mspire 0.4.9 → 0.5.0

data/Rakefile

@@ -1,330 +0,0 @@
-require 'rake'
-require 'rubygems'
-require 'rake/rdoctask'
-require 'rake/gempackagetask'
-require 'rake/clean'
-require 'fileutils'
-require 'spec/rake/spectask'
-
-###############################################
-# GLOBAL
-###############################################
-FL = FileList
-
-NAME = "mspire"
-
-$dependencies = %w(libjtp)
-$tfiles_large = 'test_files_large'
-changelog = "changelog.txt"
-
-core_files = FL["INSTALL", "README", "README.rdoc", "Rakefile", "LICENSE", changelog, "release_notes.txt", "{lib,bin,script,specs,tutorial,test_files}/**/*"]
-big_dist_files = core_files + FL["test_files_large/**/*"]
-
-dist_files = core_files 
-# dist_files = big_dist_files
-
-###############################################
-# ENVIRONMENT
-###############################################
-
-ENV["OS"] == "Windows_NT" ? WIN32 = true : WIN32 = false
-$gemcmd = "gem"
-if WIN32
-  unless ENV["TERM"] == "cygwin"
-    $gemcmd << ".cmd"
-  end
-end
-
-###############################################
-# DOC
-###############################################
-
-def move_and_add_webgen_header(file, newfile, src_dir, heading)
-  string = IO.read file
-  with_header = heading + string
-  File.open(newfile, 'w') {|v| v.print with_header }
-  FileUtils.mv newfile, src_dir, :force => true
-end
-
-desc "copy top level files into doc/src"
-task :cp_top_level_docs do
-  string = "---
-title: TITLE
-inMenu: true
-directoryName: mspire 
----\n"
-  src = "doc/src"
-  move_and_add_webgen_header('README', 'index.page', src, string.sub('TITLE', 'Home'))
-  move_and_add_webgen_header('INSTALL', 'index.page', src + '/install', string.sub('TITLE', 'Install').sub('mspire', 'Install').sub("inMenu: true\n", ''))
-end
-
-desc "upload docs (doc/output) to server"
-task :upload_docs do
-  sh "scp -i ~/.ssh/rubyforge_key -r doc/output/* jtprince@rubyforge.org:/var/www/gforge-projects/mspire/"
-end
-
-# best to use webgen 0.3.8 right now
-# to get working (may not require all these steps):
-#    gem install RedCloth
-#    gem install BlueCloth
-#    soft link the bluecloth binary into path
-desc "creates docs in doc/html"
-task :html_docs => [:cp_top_level_docs] do
-  FileUtils.cd 'doc' do
-    sh "webgen"
-  end
-  FileUtils.cp 'doc/src/archive/t2x', 'doc/output/archive/t2x'
-end
-
-desc "does html_docs and rdoc and puts rdoc inside html_docs"
-task :all_docs => [:html_docs, :rdoc] do
-  FileUtils.mv 'html', 'doc/output/rdoc'
-end
-
-#rdoc_options = ['--main', 'README', '--title', NAME]
-rdoc_options = ['--main', 'README.rdoc', '--title', NAME]
-#rdoc_extra_includes = ["README", "INSTALL", "LICENSE"]
-rdoc_extra_includes = ['README.rdoc']
-
-Rake::RDocTask.new do |rd|
-  rd.main = "README.rdoc"
-  rd.rdoc_files.include("lib/**/*.rb", *rdoc_extra_includes )
-  rd.options.push( *rdoc_options )
-end
-
-###############################################
-# TESTS
-###############################################
-
-namespace :spec do
-  task :autotest do
-    require './specs/rspec_autotest'
-    RspecAutotest.run
-  end
-end
-
-
-task :ensure_dependencies do
-  $dependencies.each do |dep|
-    unless `#{$gemcmd} list -l #{dep}`.include?(dep)
-      abort "ABORTING: install #{dep} before testing!"
-    end
-  end
-end
-
-task :ensure_large_testfiles do
-  if !File.exist?($tfiles_large) and !ENV['SPEC_LARGE'].nil?
