bio-ngs 0.3.2.alpha.01 → 0.4.2.alpha.01

data/Gemfile

@@ -5,7 +5,7 @@ source "http://rubygems.org"
 
 gem "bio", ">= 1.4.2"
 gem "bio-bwa", ">= 0.2.2"
-gem "bio-samtools", ">= 0.0.0"
+gem "bio-samtools", ">= 0.3.2"
 gem "thor", ">= 0.14.6"
 gem "rubyvis", ">= 0.5.0"
 gem "daemons", ">= 1.1.0"
@@ -14,6 +14,7 @@ gem "activerecord",">= 3.0.5"
 gem "sqlite3", ">= 1.3.3"
 gem "bio-blastxmlparser"
 gem "progressbar",">= 0.9.0"
+gem "rake", "0.9.2.2"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -21,14 +22,14 @@ group :development do
   gem "shoulda", ">= 0"
   gem "bundler", "~> 1.0.0"
   gem "jeweler", "~> 1.5.2"
-  gem "rcov", ">= 0"
+  gem "rcov", "~> 0.9.11"
   gem "bio", ">= 1.4.2"
   gem "thor", ">= 0.14.6"
   gem "ffi", ">= 1.0.6"
   gem "rubyvis", ">= 0.5.0"
   gem "rspec", ">= 2.5.0"
   gem "daemons", ">= 1.1.0"
-  gem "bio-samtools", ">= 0.0.0"
+  gem "bio-samtools", ">= 0.3.2"
   gem "ruby-ensembl-api", ">= 1.0.1"
   gem 'bio-bwa', ">= 0.2.2"
   gem "activerecord",">= 3.0.5"
@@ -36,4 +37,5 @@ group :development do
   gem "bio-blastxmlparser"
   gem "progressbar",">= 0.9.0"
   gem "json"
+  gem "rake", "0.9.2.2"
 end

data/Gemfile.lock

@@ -1,18 +1,18 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activemodel (3.1.1)
-      activesupport (= 3.1.1)
+    activemodel (3.2.1)
+      activesupport (= 3.2.1)
       builder (~> 3.0.0)
-      i18n (~> 0.6)
-    activerecord (3.1.1)
-      activemodel (= 3.1.1)
-      activesupport (= 3.1.1)
-      arel (~> 2.2.1)
+    activerecord (3.2.1)
+      activemodel (= 3.2.1)
+      activesupport (= 3.2.1)
+      arel (~> 3.0.0)
       tzinfo (~> 0.3.29)
-    activesupport (3.1.1)
+    activesupport (3.2.1)
+      i18n (~> 0.6)
       multi_json (~> 1.0)
-    arel (2.2.1)
+    arel (3.0.0)
     bio (1.4.2)
     bio-blastxmlparser (1.0.1)
       bio-logger (>= 1.0.0)
@@ -20,44 +20,49 @@ GEM
     bio-bwa (0.2.2)
     bio-logger (1.0.0)
       log4r (>= 1.1.9)
-    bio-samtools (0.2.4)
-      bio (>= 1.4.1)
+    bio-samtools (0.5.0)
+      bio (>= 1.4.2)
       ffi
     builder (3.0.0)
-    daemons (1.1.4)
+    daemons (1.1.8)
     diff-lcs (1.1.3)
-    ffi (1.0.9)
+    ffi (1.0.11)
+    ffi (1.0.11-java)
     git (1.2.5)
     i18n (0.6.0)
     jeweler (1.5.2)
       bundler (~> 1.0.0)
       git (>= 1.2.5)
       rake
-    json (1.6.1)
-    log4r (1.1.9)
-    multi_json (1.0.3)
+    json (1.6.5)
+    json (1.6.5-java)
+    log4r (1.1.10)
+    multi_json (1.0.4)
     nokogiri (1.5.0)
-    progressbar (0.9.1)
-    rake (0.9.2)
+    nokogiri (1.5.0-java)
+    progressbar (0.10.0)
+    rake (0.9.2.2)
     rcov (0.9.11)
-    rspec (2.6.0)
-      rspec-core (~> 2.6.0)
-      rspec-expectations (~> 2.6.0)
-      rspec-mocks (~> 2.6.0)
-    rspec-core (2.6.4)
-    rspec-expectations (2.6.0)
+    rcov (0.9.11-java)
+    rspec (2.8.0)
+      rspec-core (~> 2.8.0)
+      rspec-expectations (~> 2.8.0)
+      rspec-mocks (~> 2.8.0)
+    rspec-core (2.8.0)
+    rspec-expectations (2.8.0)
       diff-lcs (~> 1.1.2)
-    rspec-mocks (2.6.0)
+    rspec-mocks (2.8.0)
     ruby-ensembl-api (1.0.1)
       activerecord
       bio (>= 1)
-    rubyvis (0.5.0)
+    rubyvis (0.5.1)
     shoulda (2.11.3)
-    sqlite3 (1.3.4)
+    sqlite3 (1.3.5)
     thor (0.14.6)
-    tzinfo (0.3.30)
+    tzinfo (0.3.31)
 
