version_requirements: *id002
 - !ruby/object:Gem::Dependency 
-  name: arrayclass
+  name: trollop
+  prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
         segments: 
-        - 0
         - 1
-        - 0
-        version: 0.1.0
+        - 16
+        version: "1.16"
   type: :runtime
-  prerelease: false
   version_requirements: *id003
 - !ruby/object:Gem::Dependency 
-  name: trollop
+  name: jeweler
+  prerelease: false
   requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -71,13 +71,14 @@ dependencies:
       - !ruby/object:Gem::Version 
         segments: 
         - 1
-        - 16
-        version: "1.16"
-  type: :runtime
-  prerelease: false
+        - 5
+        - 2
+        version: 1.5.2
+  type: :development
   version_requirements: *id004
 - !ruby/object:Gem::Dependency 
   name: ms-testdata
+  prerelease: false
   requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -89,10 +90,10 @@ dependencies:
         - 1
         version: 0.1.1
   type: :development
-  prerelease: false
   version_requirements: *id005
 - !ruby/object:Gem::Dependency 
   name: spec-more
+  prerelease: false
   requirement: &id006 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
@@ -102,51 +103,7 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  prerelease: false
   version_requirements: *id006
-- !ruby/object:Gem::Dependency 
-  name: bundler
-  requirement: &id007 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 0
-        - 0
-        version: 1.0.0
-  type: :development
-  prerelease: false
-  version_requirements: *id007
-- !ruby/object:Gem::Dependency 
-  name: jeweler
-  requirement: &id008 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ~>
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 1
-        - 5
-        - 2
-        version: 1.5.2
-  type: :development
-  prerelease: false
-  version_requirements: *id008
-- !ruby/object:Gem::Dependency 
-  name: rcov
-  requirement: &id009 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        version: "0"
-  type: :development
-  prerelease: false
-  version_requirements: *id009
 description: reads .SRF, .SQT and supports conversions
 email: jtprince@gmail.com
 executables: 
@@ -161,8 +118,6 @@ extra_rdoc_files:
 files: 
 - .autotest
 - .gitmodules
-- Gemfile
-- Gemfile.lock
 - History
 - LICENSE
 - README.rdoc
@@ -217,7 +172,6 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: -385266015474839792
       segments: 
       - 0
       version: "0"

data/Gemfile

@@ -1,21 +0,0 @@
-source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-#   gem "activesupport", ">= 2.3.5"
-gem "ms-ident", ">= 0.0.17"
-gem "ms-core", ">= 0.0.17"
-gem "arrayclass", ">= 0.1.0"
-#gem "ms-msrun", ">= 0.3.3"
-gem "trollop", "~> 1.16"
-
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
-group :development do
-  gem "ms-testdata", ">= 0.1.1"
-  gem "spec-more", ">= 0"
-  gem "bundler", "~> 1.0.0"
-  gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
-end
-
-

data/Gemfile.lock

@@ -1,39 +0,0 @@
-GEM
-  remote: http://rubygems.org/
-  specs:
-    andand (1.3.1)
-    arrayclass (0.1.1)
-    bacon (1.1.0)
-    bio (1.4.1)
-    git (1.2.5)
-    jeweler (1.5.2)
-      bundler (~> 1.0.0)
-      git (>= 1.2.5)
-      rake
-    ms-core (0.0.17)
-      bio (>= 1.4.1)
-    ms-ident (0.0.17)
-      andand
-      ms-core (>= 0.0.12)
-      nokogiri
-    ms-testdata (0.1.1)
-    nokogiri (1.4.4)
-    rake (0.8.7)
-    rcov (0.9.9)
-    spec-more (0.0.4)
-      bacon
-    trollop (1.16.2)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  arrayclass (>= 0.1.0)
-  bundler (~> 1.0.0)
-  jeweler (~> 1.5.2)
-  ms-core (>= 0.0.17)
-  ms-ident (>= 0.0.17)
-  ms-testdata (>= 0.1.1)
-  rcov
-  spec-more
-  trollop (~> 1.16)