-    warn "Not running with large files since #{$tfiles_large} does not exist!"
-    warn "Removing SPEC_LARGE from ENV!"
-    ENV.delete('SPEC_LARGE')
-  end
-end
-
-task :ensure_gem_is_uninstalled do
-  reply = `#{$gemcmd} list -l #{NAME}`
-  if reply.include? NAME + " ("
-    puts "GOING to uninstall gem '#{NAME}' for testing"
-    if WIN32
-      %x( #{$gemcmd} uninstall -x #{NAME} )
-    else
-      %x( sudo #{$gemcmd} uninstall -x #{NAME} )
-    end
-  end
-end
-
-desc "Run all specs"
-Spec::Rake::SpecTask.new('spec') do |t|
-  Rake::Task[:ensure_gem_is_uninstalled].invoke
-  Rake::Task[:ensure_dependencies].invoke
-  Rake::Task[:ensure_large_testfiles].invoke
-  t.libs = 
-    if !ENV['LIB'].nil?
-      [ENV['LIB']]
-    else
-      ['lib']
-    end
-  #t.ruby_opts = ['-I', 'lib']
-  t.spec_files = FileList['specs/**/*_spec.rb']
-end
-
-desc "Run all specs"
-Spec::Rake::SpecTask.new('specl') do |t|
-  Rake::Task[:ensure_gem_is_uninstalled].invoke
-  Rake::Task[:ensure_dependencies].invoke
-  Rake::Task[:ensure_large_testfiles].invoke
-  t.spec_files = FileList['specs/**/*_spec.rb']
-  t.libs = 
-    if !ENV['LIB'].nil?
-      [ENV['LIB']]
-    else
-      ['lib']
-    end
-  #t.libs = ['lib']
-  #t.ruby_opts = ['-I', 'lib']
-  t.spec_opts = ['--format', 'specdoc' ]
-end
-
-desc "Run all specs with RCov"
-Spec::Rake::SpecTask.new('rcov') do |t|
-  Rake::Task[:ensure_gem_is_uninstalled].invoke
-  Rake::Task[:ensure_dependencies].invoke
-  Rake::Task[:ensure_large_testfiles].invoke
-  t.spec_files = FileList['specs/**/*_spec.rb']
-  t.rcov = true
-  t.libs = 
-    if !ENV['LIB'].nil?
-      [ENV['LIB']]
-    else
-      ['lib']
-    end
-  #t.ruby_opts = ['-I', 'lib']
-  t.rcov_opts = ['--exclude', 'specs']
-end
-
-task :speci => [:ensure_gem_is_uninstalled, :ensure_dependencies, :ensure_large_testfiles] do
-  # files that match a key word
-  files_to_run = ENV['SPEC'] || FileList['specs/**/*_spec.rb']
-  if ENV['SPECM']
-    files_to_run = files_to_run.select do |file|
-      file.include?(ENV['SPECM'])
-    end
-  end
-  lib = 
-    if !ENV['LIB'].nil?
-      ENV['LIB']
-    else
-      'lib'
-    end
-  files_to_run.each do |spc|
-    puts "------ SPEC=#{spc} ------"
-    system "ruby -I #{lib} -S spec #{spc} --format specdoc"
-  end
-end
-
-#Spec::Rake::SpecTask.new(:spec) do |t|
-#  uninstall_gem
-#  t.spec_files = FileList['spec/**/spec_*.rb']
-#  t.libs = FileList['lib']
-#  t.spec_opts = ['--format', 'specdoc']
-#end
-
-
-#desc "Run unit tests."
