RubyGems - ms-sequest - Versions diffs - 0.0.12 → 0.0.13 - Mend

ms-sequest 0.0.12 → 0.0.13

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Files changed (12) hide show

data/History +6 -0
data/README.rdoc +2 -0
data/Rakefile +2 -67
data/VERSION +1 -1
data/bin/srf_to_search.rb +0 -37
data/bin/srf_to_sqt.rb +22 -26
data/lib/ms/sequest/params.rb +8 -4
data/lib/ms/sequest/srf/sqt.rb +4 -26
data/spec/ms/sequest/params_spec.rb +6 -1
metadata +57 -44
data/lib/ms/sequest/srf/search/tap.rb +0 -39
data/tap.yml +0 -0

data/History CHANGED Viewed

@@ -1,3 +1,9 @@
+== 0.0.13 / 2010-08-16
+* compatible with ruby 1.9
+* simplified Rakefile, ditching efforts at gh-pages converter for now
+* removed dependency on Tap
 == 0.0.12 / 2010-01-01
 * moved over to jeweler and tests to bacon (spec/more)

data/README.rdoc CHANGED Viewed

@@ -13,8 +13,10 @@ Can read and convert Bioworks Sequest Results Files (SRF).
 Conversions (see api for options):
+    require 'ms/sequest/srf/sqt'  # require this in addition to 'ms/sequest/srf'
     srf.to_sqt            # (outputs a file) -> file.sqt
+    require 'ms/sequest/srf/search' # require this in addition to 'ms/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)

data/Rakefile CHANGED Viewed

@@ -1,4 +1,3 @@
 require 'rubygems'
 require 'rake'
 require 'jeweler'
@@ -6,8 +5,6 @@ require 'rake/testtask'
 require 'rcov/rcovtask'
 NAME = "ms-sequest"
-WEBSITE_BASE = "website"
-WEBSITE_OUTPUT = WEBSITE_BASE + "/output"
 gemspec = Gem::Specification.new do |s|
   s.name = NAME
@@ -20,13 +17,11 @@ gemspec = Gem::Specification.new do |s|
   s.add_dependency("arrayclass", ">= 0.1.0")
   s.add_dependency("ms-core", ">= 0.0.2")
-  s.add_dependency("tap", ">= 0.17.1")
-  s.add_dependency("ms-fasta", ">= 0.2.3")
+  s.add_dependency("ms-fasta", ">= 0.4.1")
   s.add_development_dependency("ms-testdata", ">= 0.18.0")
-  s.add_development_dependency("spec/more")
+  s.add_development_dependency("spec-more")
 end
 Jeweler::Tasks.new(gemspec)
 Rake::TestTask.new(:spec) do |t|
@@ -46,65 +41,5 @@ Rcov::RcovTask.new do |spec|
   spec.verbose = true
 end
-def rdoc_redirect(base_rdoc_output_dir, package_website_page, version)
-  content = %Q{
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<html><head><title>mspire: } + NAME + %Q{rdoc</title>
-<meta http-equiv="REFRESH" content="0;url=#{package_website_page}/rdoc/#{version}/">
-</head> </html>
-  }
-  FileUtils.mkpath(base_rdoc_output_dir)
-  File.open("#{base_rdoc_output_dir}/index.html", 'w') {|out| out.print content }
-end
-require 'rake/rdoctask'
-Rake::RDocTask.new do |rdoc|
-  base_rdoc_output_dir = WEBSITE_OUTPUT + '/rdoc'
-  version = File.read('VERSION')
-  rdoc.rdoc_dir = base_rdoc_output_dir + "/#{version}"
-  rdoc.title = NAME + ' ' + version
-  rdoc.rdoc_files.include('README*')
-  rdoc.rdoc_files.include('lib/**/*.rb')
-end
-task :create_redirect do
-  base_rdoc_output_dir = WEBSITE_OUTPUT + '/rdoc'
-  rdoc_redirect(base_rdoc_output_dir, gemspec.homepage,version)
-end
-task :rdoc => :create_redirect
-namespace :website do
-  desc "checkout and configure the gh-pages submodule"
-  task :init do
-    if File.exist?(WEBSITE_OUTPUT + "/.git")
-      puts "!! not doing anything, #{WEBSITE_OUTPUT + "/.git"} already exists !!"
-    else
-      puts "(not sure why this won't work programmatically)"
-      puts "################################################"
-      puts "[Execute these commands]"
-      puts "################################################"
-      puts "git submodule init"
-      puts "git submodule update"
-      puts "pushd #{WEBSITE_OUTPUT}"
-      puts "git co --track -b gh-pages origin/gh-pages ;"
-      puts "popd"
-      puts "################################################"
-      # not sure why this won't work!
-      #%x{git submodule init}
-      #%x{git submodule update}
-      #Dir.chdir(WEBSITE_OUTPUT) do
-      #  %x{git co --track -b gh-pages origin/gh-pages ;}
-      #end
-    end
-  end
-end
 task :default => :spec
-task :build => :gemspec
-# credit: Rakefile modeled after Jeweler's