 PLATFORMS
+  java
   ruby
 
 DEPENDENCIES
@@ -65,14 +70,15 @@ DEPENDENCIES
   bio (>= 1.4.2)
   bio-blastxmlparser
   bio-bwa (>= 0.2.2)
-  bio-samtools (>= 0.0.0)
+  bio-samtools (>= 0.3.2)
   bundler (~> 1.0.0)
   daemons (>= 1.1.0)
   ffi (>= 1.0.6)
   jeweler (~> 1.5.2)
   json
   progressbar (>= 0.9.0)
-  rcov
+  rake (= 0.9.2.2)
+  rcov (~> 0.9.11)
   rspec (>= 2.5.0)
   ruby-ensembl-api (>= 1.0.1)
   rubyvis (>= 0.5.0)

data/README.rdoc

@@ -67,6 +67,13 @@ Most of this tasks create sub-processes to speed up conversions
 
 = ForDevelopers
 
+== Contribute 
+=== Clone Main Repository
+This command will crate a local copy of the main repository
+    git clone https://github.com/helios/bioruby-ngs
+=== Install Bioinformatics Tools into the repository directory
+    rake devenv:bio_tools
+
 == Wrapper
 Bio-Ngs comes with a build-in wrapper to map binary software directly in BioRuby as objects. From this wrapper object is possible to create Thor task as well, with a lot of sugar.
 === Wrapping a binary
@@ -187,6 +194,32 @@ You can create a new wrapper and configure it and run it from inside a Thor's ta
       end #Ngs
     end #Bio
 
+== Features
+=== Iterators for output files
+
+Example CuffDiff.  In this class is possible to define an iterator for a specific set of output files: genes, isoforms, tss_groups, cds.
+To activate the iterator is just a matter of call a class method in the class definition
+    class Bio::Ngs::Cufflinks::Diff
+      #... all the previous definitions
+      #define iterators
+      add_iterator_for :genes
+      add_iterator_for :isoforms
+      add_iterator_for :cds
+      add_iterator_for :tss_groups
+    end
+  
+This is an example of CuffDiff, parsing genes.fpkm_tracking file:
+
+    Bio::Ngs::Cufflinks::Diff.foreach_gene_tracked("path_to_cuffdiff_output_directory") do |gene_fpkm_track|
+      expression_profile = (1..7).map do |sample_idx|
+        gene_fpkm_track["q#{sample_idx}_FPKM"].to_f
+      end
+      
+      #do your stuff accessing this tabular file with gene_fpkm_track["name of the field"]
+    end
+
+In this case internally CSV library has been used to parse in an easy way the file, there is a lack of performances with huge files, gaining in flexibility.
+
 === Notes
 * It's possible to add more sugar and we are working hard on it
 * aliases are not well supported at this time. ToDo

data/VERSION

@@ -1 +1 @@
-0.3.2.alpha.01
+0.4.2.alpha.01

data/bio-ngs.gemspec

@@ -4,16 +4,16 @@
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{bio-ngs}
-  s.version = "0.3.2.alpha.01"
+  s.name = "bio-ngs"
+  s.version = "0.4.2.alpha.01"
 