-#Rake::TestTask.new do |t|
-#  uninstall_gem
-#  #  t.libs << "lib"  ## done by default
-#  t.test_files = FL["test/tc_*.rb"]
-#  #t.verbose = true
-#end
-
-
-
-#desc "Run unit tests individual on each test"
-#task :test_ind do |t|
-#  reply = `#{$gemcmd} list -l #{NAME}`
-#  if reply.include? NAME + " ("
-#    %x( sudo #{$gemcmd} uninstall -x #{NAME} )
-#  end
-#
-#  #  t.libs << "lib"  ## done by default
-#  test_files = FL["test/tc_*.rb"]
-#  test_files.each do |file|
-#    puts "TESTING: #{file.sub(/test\//,'')}"
-#    puts `ruby -I lib #{file}`
-#  end
-#  #t.verbose = true
-#end
-
-
-
-
-
-#desc "Run all tests"
-#task :test_indiv do
-#  sys.cd "test" do 
-#    sys["tc_*.rb"].each do |file|
-#      sys "ruby #{file}"
-#    end
-#  end
-#end
-
-###############################################
-# PACKAGE / INSTALL / UNINSTALL
-###############################################
-
-## To release a package on rubyforge:
-## Login to rubyforge and go the 'Files' tab
-## then "To create a new release click here"
-
-tm = Time.now
-spec = Gem::Specification.new do |s|
-  s.platform = Gem::Platform::RUBY
-  s.name = NAME
-  s.version = IO.readlines(changelog).grep(/##.*version/).pop.split(/\s+/).last.chomp 
-  s.summary = "Mass Spectrometry Proteomics Objects, Scripts, and Executables"
-  s.date = "#{tm.year}-#{tm.month}-#{tm.day}"
-  s.email = "jprince@icmb.utexas.edu"
-  s.homepage = "http://mspire.rubyforge.org"
-  s.rubyforge_project = "mspire"
-  s.description = "mspire is for working with mass spectrometry proteomics data"
-  s.has_rdoc = true
-  s.authors = ["John Prince"]
-  s.files = dist_files
-  s.rdoc_options = rdoc_options
-  s.extra_rdoc_files = rdoc_extra_includes
-  s.executables = FL["bin/*"].map {|file| File.basename(file) }
-  s.add_dependency('libjtp', '~> 0.2.14')
-  s.add_dependency('axml', '~> 0.0.0')
-  s.add_dependency('arrayclass', '~> 0.1.0')
-  s.requirements << '"libxml" is the prefered xml parser right now.  libxml, xmlparser, REXML and regular expressions are used as fallback in some routines.'
-  s.requirements << 'some plotting functions will not be available without the "gnuplot" gem (and underlying gnuplot binary)'
-  s.requirements << 'the "t2x" binary (in archive) or readw.exe is required to convert .RAW files to mzXML in some applications'
-  s.requirements << '"rake" is useful for development'
-  s.requirements << '"webgen (with gems redcloth and bluecloth) is necessary to build web pages'
-  #s.test_files = FL["test/tc_*.rb"]
-  s.test_files = FL["specs/**/*_spec.rb"]
-end
-
-desc "Create packages."
-Rake::GemPackageTask.new(spec) do |pkg|
-  pkg.need_zip = true
-  pkg.need_tar = true
-end
-
-#desc "Create packages."
-#gen RubyPackage, NAME do |t|
-#  t.version = "0.1.4"
-#  t.summary = "Mass Spectrometry Proteomics Objects, Scripts, and Executables"
-#  t.files = dist_files
-#  t.bindir = "bin"
-#  t.executable = sys["bin/*"].collect {|file| File.basename(file) }
-#  t.test_files = sys["test/tc_*.rb"]
-#  t.gem_add_dependency('libjtp', '= 0.1.1')
-#  t.package_task
-#end
-
-task :remove_pkg do 
-  FileUtils.rm_rf "pkg"
-end
-
-task :install => [:reinstall]
-
-desc "uninstalls the package, packages a fresh one, and installs"
-task :reinstall => [:remove_pkg, :clean, :package] do
-  reply = `#{$gemcmd} list -l #{NAME}`
-  if reply.include?(NAME + " (")
-    %x( #{$gemcmd} uninstall -x #{NAME} )
-  end
-  FileUtils.cd("pkg") do
-    %x( #{$gemcmd} install #{NAME}*.gem )
-  end
-  
-end
-
-###############################################
-# CLEANUP
-###############################################
-
-#desc "Remove autogenerated and backup files."