data/VERSION CHANGED Viewed

	@@ -1 +1 @@
1	- 0.0.12
1	+ 0.0.13

data/bin/srf_to_search.rb CHANGED Viewed

@@ -39,40 +39,3 @@ ARGV.each do |srf_file|
     srf.to_dta_files(newfile)
   end
 end
-=begin
-#require 'tap/task'
-task_class = Ms::Sequest::Srf::SrfToSearch
-parser = ConfigParser.new do |opts|
-  opts.separator "configurations"
-  opts.add task_class.configurations
-  opts.on "--help", "Print this help" do
-    puts "usage: #{File.basename(__FILE__)} <file>.srf ..."
-    puts
-    puts opts
-    exit(0)
-  end
-end
-parser.parse!(ARGV)
-task = task_class.new(parser.config)
-ARGV.each do |file|
-  task.execute(file)
-end
-=end

data/bin/srf_to_sqt.rb CHANGED Viewed

@@ -1,39 +1,35 @@
 #!/usr/bin/env ruby
 require 'rubygems'
-require 'tap/task'
 require 'ms/sequest/srf/sqt'
-if ARGV.size == 0
-  ARGV << "--help"
+opt = {
+  :filter => true
+}
+opts = OptionParser.new do |op|
+  op.banner = "usage: #{File.basename(__FILE__)} [OPTIONS] <file>.srf ..."
+  op.separator "output: <file>.sqt ..."
+  op.separator ""
+  op.separator "options:"
+  op.on("-d", "--db-info", "calculates num aa's and md5sum on db") {|v| opt[:db_info] = v }
+  op.on("-p", "--db-path <String>", "If you need to specify the database path") {|v| opt[:new_db_path] = v }
+  op.on("-u", "--db-update", "update the sqt file to reflect --db_path") {|v| opt[:db_update] = v }
+  op.on("-n", "--no-filter", "by default, pephit must be within peptide_mass_tolerance",  "(defined in sequest.params) to be included.  Turns this off.") { opt[:filter] = false }
+  op.on("-r", "--round", "round floating point values reasonably") {|v| opt[:round] = v }
 end
+opts.parse!
-task_class = Ms::Sequest::Srf::SrfToSqt
-parser = ConfigParser.new do |opts|
-  opts.separator "configurations"
-  opts.add task_class.configurations
-  opts.on "--help", "Print this help" do
-    puts "usage: #{File.basename(__FILE__)} <file>.srf ..."
-    puts "outputs: <file>.sqt ..."
-    puts
-    #puts task_class::desc.wrap
-    #puts
-    puts opts
-    #puts
-    #puts "in tap workflow: tap run -- glob '*.srf' --:i srf_to_sqt"
-    exit(0)
-  end
+if ARGV.size == 0
+  puts(opts) || exit
 end
-parser.parse!(ARGV)
+ARGV.each do |srf_file|
+  base = srf_file.chomp(File.extname(srf_file))
+  outfile = base + '.sqt'
-task = task_class.new(parser.config)
-ARGV.each do |file|
-  task.execute(file)
+  srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => opt.delete(:filter))
+  srf.to_sqt(outfile, :db_info => db_info, :new_db_path => db_path, :update_db_path => db_update, :round => round)
 end

data/lib/ms/sequest/params.rb CHANGED Viewed

@@ -97,6 +97,10 @@ class Ms::Sequest::Params
   # returns self or nil if no sequest found in the io
   def parse_io(fh)
     # seek to the SEQUEST file
+    if fh.respond_to?(:set_encoding)
+      # this mimics ruby1.8 behavior as we read in the file
+      fh.set_encoding('ASCII-8BIT')
+    end
     loop do
       line = fh.gets
       return nil if line.nil?  # we return nil if we reach then end of the file without seeing sequest params
@@ -234,8 +238,8 @@ class Ms::Sequest::Params
   # based_on may be :precursor or :fragment
   def mass_index(based_on=:precursor)
     reply = case based_on
-            when :precursor : precursor_mass_type
-            when :fragment : fragment_mass_type
+            when :precursor ; precursor_mass_type
+            when :fragment ; fragment_mass_type
             end
     case reply
     when 'average'
@@ -257,8 +261,8 @@ class Ms::Sequest::Params
   def min_number_termini
     if e_info = @opts["enzyme_info"]
       case e_info.split(" ")[1]
-      when "1": return "2"
-      when "2": return "1"
+      when "1" ; return "2"
+      when "2" ; return "1"
       end
     end
     warn "No Enzyme termini info, using min_number_termini = '1'"