   s.required_rubygems_version = Gem::Requirement.new("> 1.3.1") if s.respond_to? :required_rubygems_version=
-  s.authors = [%q{Francesco Strozzi}, %q{Raoul J.P. Bonnal}]
-  s.date = %q{2011-10-10}
-  s.description = %q{bio-ngs provides a framework for handling NGS data with BioRuby}
-  s.email = %q{francesco.strozzi@gmail.com}
-  s.executables = [%q{biongs}]
-  s.extensions = [%q{ext/mkrf_conf.rb}]
+  s.authors = ["Francesco Strozzi", "Raoul J.P. Bonnal"]
+  s.date = "2012-02-13"
+  s.description = "bio-ngs provides a framework for handling NGS data with BioRuby"
+  s.email = "francesco.strozzi@gmail.com"
+  s.executables = ["biongs"]
+  s.extensions = ["ext/mkrf_conf.rb"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -34,6 +34,7 @@ Gem::Specification.new do |s|
     "lib/bio/appl/ngs/blast.rb",
     "lib/bio/appl/ngs/bowtie-inspect.rb",
     "lib/bio/appl/ngs/cufflinks.rb",
+    "lib/bio/appl/ngs/cufflinks/iterators.rb",
     "lib/bio/appl/ngs/fastx.rb",
     "lib/bio/appl/ngs/samtools.rb",
     "lib/bio/appl/ngs/sff_extract.rb",
@@ -68,6 +69,7 @@ Gem::Specification.new do |s|
     "lib/tasks/history.thor",
     "lib/tasks/homology.thor",
     "lib/tasks/ontology.thor",
+    "lib/tasks/pre.thor",
     "lib/tasks/project.thor",
     "lib/tasks/quality.thor",
     "lib/tasks/rna.thor",
@@ -95,11 +97,11 @@ Gem::Specification.new do |s|
     "test/test_ontology.rb",
     "test/test_utils.rb"
   ]
-  s.homepage = %q{http://github.com/helios/bioruby-ngs}
-  s.licenses = [%q{MIT}]
-  s.require_paths = [%q{lib}]
-  s.rubygems_version = %q{1.8.6}
-  s.summary = %q{bio-ngs provides a framework for handling NGS data with BioRuby}
+  s.homepage = "http://github.com/helios/bioruby-ngs"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "bio-ngs provides a framework for handling NGS data with BioRuby"
   s.test_files = [
     "spec/converter_qseq_spec.rb",
     "spec/quality_spec.rb",
@@ -122,7 +124,7 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<bio>, [">= 1.4.2"])
       s.add_runtime_dependency(%q<bio-bwa>, [">= 0.2.2"])
-      s.add_runtime_dependency(%q<bio-samtools>, [">= 0.0.0"])
+      s.add_runtime_dependency(%q<bio-samtools>, [">= 0.3.2"])
       s.add_runtime_dependency(%q<thor>, [">= 0.14.6"])
       s.add_runtime_dependency(%q<rubyvis>, [">= 0.5.0"])
       s.add_runtime_dependency(%q<daemons>, [">= 1.1.0"])
@@ -131,17 +133,18 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<sqlite3>, [">= 1.3.3"])
       s.add_runtime_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_runtime_dependency(%q<progressbar>, [">= 0.9.0"])
+      s.add_runtime_dependency(%q<rake>, ["= 0.9.2.2"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<rcov>, ["~> 0.9.11"])
       s.add_development_dependency(%q<bio>, [">= 1.4.2"])
       s.add_development_dependency(%q<thor>, [">= 0.14.6"])
       s.add_development_dependency(%q<ffi>, [">= 1.0.6"])
       s.add_development_dependency(%q<rubyvis>, [">= 0.5.0"])
       s.add_development_dependency(%q<rspec>, [">= 2.5.0"])
       s.add_development_dependency(%q<daemons>, [">= 1.1.0"])
-      s.add_development_dependency(%q<bio-samtools>, [">= 0.0.0"])
+      s.add_development_dependency(%q<bio-samtools>, [">= 0.3.2"])
       s.add_development_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
       s.add_development_dependency(%q<bio-bwa>, [">= 0.2.2"])
       s.add_development_dependency(%q<activerecord>, [">= 3.0.5"])
@@ -149,10 +152,11 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_development_dependency(%q<progressbar>, [">= 0.9.0"])
       s.add_development_dependency(%q<json>, [">= 0"])
+      s.add_development_dependency(%q<rake>, ["= 0.9.2.2"])
     else
       s.add_dependency(%q<bio>, [">= 1.4.2"])
       s.add_dependency(%q<bio-bwa>, [">= 0.2.2"])
-      s.add_dependency(%q<bio-samtools>, [">= 0.0.0"])
+      s.add_dependency(%q<bio-samtools>, [">= 0.3.2"])
       s.add_dependency(%q<thor>, [">= 0.14.6"])
       s.add_dependency(%q<rubyvis>, [">= 0.5.0"])
       s.add_dependency(%q<daemons>, [">= 1.1.0"])
@@ -161,17 +165,18 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<sqlite3>, [">= 1.3.3"])
       s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_dependency(%q<progressbar>, [">= 0.9.0"])
+      s.add_dependency(%q<rake>, ["= 0.9.2.2"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<bundler>, ["~> 1.0.0"])
       s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<rcov>, ["~> 0.9.11"])
       s.add_dependency(%q<bio>, [">= 1.4.2"])
       s.add_dependency(%q<thor>, [">= 0.14.6"])
       s.add_dependency(%q<ffi>, [">= 1.0.6"])
       s.add_dependency(%q<rubyvis>, [">= 0.5.0"])
       s.add_dependency(%q<rspec>, [">= 2.5.0"])
       s.add_dependency(%q<daemons>, [">= 1.1.0"])
-      s.add_dependency(%q<bio-samtools>, [">= 0.0.0"])
+      s.add_dependency(%q<bio-samtools>, [">= 0.3.2"])
       s.add_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
       s.add_dependency(%q<bio-bwa>, [">= 0.2.2"])
       s.add_dependency(%q<activerecord>, [">= 3.0.5"])
@@ -179,11 +184,12 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
       s.add_dependency(%q<progressbar>, [">= 0.9.0"])
       s.add_dependency(%q<json>, [">= 0"])
+      s.add_dependency(%q<rake>, ["= 0.9.2.2"])
     end
   else
     s.add_dependency(%q<bio>, [">= 1.4.2"])
     s.add_dependency(%q<bio-bwa>, [">= 0.2.2"])
-    s.add_dependency(%q<bio-samtools>, [">= 0.0.0"])
+    s.add_dependency(%q<bio-samtools>, [">= 0.3.2"])
     s.add_dependency(%q<thor>, [">= 0.14.6"])
     s.add_dependency(%q<rubyvis>, [">= 0.5.0"])
     s.add_dependency(%q<daemons>, [">= 1.1.0"])
@@ -192,17 +198,18 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<sqlite3>, [">= 1.3.3"])
     s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
     s.add_dependency(%q<progressbar>, [">= 0.9.0"])
+    s.add_dependency(%q<rake>, ["= 0.9.2.2"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<bundler>, ["~> 1.0.0"])
     s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
-    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<rcov>, ["~> 0.9.11"])
     s.add_dependency(%q<bio>, [">= 1.4.2"])
     s.add_dependency(%q<thor>, [">= 0.14.6"])
     s.add_dependency(%q<ffi>, [">= 1.0.6"])
     s.add_dependency(%q<rubyvis>, [">= 0.5.0"])
     s.add_dependency(%q<rspec>, [">= 2.5.0"])
     s.add_dependency(%q<daemons>, [">= 1.1.0"])
-    s.add_dependency(%q<bio-samtools>, [">= 0.0.0"])
+    s.add_dependency(%q<bio-samtools>, [">= 0.3.2"])
     s.add_dependency(%q<ruby-ensembl-api>, [">= 1.0.1"])
     s.add_dependency(%q<bio-bwa>, [">= 0.2.2"])
     s.add_dependency(%q<activerecord>, [">= 3.0.5"])
@@ -210,6 +217,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<bio-blastxmlparser>, [">= 0"])
     s.add_dependency(%q<progressbar>, [">= 0.9.0"])
     s.add_dependency(%q<json>, [">= 0"])
+    s.add_dependency(%q<rake>, ["= 0.9.2.2"])
   end
 end
 