-#gen Clean
-#var[:clean].include "pkg", "*~", tutorial_files

data/bin/aafreqs.rb

@@ -1,23 +0,0 @@
-#!/usr/bin/ruby -w
-
-require 'fasta'
-require 'spec_id/aa_freqs'
-
-if ARGV.size < 1
-  puts "usage: #{File.basename(__FILE__)} <file>.fasta ..."
-  puts "prints the amino acid frequencies of every amino acid in each fasta file"
-  exit
-end
-
-ARGV.each do |file|
-  obj = SpecID::AAFreqs.new(Fasta.new(file))
-  puts file
-  obj.aafreqs.sort_by{|v| v.to_s }.each do |k,v|
-    puts "#{k}: #{v}"
-  end
-  puts ""
-end
-
-
-
-

data/bin/bioworks2excel.rb

@@ -1,14 +0,0 @@
-#!/usr/bin/ruby -w
-
-require 'spec_id/bioworks'
-
-if ARGV.size < 1
-  puts "usage: #{File.basename(__FILE__)} bioworks.xml ..."
-  exit
-end
-
-ARGV.each do |file|
-  newfile = file.gsub(".xml", ".txt")
-  obj = Bioworks.new(file)
-  obj.to_excel(newfile)
-end

data/bin/bioworks_to_pepxml.rb

@@ -1,148 +0,0 @@
-#!/usr/bin/ruby -w
-
-##############################################################
-# GLOBAL CONSTANTS
-
-DEFAULT_DATABASE_PATH = "/project/marcotte/marcotte/ms/database"
-DEFAULT_MZ_PATH = "."
-DEFAULT_OUTDIR = "pepxml"
-DEFAULT_PARAMS_GLOB = "*.params"
-DEFAULT_PARAMS_FILE = Dir[DEFAULT_PARAMS_GLOB].first
-DEFAULT_MS_MODEL = 'LCQ'
-DEFAULT_MASS_ANALYZER = 'Ion Trap'
-##############################################################
-
-#require 'spec_id/sequest/pepxml'  # dies of this guy is called (why???)
-require 'spec_id/proph/pep_summary'  # <- he requests the above...hmmm
-require 'spec_id'
-require 'optparse'
-require 'ostruct'
-require 'fileutils'
-require 'spec_id/srf'
-
-# establish the default database path after examining env vars
-def_dbpath = nil
-db_env_var = ENV["BIOWORKS_DBPATH"]
-if db_env_var
-  def_dbpath = db_env_var
-else
-  def_dbpath = DEFAULT_DATABASE_PATH
-end
-
-opt = OpenStruct.new
-
-opt_obj = OptionParser.new do |op|
-  progname = File.basename(__FILE__)
-  op.banner = "\nusage: #{progname} [options] <file>.srf ..."
-  op.separator "usage: #{progname} [options] <bioworks>.srg"
-  op.separator "usage: #{progname} [options] <bioworks>.xml"
-  op.separator ""
-  op.separator "Takes srf files or the xml exported output of Bioworks multi-consensus view"
-  op.separator "(no filtering) and outputs pepXML files (to feed the trans-proteomic pipeline)."
