mspire 0.8.6.2 → 0.8.7

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: b2a81f049d60fc8583b6983a65bba777cb099859
+  data.tar.gz: 801edda8a819a0555966b7039dea2dcedf75f22c
+SHA512:
+  metadata.gz: 078df42a60519c0a9431be10957c4bab2f8a2060c7a53e6d6d1e58962654149eaff385328d5f19c79b4885938d488e0db25c68a7259a2d75702d96868bf991ec
+  data.tar.gz: cc584e4bb9df969d60d497db14e9af86dd5332254a5fc9fefbf9186cc040891a8e9ae40b09dd5caa3a7685df8cf08ae635d33a1aa4cf663c0a6e6c267a08602b

data/.gitignore

@@ -0,0 +1,7 @@
+pkg
+test_files_large
+doc/output/*
+.*.swp
+*.gemspec
+playing_around_with
+coverage

data/.travis.yml

@@ -0,0 +1,6 @@
+language: ruby
+rvm:
+  - 2.0.0
+  - 1.9.3
+#  - jruby-19mode # JRuby in 1.9 mode
+#  - rbx-19mode

data/Gemfile

@@ -0,0 +1,6 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in mspire.gemspec
+gemspec
+
+gem 'coveralls', require: false

data/README.md

@@ -1,5 +1,10 @@
 # mspire
 
+[![Gem Version][GV img]][Gem Version]
+[![Build Status][BS img]][Build Status]
+[![Dependency Status][DS img]][Dependency Status]
+[![Code Climate][CC img]][Code Climate]
+
 Mspire is a full featured library for working with mass spectrometry data,
 particularly proteomic, metabolomic and lipidomic data sets.  It aims to be
 fast, robust, and beautiful.
@@ -159,3 +164,14 @@ trypsin.digest("AACCKDDEERFFKPGG") # => ["AACCK", "DDEER", "FFKPGG"]
 ## Copyright
 
 MIT license.  See LICENSE for details.
+
+[Gem Version]: https://rubygems.org/gems/mspire
+[Build Status]: https://travis-ci.org/princelab/mspire
+[travis pull requests]: https://travis-ci.org/princelab/mspire/pull_requests
+[Dependency Status]: https://gemnasium.com/princelab/mspire
+[Code Climate]: https://codeclimate.com/github/princelab/mspire
+
+[GV img]: https://badge.fury.io/rb/mspire.png
+[BS img]: https://travis-ci.org/princelab/mspire.png
+[DS img]: https://gemnasium.com/princelab/mspire.png
+[CC img]: https://codeclimate.com/github/princelab/mspire.png

data/Rakefile

@@ -1,33 +1,4 @@
-require 'rubygems'
-require 'rake'
-require 'rspec/core/rake_task'
-require 'yard'
-
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
-  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
-  gem.name = "mspire"
-  gem.homepage = "http://github.com/princelab/mspire"
-  gem.license = "MIT"
-  gem.summary = %Q{mass spectrometry proteomics, lipidomics, and tools}
-  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", "~> 1.5.9"
-  gem.add_dependency "bsearch", ">= 1.5.0"
-  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"
-  # 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", "~> 2.13"
-  gem.add_development_dependency "jeweler", "~> 1.8.4"
-  #gem.add_development_dependency "rcov", ">= 0"
-end
-Jeweler::RubygemsDotOrgTasks.new
+require "bundler/gem_tasks"
 
 require 'rspec/core'
 require 'rspec/core/rake_task'
@@ -35,23 +6,6 @@ RSpec::Core::RakeTask.new(:spec) do |spec|
   spec.pattern = FileList['spec/**/*_spec.rb']
 end
 
-YARD::Rake::YardocTask.new do |t|
-  t.files   = ['lib/**/*.rb', 'obo/**/*', 'README.md', 'script/**/*']   # optional
-  #t.options = ['--any', '--extra', '--opts'] # optional
-end
-
-RSpec::Core::RakeTask.new(:rcov) do |spec|
-  spec.pattern = 'spec/**/*_spec.rb'
-  spec.rcov = 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
 
 require 'rdoc/task'
@@ -59,7 +13,7 @@ Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 
   rdoc.rdoc_dir = 'rdoc'
-  rdoc.title = "mspire #{version}"
+  rdoc.title = "rubabel #{version}"
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
 end

data/lib/mspire/ident/pepxml/modifications.rb

@@ -72,7 +72,7 @@ class Mspire::Ident::Pepxml::TerminalModification
   def to_xml(builder=nil)
     xmlb = builder || Nokogiri::XML::Builder.new
     #short_element_xml_from_instance_vars("terminal_modification")
-   attrs = [:terminus, :massdiff, :mass, :variable, :protein_terminus, :description].map {|at| v=send(at) ; [at,v] if v }
+   attrs = [:terminus, :massdiff, :mass, :variable, :protein_terminus, :description].map {|at| v=send(at) ; [at,v] if v }.compact
    hash = Hash[attrs] 
     hash[:massdiff] = hash[:massdiff].to_plus_minus_string
     xmlb.terminal_modification(hash)

