bioinform 0.2.1 → 0.2.4

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 65e5cdc14dec4d99cb0266d8d4bf589ef44efb99
+SHA256:
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+  data.tar.gz: 7fe03d3cb26177146233d5db6715c49f7a72338c05bbcbf35dc54b5cb7e8093b
 SHA512:
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data/lib/bioinform/conversion_algorithms/pcm2pwm_converter.rb

@@ -17,7 +17,7 @@ module Bioinform
         when Numeric
           @pseudocount
         when :log
-          Math.log(pcm.count)
+          Math.log([pcm.count, 2].max)
         when :sqrt
           Math.sqrt(pcm.count)
         when Proc

data/lib/bioinform/data_models/named_model.rb

@@ -16,8 +16,8 @@ module Bioinform
 
       private :motif_klasses, :motif?
 
-      def method_missing(meth, *args, &block)
-        result = model.public_send(meth, *args, &block)
+      def method_missing(meth, *args, **kwargs, &block)
+        result = model.public_send(meth, *args, **kwargs, &block)
         if motif?(result) && ! result.is_a?(self.class)
           self.class.new(result, name)
         else

data/lib/bioinform/parsers/matrix_parser.rb

@@ -16,7 +16,7 @@ module Bioinform
     end
 
     def need_transpose?(matrix)
-      (matrix.size == @fix_nucleotides_number) && (matrix.first.size != 4)
+      (matrix.size == @fix_nucleotides_number) && (matrix.first.size != @fix_nucleotides_number)
     end
     private :need_transpose?
 

data/lib/bioinform/version.rb

@@ -1,3 +1,3 @@
 module Bioinform
-  VERSION = "0.2.1"
+  VERSION = "0.2.4"
 end

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: bioinform
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.2.4
 platform: ruby
 authors:
 - Ilya Vorontsov
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-20 00:00:00.000000000 Z
+date: 1980-01-02 00:00:00.000000000 Z
 dependencies: []
 description: A bunch of useful classes for bioinformatics
 email:
@@ -104,7 +103,6 @@ files:
 homepage: ''
 licenses: []
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -119,9 +117,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.4.1
-signing_key: 
+rubygems_version: 3.7.2
 specification_version: 4
 summary: Classes for work with different input formats of positional matrices and
   IUPAC-words and making simple transform and statistics with them. Also module includes