data/lib/ms/sequest/srf/sqt.rb CHANGED Viewed

@@ -38,7 +38,7 @@ module Ms
           if params.precursor_mass_type == 'average' ; 'AVG'
           else ; 'MONO'
           end
         mass_index = params.mass_index
         static_mods = params.static_mods.map do |k,v|
           key =  k.split(/_/)[1]
@@ -71,9 +71,9 @@ module Ms
         apmu =
           case params.peptide_mass_units
-          when '0' : 'amu'
-          when '1' : 'mmu'
-          when '2' : 'ppm'
+          when '0' ; 'amu'
+          when '1' ; 'mmu'
+          when '2' ; 'ppm'
           end
         hh =  {
@@ -163,28 +163,6 @@ module Ms
           end
         end # close the filehandle
       end # method
-      # SrfToSqt::task convert .srf to .sqt files
-      class SrfToSqt < Tap::Task
-        config :db_info, false, :short => 'd', &c.flag   # calculates num aa's and md5sum on db
-        # if your database path has changed
-        # and you want db-info, then give the
-        # path to the new *directory*
-        # e.g. /my/new/path
-        config :db_path, nil, :short => 'p'
-        config :db_update, false, :short => 'u', &c.flag # update the sqt file to reflect --db_path
-        config :no_filter, false, :short => 'n', &c.flag # by default, pephit must be within peptide_mass_tolerance (defined in sequest.params) to be included.  Turns this off.
-        config :round, false, :short => 'r', &c.flag     # round floating point values reasonably
-        def process(srf_file)
-          new_filename = srf_file.sub(/\.srf$/i, '') << '.sqt'
-          srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => !no_filter)
-          srf.to_sqt(new_filename, :db_info => db_info, :new_db_path => db_path, :update_db_path => db_update, :round => round)
-        end # process
-      end # SrfToSqt
     end # Srf
   end # Sequest
 end # Ms

data/spec/ms/sequest/params_spec.rb CHANGED Viewed

@@ -5,7 +5,12 @@ require 'ms/sequest/params'
 # returns a hash of all params
 def simple_parse(filename)
   hash = {}
-  IO.read(filename).split(/\r?\n/).select {|v| v =~ /^[a-z]/}.each do |line|
+  data = File.open(filename) do |io|
+    # this makes it work with ruby 1.9:
+    io.set_encoding("ASCII-8BIT") if io.respond_to?(:set_encoding)
+    io.read
+  end
+  data.split(/\r?\n/).select {|v| v =~ /^[a-z]/}.each do |line|
     if line =~ /([^\s]+)\s*=\s*([^;]+)\s*;?/
       hash[$1.dup] = $2.rstrip
     end