data/lib/mspire/ident/pepxml/search_hit/modification_info.rb

@@ -44,7 +44,8 @@ Mspire::Ident::Pepxml::SearchHit::ModificationInfo = Struct.new(:modified_peptid
     ## Collect the modifications:
     ## Create the attribute string:
     atts = [:mod_nterm_mass, :mod_cterm_mass, :modified_peptide]
-    atts.map! {|at| (v=send(at)) && [at, v] }.compact
+    atts.map! {|at| (v=send(at)) && [at, v] }
+    atts.compact!
     xmlb.modification_info(Hash[atts]) do |xmlb|
       mod_aminoacid_masses.andand.each do |mod_aa_mass|
         mod_aa_mass.to_xml(xmlb)

data/lib/mspire/ident/pepxml/search_hit.rb

@@ -137,7 +137,7 @@ class Mspire::Ident::Pepxml
       self
     end
 
-    Simple = Struct.new(:id, :search, :aaseq, :charge, :search_scores)
+    Simple = Struct.new(:id, :search, :aaseq, :charge, :search_scores, :analysis_results)
   end
 
 end

data/lib/mspire/ident/pepxml/spectrum_query.rb

@@ -49,7 +49,7 @@ class Mspire::Ident::Pepxml::SpectrumQuery
   def to_xml(builder=nil)
     xmlb = builder || Nokogiri::XML::Builder.new
     # all through search_specification
-    attrs = members[0, 8].map {|at| v=send(at) ; [at, v] if v }
+    attrs = members[0, 8].map {|at| v=send(at) ; [at, v] if v }.compact
     attrs_hash = Hash[attrs]
     case pepxml_version
     when 18

data/lib/mspire/ident/pepxml.rb

@@ -24,8 +24,11 @@ class Mspire::Ident::Pepxml
 
   attr_accessor :msms_pipeline_analysis
 
-  # returns an array of Mspire::Ident::Pepxml::SearchHit::Simple structs
-  def self.simple_search_hits(file)
+  # returns an array of Mspire::Ident::Pepxml::SearchHit::Simple structs will
+  # only process last result if duplicate search scores are included.  Score
+  # keys returned as symbols and values cast as Floats while analysis results
+  # are all returned as strings.
+  def self.simple_search_hits(file, &block)
     hit_values = File.open(file) do |io|
       doc = Nokogiri::XML.parse(io, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS | Nokogiri::XML::ParseOptions::STRICT)
       # we can work with namespaces, or just remove them ...
@@ -35,12 +38,24 @@ class Mspire::Ident::Pepxml
       search_hits.each_with_index.map do |search_hit,i| 
         aaseq = search_hit['peptide']
         charge = search_hit.parent.parent['assumed_charge'].to_i
-        search_score_nodes = search_hit.children.select {|node| node.name == 'search_score' }
+        nodes_by_name = search_hit.children.group_by(&:name)
         search_scores = {}
-        search_score_nodes.each do |node|
+        nodes_by_name['search_score'].each do |node|
           search_scores[node['name'].to_sym] = node['value'].to_f
         end
-        Mspire::Ident::Pepxml::SearchHit::Simple.new("hit_#{i}", Mspire::Ident::Search.new(file.chomp(File.extname(file))), aaseq, charge, search_scores)
+        analysis_results = {}
+        nodes_by_name['analysis_result'].each do |node|
+          analysis_results[node['analysis']] = node.children.map do |atnode| 
+            atnode.attribute_nodes.each_with_object({}) do |attribute, hash|
+              hash[attribute.name] = attribute.value
+            end
+          end
+        end
+        hit = Mspire::Ident::Pepxml::SearchHit::Simple.new("hit_#{i}", Mspire::Ident::Search.new(file.chomp(File.extname(file))), aaseq, charge, search_scores, analysis_results)
+        if block
+          block.call(search_hit_n.parent.parent)
+        end
+        hit
       end
     end
   end

data/lib/mspire/version.rb

@@ -0,0 +1,3 @@
+module Mspire
+  VERSION = "0.8.7"
+end

data/lib/mspire.rb

@@ -1,7 +1,5 @@
-
-require 'mspire/mass/aa' # requires mspire/mass & therefore mspire/molecular_formula
+require 'mspire/version'
 
 module Mspire
-  VERSION = IO.read(File.join(File.dirname(__FILE__), '..', 'VERSION')).chomp
   CITE = "Prince JT, Marcotte EM. mspire: mass spectrometry proteomics in Ruby. Bioinformatics. 2008. 24(23):2796-7."
 end