wrnap 0.9.0 → 0.10.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 968842380493afb6092cce95df09d3c4d61bb3c4
+  metadata.gz: ce3134651886e323b97794153a83b97ada50a5db
+  data.tar.gz: a01c0eb283ca43609e06997deee79787dc98de00
 SHA512:
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+  data.tar.gz: 91d22c1f48cc245ba1135324f874858d8f2ffc0834e4b9d0383d44ed8425ecf53a3070ca8e189d9a9cbd2ce467803022185eb26deb1f1c948e2caca7c5ec97c1

data/lib/wrnap/etl/infernal.rb

@@ -0,0 +1,23 @@
+module Wrnap
+  module Etl
+    module Infernal
+      class << self
+        def parse_hit(output)
+          Stockholm.fit_structure_to_sequence(
+            *output.split(?\n).as do |infernal|
+              [
+                infernal.select { |line| line =~ /^.*\d+\s+.*\s+\d+\s*$/ }.last.match(/^.*\s+(.*)\s+\d+\s*$/)[1].upcase.gsub(/[^AUGC]/, ?.),
+                convert_infernal_to_dot_bracket(infernal.find { |line| line =~ /CS\s*$/ }.gsub(/\s+CS\s*$/, "").strip)
+              ]
+            end
+          )
+        end
+
+        def convert_infernal_to_dot_bracket(structure)
+          # http://jalview-rnasupport.blogspot.com/2010/06/parsing-wuss-notation-of-rna-secondary.html
+          structure.gsub(/[:,_-]/, ?.).gsub(/[<\[\{]/, ?().gsub(/[>\]\}]/, ?))
+        end
+      end
+    end
+  end
+end

data/lib/wrnap/etl/stockholm.rb

@@ -0,0 +1,49 @@
+module Wrnap
+  module Etl
+    module Stockholm
+      class << self
+        def load_all(file)
+          entries   = Bio::Stockholm::Reader.parse_from_file(file)[0]
+          sequences = entries.records.map(&:last).map(&:sequence)
+          structure = dot_bracket_from_stockholm(entries.gc_features["SS_cons"])
+
+          sequences.map { |sequence| fit_structure_to_sequence(sequence, structure) }
+        end
+
+        def dot_bracket_from_stockholm(structure)
+          structure.gsub(/</, ?().gsub(/>/, ?))
+        end
+
+        def fit_structure_to_sequence(sequence, consensus_structure)
+          theta_filter(prune_gaps(balanced_consensus_from_sequence(sequence, consensus_structure)))
+        end
+
+        def balanced_consensus_from_sequence(sequence, structure)
+          Wrnap::Global::Rna.init_from_string(
+            sequence,
+            Wrnap::Global::Rna.structure_from_bp_list(
+              sequence.length,
+              sequence.split(//).zip(structure.split(//)).each_with_index.inject(
+                Wrnap::Global::Rna.base_pairs(structure).map(&:to_a).select { |i, j| Wrnap::Global::Rna::CANONICAL_BASES.include?(Set.new([sequence[i], sequence[j]])) }
+              ) do |valid_bases, ((bp, symbol), i)|
+                valid_bases - (bp == ?. && symbol != ?. ? (valid_bases.select { |bps| bps.any? { |j| i == j } }) : [])
+              end
+            )
+          )
+        end
+
+        def prune_gaps(rna)
+          Wrnap::Global::Rna.init_from_array(rna.seq.split(//).zip(rna.str.split(//)).reject { |nucleotide, _| nucleotide == ?. }.transpose.map(&:join))
+        end
+
+        def theta_filter(rna)
+          # Needs to happen after gap pruning.
+          Wrnap::Global::Rna.init_from_string(
+            rna.seq,
+            Wrnap::Global::Rna.structure_from_bp_list(rna.seq.length, rna.base_pairs.map(&:to_a).select { |i, j| (j - i).abs > 3 })
+          )
+        end
+      end
+    end
+  end
+end

data/lib/wrnap/global/rna.rb

@@ -3,6 +3,8 @@ module Wrnap
     class Rna
       include Extensions
 
+      CANONICAL_BASES = Set.new << Set.new([?G, ?C]) << Set.new([?A, ?U]) << Set.new([?G, ?U])
+
       attr_accessor :comment
       attr_reader :sequence, :structure, :second_structure
 
@@ -124,6 +126,13 @@ module Wrnap
 
       alias :two_str :two_structures
 
+      def print_full
+        puts name  if name
+        puts seq   if seq
+        puts str_1 if str_1
+        puts str_2 if str_2
+      end
+
       def write_fa!(filename)
         filename.tap do |filename|
           File.open(filename, ?w) do |file|

data/lib/wrnap/version.rb

@@ -1,3 +1,3 @@
 module Wrnap
-  VERSION = "0.9.0"
+  VERSION = "0.10.0"
 end

data/lib/wrnap.rb

@@ -7,6 +7,7 @@ require "tempfile"
 require "bigdecimal"
 require "rroc"
 require "bio"
+require "bio-stockholm"
 require "entrez"
 require "active_support/inflector"
 require "active_support/core_ext/class"
@@ -19,6 +20,8 @@ require "wrnap/global/chainer"
 require "wrnap/global/entrez"
 require "wrnap/global/parser"
 require "wrnap/global/runner"
+require "wrnap/etl/infernal"
+require "wrnap/etl/stockholm"
 require "wrnap/graphing/r"
 require "wrnap/package/base"
 

data/wrnap.gemspec

@@ -28,5 +28,6 @@ Gem::Specification.new do |spec|
   spec.add_runtime_dependency "rinruby",       "~> 2.0"
   spec.add_runtime_dependency "rroc",          "~> 0.1"
   spec.add_runtime_dependency "bio",           "~> 1.4"
+  spec.add_runtime_dependency "bio-stockholm", "~> 0.0.1"
   spec.add_runtime_dependency "entrez",        "~> 0.5"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: wrnap
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.10.0
 platform: ruby
 authors:
 - Evan Senter
@@ -108,6 +108,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: bio-stockholm
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.1
 - !ruby/object:Gem::Dependency
   name: entrez
   requirement: !ruby/object:Gem::Requirement
@@ -135,6 +149,8 @@ files:
 - README.md
 - Rakefile
 - lib/wrnap.rb
+- lib/wrnap/etl/infernal.rb
+- lib/wrnap/etl/stockholm.rb
 - lib/wrnap/global/chainer.rb
 - lib/wrnap/global/entrez.rb
 - lib/wrnap/global/parser.rb