metadata CHANGED Viewed

@@ -1,7 +1,12 @@
 --- !ruby/object:Gem::Specification
 name: ms-sequest
 version: !ruby/object:Gem::Version
-  version: 0.0.12
+  prerelease: false
+  segments:
+  - 0
+  - 0
+  - 13
+  version: 0.0.13
 platform: ruby
 authors:
 - John T. Prince
@@ -9,69 +14,77 @@ autorequire:
 bindir: bin
 cert_chain: []
-date: 2010-01-01 00:00:00 -07:00
+date: 2010-08-17 00:00:00 -06:00
 default_executable:
 dependencies:
 - !ruby/object:Gem::Dependency
   name: arrayclass
-  type: :runtime
-  version_requirement:
-  version_requirements: !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
+        segments:
+        - 0
+        - 1
+        - 0
         version: 0.1.0
-    version:
+  type: :runtime
+  version_requirements: *id001
 - !ruby/object:Gem::Dependency
   name: ms-core
-  type: :runtime
-  version_requirement:
-  version_requirements: !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
+        segments:
+        - 0
+        - 0
+        - 2
         version: 0.0.2
-    version:
-- !ruby/object:Gem::Dependency
-  name: tap
   type: :runtime
-  version_requirement:
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.17.1
-    version:
+  version_requirements: *id002
 - !ruby/object:Gem::Dependency
   name: ms-fasta
-  type: :runtime
-  version_requirement:
-  version_requirements: !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.2.3
-    version:
+        segments:
+        - 0
+        - 4
+        - 1
+        version: 0.4.1
+  type: :runtime
+  version_requirements: *id003
 - !ruby/object:Gem::Dependency
   name: ms-testdata
-  type: :development
-  version_requirement:
-  version_requirements: !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
+        segments:
+        - 0
+        - 18
+        - 0
         version: 0.18.0
-    version:
-- !ruby/object:Gem::Dependency
-  name: spec/more
   type: :development
-  version_requirement:
-  version_requirements: !ruby/object:Gem::Requirement
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency
+  name: spec-more
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
+        segments:
+        - 0
         version: "0"
-    version:
+  type: :development
+  version_requirements: *id005
 description: reads .SRF, .SQT and supports conversions
 email: jtprince@gmail.com
 executables:
@@ -100,7 +113,6 @@ files:
 - lib/ms/sequest/sqt.rb
 - lib/ms/sequest/srf.rb
 - lib/ms/sequest/srf/search.rb
-- lib/ms/sequest/srf/search/tap.rb
 - lib/ms/sequest/srf/sqt.rb
 - script/fasta_ipi_to_ncbi-ish.rb
 - spec/ms/sequest/bioworks_spec.rb
@@ -121,7 +133,6 @@ files:
 - spec/testfiles/corrupted_900.srf
 - spec/testfiles/small.sqt
 - spec/testfiles/small2.sqt
-- tap.yml
 has_rdoc: true
 homepage: http://jtprince.github.com/ms-sequest
 licenses: []
@@ -135,30 +146,32 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
+      segments:
+      - 0
       version: "0"
-  version:
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
+      segments:
+      - 0
       version: "0"
-  version:
 requirements: []
 rubyforge_project: mspire
-rubygems_version: 1.3.5
+rubygems_version: 1.3.6
 signing_key:
 specification_version: 3
 summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc
 test_files:
+- spec/ms/sequest/srf_spec_helper.rb
+- spec/ms/sequest/pepxml_spec.rb
+- spec/ms/sequest/bioworks_spec.rb
 - spec/ms/sequest/srf/search_spec.rb
-- spec/ms/sequest/srf/sqt_spec.rb
 - spec/ms/sequest/srf/search_spec_helper.rb
-- spec/ms/sequest/sqt_spec.rb
+- spec/ms/sequest/srf/sqt_spec.rb
+- spec/ms/sequest/sqt_spec_helper.rb
 - spec/ms/sequest/params_spec.rb
-- spec/ms/sequest/bioworks_spec.rb
+- spec/ms/sequest/sqt_spec.rb
 - spec/ms/sequest/srf_spec.rb
-- spec/ms/sequest/srf_spec_helper.rb
-- spec/ms/sequest/sqt_spec_helper.rb
-- spec/ms/sequest/pepxml_spec.rb
 - spec/spec_helper.rb

data/lib/ms/sequest/srf/search/tap.rb DELETED Viewed

@@ -1,39 +0,0 @@
-require 'tap/task'
-module Ms
-  module Sequest
-    class Srf
-      # Ms::Sequest::Srf::SrfToSearch::task converts to MS formats for DB
-      # searching
-      #
-      # outputs the appropriate file or directory structure for <file>.srf:
-      #     <file>.mgf    # file for mgf
-      #     <file>        # the basename directory for dta
-      class SrfToSearch < Tap::Task
-        config :format, "mgf", :short => 'f' # mgf|dta (default: mgf)
-        def process(srf_file)
-          base = srf_file.sub(/\.srf$/i, '')
-          newfile =
-            case format
-            when 'dta'
-              base
-            when 'mgf'
-              base << '.' << format
-            end
-          srf = Ms::Sequest::Srf.new(srf_file, :link_protein_hits => false, :filter_by_precursor_mass_tolerance => false, :read_pephits => false )
-          # options just speed up reading since we don't need .out info anyway
-          case format
-          when 'mgf'
-            srf.to_mgf(newfile)
-          when 'dta'
-            srf.to_dta(newfile)
-          end
-        end
-      end
-    end # Srf
-  end # Sequest
-end # Ms

data/tap.yml DELETED Viewed

File without changes