sequence_logo 1.2.1 → 1.2.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 3828e40c98389a3aac1a0c04cb13d766fcf70188
+  metadata.gz: 49b8d62c88fef94b51afe103ca310f00916efdec
+  data.tar.gz: bd8990d9f2ae74d63a2565152ef5f9a32044c4b2
 SHA512:
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+  data.tar.gz: 51dd020446c145136fad74b845cd6711423439bfa41a3d4cd895b2fb2fbd910f307d175fd83aaeb5d828377bf897c173141ab01a7032e762b25e66f418591f12

data/lib/sequence_logo/di_pm.rb

@@ -89,7 +89,7 @@ module Bioinform
           sum_dependent_on_first_letter(pos)
         } + [ sum_dependent_on_second_letter(matrix.last) ]
 
-        PCM.new(mono_matrix)
+        PCM.new(mono_matrix, validator: Bioinform::MotifModel::PCM::DIFFERENT_COUNTS_VALIDATOR)
       end
     end
 

data/lib/sequence_logo/exec/glue_logos.rb

@@ -9,7 +9,7 @@ def load_alignment_infos(alignment_lines)
     shift = shift.to_i
     orientation = orientation.downcase.to_sym
 
-    ppm = Bioinform::MotifModel::PCM.from_file(filename)
+    ppm = Bioinform::MotifModel::PCM.from_file(filename, validator: Bioinform::MotifModel::PCM::DIFFERENT_COUNTS_VALIDATOR)
     ppm.name ||= motif_name
 
     raise 'Unknown orientation'  unless [:direct, :revcomp].include?(orientation)

data/lib/sequence_logo/exec/sequence_logo.rb

@@ -113,7 +113,7 @@ begin
       if options[:from_dinucleotide]
         ppm = Bioinform::MotifModel::DiPCM.from_file(filename).to_mono
       else
-        ppm = Bioinform::MotifModel::PCM.from_file(filename)
+        ppm = Bioinform::MotifModel::PCM.from_file(filename, validator: Bioinform::MotifModel::PCM::DIFFERENT_COUNTS_VALIDATOR)
       end
 
       logo = SequenceLogo::PPMLogo.new( ppm,

data/lib/sequence_logo/version.rb

@@ -1,3 +1,3 @@
 module SequenceLogo
-  VERSION = "1.2.1"
+  VERSION = "1.2.2"
 end

data/sequence_logo.gemspec

@@ -18,4 +18,5 @@ Gem::Specification.new do |gem|
   gem.version       = SequenceLogo::VERSION
   
   gem.add_dependency('rmagick', '~> 2.13')
+  gem.add_dependency('bioinform', '~> 0.3.1')
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sequence_logo
 version: !ruby/object:Gem::Version
-  version: 1.2.1
+  version: 1.2.2
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-20 00:00:00.000000000 Z
+date: 2016-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rmagick
@@ -24,6 +24,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.13'
+- !ruby/object:Gem::Dependency
+  name: bioinform
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.3.1
 description: |
   SequenceLogo is a tool for drawing sequence logos of motifs. It gets Positional Count Matrices(PCMs) or IUPAC sequences as input and generates png-logos for a motif. Also one can create logo for reverse complement or even generate logos for a whole collection of motifs.
     Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence (see http://weblogo.berkeley.edu/)