-  op.separator "Additionally, will group .srf files into an .srg file (like 'srf_group.rb')"
-  op.separator ""
-  op.separator "Options:"
-  op.on('-h', '--help', "display this and more notes and exit") {|v| opt.help = v }
-  op.on('-o', '--outdir path', "output directory     d: '#{DEFAULT_OUTDIR}'") {|v| opt.outdir = v }
-  op.on('--sample_enzyme <type>', "For digested samples run with no enzymatic",
-                                  "search constraint, the enzyme used for",
-                                  "digestion, options: 'Trypsin_KR_P'") {|v| 
-    case v
-    when 'Trypsin_KR_P'
-      opt.sample_enzyme = SampleEnzyme.new("trypsin")
-    else
-      raise ArgumentError, "Don't recognize enzyme: #{v}"
-    end
-  } 
-  op.on('-a', '--all_hits', "includes all hits, not just top xcorr") {|v| opt.all_hits = v }
-  op.on('--deltacn_orig', "top hit deltacn = 0.0, (no deltacnstar att)") {|v| opt.deltacn_orig = v }
-  op.on('-m', '--mspath path', "path to MS files     d: '#{DEFAULT_MZ_PATH}'") {|v| opt.mspath = v }
-  op.on('--copy_mzxml', "copies mzXML files to outdir path"){|v| opt.copy_mzxml = v }
-
-  op.separator ""
-  op.separator "bioworks.xml files may require additional options:"
-  op.separator ""
-  op.on('-p', '--params file', "sequest params file  d: '#{DEFAULT_PARAMS_FILE}'") {|v| opt.params = v }
-  op.on('-d', '--dbpath path', "path to databases    d: '#{DEFAULT_DATABASE_PATH}'") {|v| opt.dbpath = v }
-  op.on('--model <LCQ|Orbi|string>', "MS model      (xml)  d: '#{DEFAULT_MS_MODEL}'") {|v| opt.model = v }
-  op.on('--mass_analyzer <string>',  "Mass Analyzer (xml)  d: '#{DEFAULT_MASS_ANALYZER}'") {|v| opt.mass_analyzer = v }
-
-end
-
-more_notes = "
-Notes:
-
-  mspath: Directory to RAW or mzXML files.
-          This option is needed to view Pep3D files 
-          and is critical with Bioworks 3.2 xml export files
-  outdir: Path will be created if it does not already exist.
-  (xml) : only bioworks.xml files need to include this information
-  model : LCQ -> 'LCQ Deca XP Plus'
-        : Orbi -> 'LTQ Orbitrap'
-        : other string -> That's the string that will be used.
-
-  options with spaces should be quoted: e.g., \"Time of Flight\"
-
-Database Path:
-
-  If the database path in the sequest.params file is valid, that will be used.
-  Otherwise, will try (in order):
-      1. --dbpath or -d option
-      1. environmental variable BIOWORKS_DBPATH (currently: '#{db_env_var}')
-      2. constant at top of this script         (currently: '#{DEFAULT_DATABASE_PATH}')
-  "
-
-
-
-opt_obj.parse!
-
-# intercept before argv count
-if opt.help
-  puts opt_obj
-  puts more_notes
-  exit
-end
-
-if ARGV.size < 1
-  puts opt_obj 
-  exit
-end
-
-
-
-opt.outdir ||= DEFAULT_OUTDIR
-
-
-files = ARGV.to_a
-bioworks_file = files[0]
-if files[0] =~ /\.srf/i
-  srg_file = 'bioworks.srg'
-  if File.exist? srg_file
-    srg_file = 'bioworks.tmp.srg'
-  end
-  srg = SRFGroup.new(files)
-  srg.to_srg(srg_file)
-unless File.exist? srg_file
-  abort "couldn't create #{srg_file} from: #{files.join(', ')}" 
-end
-bioworks_file = srg_file
-end
-
-
-case opt.model
-when "LCQ"
-  model = 'LCQ Deca XP Plus'
-when "Orbi"
-  model = 'LTQ Orbitrap'
-else
-  model = opt.model
-end
-
-opt.dbpath ||= def_dbpath
-opt.mspath ||= DEFAULT_MZ_PATH
-opt.params ||= DEFAULT_PARAMS_FILE
-opt.mass_analyzer ||= DEFAULT_MASS_ANALYZER
-opt.model ||= DEFAULT_MS_MODEL
-
-xml_objs = Sequest::PepXML.set_from_bioworks(bioworks_file, {:params => opt.params, :ms_data => opt.mspath, :out_path => opt.outdir, :model => model, :backup_db_path => opt.dbpath, :copy_mzxml => opt.copy_mzxml, :ms_mass_analyzer => opt.mass_analyzer, :print => true, :all_hits => opt.all_hits, :deltacn_orig => opt.deltacn_orig, :sample_enzyme => opt.sample_enzyme})
-