transrate 0.0.5 → 0.0.6

data/lib/transrate/assembly.rb

@@ -3,103 +3,107 @@ require 'bettersam'
 require 'csv'
 require 'forwardable'
 
-class Assembly
+module Transrate
 
-  include Enumerable
-  extend Forwardable
-  def_delegators :@assembly, :each, :<<
+  class Assembly
 
-  attr_accessor :ublast_db
-  attr_accessor :orfs_ublast_db
-  attr_accessor :protein
+    include Enumerable
+    extend Forwardable
+    def_delegators :@assembly, :each, :<<
 
-  # number of bases in the assembly
-  attr_writer :n_bases
+    attr_accessor :ublast_db
+    attr_accessor :orfs_ublast_db
+    attr_accessor :protein
 
-  # assembly filename
-  attr_accessor :file
+    # number of bases in the assembly
+    attr_writer :n_bases
 
-  # assembly n50
-  attr_reader :n50
+    # assembly filename
+    attr_accessor :file
 
-  # Reuturn a new Assembly.
-  #
-  # - +:file+ - path to the assembly FASTA file
-  def initialize file
-    @file = file
-    @assembly = []
-    @n_bases = 0
-    Bio::FastaFormat.open(file).each do |entry|
-      @n_bases += entry.length
-      @assembly << entry
+    # assembly n50
+    attr_reader :n50
+
+    # Reuturn a new Assembly.
+    #
+    # - +:file+ - path to the assembly FASTA file
+    def initialize file
+      @file = file
+      @assembly = []
+      @n_bases = 0
+      Bio::FastaFormat.open(file).each do |entry|
+        @n_bases += entry.length
+        @assembly << entry
+      end
+      @assembly.sort_by! { |x| x.length }
     end
-    @assembly.sort_by! { |x| x.length }
-  end
 
-  # Return a new Assembly object by loading sequences
-  # from the FASTA-format +:file+
-  def self.stats_from_fasta file
-    a = Assembly.new file
-    a.basic_stats
-  end
+    # Return a new Assembly object by loading sequences
+    # from the FASTA-format +:file+
+    def self.stats_from_fasta file
+      a = Assembly.new file
+      a.basic_stats
+    end
 
-  def run
-    stats = self.basic_stats
-    stats.each_pair do |key, value|
-      ivar = "@#{key.gsub(/ /, '_')}".to_sym
-      self.instance_variable_set(key, value)
+    def run
+      stats = self.basic_stats
+      stats.each_pair do |key, value|
+        ivar = "@#{key.gsub(/ /, '_')}".to_sym
+        self.instance_variable_set(key, value)
+      end
     end
-  end
 
-  # Return a hash of statistics about this assembly
-  def basic_stats
-    cumulative_length = 0.0
-    # we'll calculate Nx for all these x
-    x = [90, 70, 50, 30, 10]
-    x2 = x.clone
-    cutoff = x2.pop / 100.0
-    res = []
-    n1k = 0
-    n10k = 0
-    @assembly.each do |s|
-      new_cum_len = cumulative_length + s.length
-      prop = new_cum_len / self.n_bases
-      n1k += 1 if s.length > 1_000
-      n10k += 1 if s.length > 10_000
-      if prop >= cutoff
-        res << s.length
-        break if x2.empty?
-        cutoff = x2.pop / 100.0
+    # Return a hash of statistics about this assembly
+    def basic_stats
+      cumulative_length = 0.0
+      # we'll calculate Nx for all these x
+      x = [90, 70, 50, 30, 10]
+      x2 = x.clone
+      cutoff = x2.pop / 100.0
+      res = []
+      n1k = 0
+      n10k = 0
+      @assembly.each do |s|
+        new_cum_len = cumulative_length + s.length
+        prop = new_cum_len / self.n_bases
+        n1k += 1 if s.length > 1_000
+        n10k += 1 if s.length > 10_000
+        if prop >= cutoff
+          res << s.length
+          break if x2.empty?
+          cutoff = x2.pop / 100.0
+        end
+        cumulative_length = new_cum_len
       end
-      cumulative_length = new_cum_len
+      mean = cumulative_length / @assembly.size
+      ns = Hash[x.map { |n| "N#{n}" }.zip(res)]
+      {
+        "n_seqs" => @assembly.size,
+        "smallest" => @assembly.first.length,
+        "largest" => @assembly.last.length,
+        "n_bases" => @n_bases,
+        "mean_len" => mean,
+        "n > 1k" => n1k,
+        "n > 10k" => n10k
+      }.merge ns
     end
-    mean = cumulative_length / @assembly.size
-    ns = Hash[x.map { |n| "N#{n}" }.zip(res)]
-    {
-      "n_seqs" => @assembly.size,
-      "smallest" => @assembly.first.length,
-      "largest" => @assembly.last.length,
-      "n_bases" => @n_bases,
-      "mean_len" => mean,
-      "n > 1k" => n1k,
-      "n > 10k" => n10k
-    }.merge ns
-  end
 
-  # return the number of bases in the assembly, calculating
-  # from the assembly if it hasn't already been done.
-  def n_bases
-    unless @n_bases
-      @n_bases = 0
-      @assembly.each { |s| @n_bases += s.length }
+    # return the number of bases in the assembly, calculating
+    # from the assembly if it hasn't already been done.
+    def n_bases
+      unless @n_bases
+        @n_bases = 0
+        @assembly.each { |s| @n_bases += s.length }
+      end
+      @n_bases
+    end
+
+    def print_stats
+      self.basic_stats.map do |k, v| 
+        "#{k}#{" " * (20 - (k.length + v.to_i.to_s.length))}#{v.to_i}"
+      end.join("\n")
     end
-    @n_bases
-  end
 
-  def print_stats
-    self.basic_stats.map do |k, v| 
-      "#{k}#{" " * (20 - (k.length + v.to_i.to_s.length))}#{v.to_i}"
-    end.join("\n")
-  end
+  end # Assembly
 
-end # Assembly
+end # Transrate

data/lib/transrate/version.rb

@@ -4,7 +4,7 @@ module Transrate
   module VERSION
     MAJOR = 0
     MINOR = 0
-    PATCH = 5
+    PATCH = 6
     BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 0.0.5
+  version: 0.0.6
   prerelease: 
 platform: ruby
 authors: