bio-gngm 0.2.0 → 0.2.1

data/test/test_bio-gngm.rb

@@ -46,7 +46,7 @@ class TestBioGngm < Test::Unit::TestCase
                      :format => :bam, 
                      :fasta => "/Users/macleand/Desktop/ngm/TAIR9_chr_all.fas", 
                      :samtools => {:r => "1:100-10000"},
-                     :histo_bin_width => 100,
+                     :histo_bin_width => 100
 
       )
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-gngm
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-15 00:00:00.000000000 Z
+date: 2012-12-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70148237802860 !ruby/object:Gem::Requirement
+  requirement: &70260854174020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *70148237802860
+  version_requirements: *70260854174020
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &70148237802000 !ruby/object:Gem::Requirement
+  requirement: &70260854172940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: 0.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *70148237802000
+  version_requirements: *70260854172940
 - !ruby/object:Gem::Dependency
   name: rinruby
-  requirement: &70148237801440 !ruby/object:Gem::Requirement
+  requirement: &70260854172180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 2.0.2
   type: :runtime
   prerelease: false
-  version_requirements: *70148237801440
+  version_requirements: *70260854172180
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &70148237800620 !ruby/object:Gem::Requirement
+  requirement: &70260854171460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70148237800620
+  version_requirements: *70260854171460
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &70148237793360 !ruby/object:Gem::Requirement
+  requirement: &70260854170300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *70148237793360
+  version_requirements: *70260854170300
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &70148237791880 !ruby/object:Gem::Requirement
+  requirement: &70260854168400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70148237791880
+  version_requirements: *70260854168400
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &70148237789480 !ruby/object:Gem::Requirement
+  requirement: &70260854166740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70148237789480
+  version_requirements: *70260854166740
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &70148237788820 !ruby/object:Gem::Requirement
+  requirement: &70260854158740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,10 +98,10 @@ dependencies:
         version: 1.4.2
   type: :development
   prerelease: false
-  version_requirements: *70148237788820
+  version_requirements: *70260854158740
 - !ruby/object:Gem::Dependency
   name: bio-samtools
-  requirement: &70148237788260 !ruby/object:Gem::Requirement
+  requirement: &70260854156720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -109,10 +109,10 @@ dependencies:
         version: 0.5.0
   type: :development
   prerelease: false
-  version_requirements: *70148237788260
+  version_requirements: *70260854156720
 - !ruby/object:Gem::Dependency
   name: rinruby
-  requirement: &70148237787540 !ruby/object:Gem::Requirement
+  requirement: &70260854154940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,10 +120,10 @@ dependencies:
         version: 2.0.2
   type: :development
   prerelease: false
-  version_requirements: *70148237787540
+  version_requirements: *70260854154940
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &70148237787000 !ruby/object:Gem::Requirement
+  requirement: &70260854152960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -131,7 +131,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70148237787000
+  version_requirements: *70260854152960
 description: Identify causative mutations in a model genome from NGS reads using the
   NGM method.
 email: maclean.daniel@gmail.com
@@ -151,6 +151,7 @@ files:
 - bio-gngm.gemspec
 - doc/Bio.html
 - doc/Bio/DB.html
+- doc/Bio/DB/FastaLengthDB.html
 - doc/Bio/DB/Pileup.html
 - doc/Bio/DB/Vcf.html
 - doc/Bio/Util.html
@@ -207,13 +208,16 @@ files:
 - doc/rdoc.css
 - doc/table_of_contents.html
 - examples/.DS_Store
+- examples/Chr1.html
+- examples/gngm_qtl_mapping_HTML_maker_set_options.rb
 - examples/make_histograms.rb
 - examples/make_threads.rb
 - examples/make_threads_isize.rb
+- examples/pileup.txt
+- examples/snps.vcf
 - examples/use_indels.rb
 - lib/bio-gngm.rb
 - lib/bio/util/bio-gngm.rb
-- lib/bio/util/mutation_effects.rb
 - scripts/get_subseq.rb
 - scripts/make_histograms_laerfyve.rb
 - scripts/make_histograms_laerfyve_stitched.rb
@@ -261,7 +265,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 729394422036910323
+      hash: -3269081301574105194
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/lib/bio/util/mutation_effects.rb

@@ -1,39 +0,0 @@
-require 'bio'
-
-
-module Bio
-  class Util
-    def self.read_gff3(fn)
-      genearray=Array.new
-      mRNAhash=Hash.new
-      exonhash=Hash.new
-      tehash=Hash.new
-      lastid = ''
-      lastrecord = nil
-      gff3 = Bio::GFF::GFF3.new(File.read(fn))
-      gff3.records.each do | record |
-       feature_type = record.feature_type
-       if(feature_type == 'gene')
-         genearray << record.id
-       elsif(feature_type == 'mRNA')
-         parent = record.get_attribute('Parent')
-        if mRNAhash[parent] == nil
-          mRNAhash[parent] = [record]
-        else 
-          mRNAhash[parent] << record
-        end
-       elsif(feature_type == 'transposable_element')
-        #--- not yet implemented
-       elsif(feature_type == 'exon')
-        parents = record.get_attributes('Parent')
-        parents.each do |parent|
-         if exonhash[parent] == nil
-          exonhash[parent] = Array.new
-         end
-         exonhash[parent] << record
-         end
-       end
-      end
-    end
-  end
-end