data/ext/mkrf_conf.rb

@@ -57,8 +57,6 @@ path_binary = File.join(path_external,"bin","common")
     task :compile do
       ["common", Bio::Ngs::Utils.os_type].each do |kind_software|
         path_binary = File.join("#{path_external}", 'bin', kind_software)
-        #download common libraries or tools
-        #download specific OS binaries or libraries    
         versions[kind_software].each do |tool, info|
           Bio::Ngs::Utils.compile_source(tool, info, "#{path_external}", path_binary) if info["type"]=="source"
         end #versions

data/lib/bio/appl/ngs/cufflinks/iterators.rb

@@ -0,0 +1,35 @@
+
+#use CSV to iterate over all the genes expressed during the differential expression.
+
+module Bio
+  module Ngs          
+    module Cufflinks
+        module Utils
+          
+          def self.included(base)
+            base.extend(ClassMethods)
+          end            
+          
+          module ClassMethods
+            require 'csv'            
+            # Create an iterator using the specified type_name file.
+            # in case of Cufflinks type_file_name can be gene,isoform, cds, tss_group
+            def add_iterator_for( type_file_name, opts={})
+              plural_name = type_file_name = type_file_name.to_s
+              if %w(genes isoforms cds tss_groups).include?(type_file_name)
+                type_file_name=type_file_name[0..-2] if type_file_name!="cds"
+                self.class.send  :define_method, "foreach_#{type_file_name}_tracked" do |path = '.', &block|
+                  file_name = File.join(path,"#{plural_name}.fpkm_tracking")
+                  CSV.foreach(file_name, headers: true, converters: :numeric, col_sep:"\t") do |data|
+                    block.call(data)
+                  end #cvs_foreach
+                end #define_method
+             else
+                raise "#{type_file_name} is not a valid base name for cuffdiff's output, must be plural and in this set: genes, cds, isoforms, tss_groups"
+             end #if
+            end #iterator
+          end #ClassMethod
+        end #Utils
+    end #Cufflinks
+  end #Ngs
+end #Bio