transrate 0.0.12 → 0.0.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f5f7d2d65376b69682c5e29c318ad35f43a5ea9a
-  data.tar.gz: 794238eafb17705f68d82296e53ffa6128bf7141
+  metadata.gz: 8e95b284158f18e48f07d5d0dbfffadab014f4f9
+  data.tar.gz: 7bbaa794b374538e2fc3d422d9256e0e501e14ac
 SHA512:
-  metadata.gz: 101280a09d847f28165d0a4394bb849af5e339bf782a25b7e09ad45e1fbdd694f441809b09f078848c69ff0607bedc1aff91e87c50839cd0be3a997038f381a8
-  data.tar.gz: 1cf8a710b6e7d83139eabd4b8d820a056de19715307b822c3096458cefdec89f195d0727a8b49ccc5ac648bba9e1e8ec007092abcc94796e5a3f6b3ba4c6df99
+  metadata.gz: 71163763618dc38fed73de88e677f3db6d375e28f31d33f4c03bcbb4aece341ee9e849bf5e6654967a9635cd2b9225ca9025645f8cb9bfff1f3e313e2e44e23c
+  data.tar.gz: b6c297fa15496cc78195e11780cecac0a75dbfce971358c5814b3dc0a6c2e9ee6766556b8a32ac303d487c12967afbb63551d2aa78b543bdfbb19a77d4459ad4

data/.gitignore

@@ -12,6 +12,7 @@ spec/reports
 test/tmp
 test/version_tmp
 tmp
+*~
 
 # YARD artifacts
 .yardoc

data/bin/transrate

@@ -88,7 +88,9 @@ end
 if opts.reference
   puts "\nCalculating comparative metrics..."
   t0 = Time.now
-  comparative_results = transrater.comparative_metrics.comp_stats
+  comparative_metrics = transrater.comparative_metrics
+  p comparative_metrics.comp_stats
+  comparative_results = comparative_metrics.comp_stats
 
   if comparative_results
     puts "\n"

data/lib/transrate.rb

@@ -11,6 +11,8 @@ require 'transrate/metric'
 require 'transrate/dimension_reduce'
 require 'transrate/express'
 
+# Transrate is a comprehensive transcriptome assembly
+# quality assessment tool.
 module Transrate
 
 end # Transrate

data/lib/transrate/assembly.rb

@@ -2,9 +2,28 @@ require 'bio'
 require 'bettersam'
 require 'csv'
 require 'forwardable'
+require 'inline'
 
 module Transrate
 
+  # Container for a transcriptome assembly and its associated
+  # metadata.
+  #
+  # @!attribute [rw] ublast_db
+  #   @return [String] path to a ublast database generated from this assembly
+  # @!attribute [rw] orss_ublast_db
+  #   @return [String] path to a ublast database generated from the orfs
+  #     extracted from this assembly
+  # @!attribute [r] assembly
+  #   @return [Array<Bio::FastaFormat>] the assembly
+  # @!attribute [r] has_run
+  #   @return [BOOL] whether the basic metrics have been generated
+  # @!attribute [w] n_bases
+  #   @return [Integer] the number of bases in the assembly
+  # @!attribute [rw] file
+  #   @return [String] path to the assembly FASTA file
+  # @!attribute [r] n50
+  #   @return [Integer] assembly n50
   class Assembly
 
     include Enumerable
@@ -13,22 +32,15 @@ module Transrate
 
     attr_accessor :ublast_db
     attr_accessor :orfs_ublast_db
-    attr_accessor :protein
     attr_reader :assembly
     attr_reader :has_run
-
-    # number of bases in the assembly
     attr_writer :n_bases
-
-    # assembly filename
     attr_accessor :file
-
-    # assembly n50
     attr_reader :n50
 
-    # Return a new Assembly.
+    # Create a new Assembly.
     #
-    # - +:file+ - path to the assembly FASTA file
+    # @param file [String] path to the assembly FASTA file
     def initialize file
       @file = file
       @assembly = []
@@ -39,13 +51,20 @@ module Transrate
       end
     end
 
-    # Return a new Assembly object by loading sequences
-    # from the FASTA-format +:file+
-    def self.stats_from20_fasta file
+    # Return basic statistics about the assembly in 
+    # the specified FASTA file
+    #
+    # @param file [String] path to assebmly FASTA file
+    #
+    # @return [Hash] basic statistics about the assembly
+    def self.stats_from_fasta file
       a = Assembly.new file
       a.basic_stats
     end
 
+    # Generate and store the basic statistics for this assembly
+    #
+    # @param threads [Integer] number of threads to use
     def run threads=8
       stats = self.basic_stats threads
       stats.each_pair do |key, value|
@@ -62,7 +81,10 @@ module Transrate
     # calculated in parallel by splitting the assembly into
     # equal-sized bins and calling Assembly#basic_bin_stat on each
     # bin in a separate thread.
-    
+    #
+    # @param threads [Integer] number of threads to use
+    #
+    # @return [Hash] basic statistics about the assembly
     def basic_stats threads=8
       
       # create a work queue to process contigs in parallel
@@ -185,14 +207,14 @@ module Transrate
       mean = cumulative_length / @assembly.size
  #     ns = Hash[x.map { |n| "N#{n}" }.zip(res)]
       {
-        "n_seqs" => bin.size,
-        "smallest" => bin.first.length,
-        "largest" => bin.last.length,
-        "n_bases" => n_bases,
-        "mean_len" => mean,
-        "n_1k" => n1k,
-        "n_10k" => n10k,
-        "orf_percent" => 300 * orf_length_sum / (@assembly.size * mean)
+        'n_seqs' => bin.size,
+        'smallest' => bin.first.length,
+        'largest' => bin.last.length,
+        'n_bases' => n_bases,
+        'mean_len' => mean,
+        'n_1k' => n1k,
+        'n_10k' => n10k,
+        'orf_percent' => 300 * orf_length_sum / (@assembly.size * mean)
       }
 #      }.merge ns
 
@@ -223,17 +245,59 @@ module Transrate
       
     end # merge_basic_stats
      
+    inline do |builder|
+
+      builder.c <<SRC
+        static
+        void
+        longest_orf(VALUE _s) {
+          int i,sl,longest=0;
+          int len[6];
+          char * c_str;
+
+          sl = RSTRING_LEN(_s);
+          c_str = StringValueCStr(_s);
+          for (i=0;i<6;i++) {
+            len[i]=0;
+          }
+          for (i=0;i<sl-2;i++) {
+            if (c_str[i]=='T' &&
+              ((c_str[i+1]=='A' && c_str[i+2]=='G') ||
+              (c_str[i+1]=='A' && c_str[i+2]=='A') ||
+              (c_str[i+1]=='G' && c_str[i+2]=='A'))) { 
+              if (len[i%3] > longest) {
+                longest = len[i%3];
+              }
+              len[i%3]=0;
+            } else {
+              len[i%3]++;
+            }
+            if (c_str[i+2]=='A' &&
+              ((c_str[i]=='C' && c_str[i+1]=='T') ||
+              (c_str[i]=='T' && c_str[i+1]=='T') ||
+              (c_str[i]=='T' && c_str[i+1]=='C'))) { 
+              if (len[3+i%3] > longest) {
+                longest = len[3+i%3];
+              }
+              len[3+i%3]=0;
+            } else {
+              len[3+i%3]++;
+            }
+          }
+          if (len[i%3] > longest) {
+            longest = len[i%3];
+          }
+          if (len[3+i%3] > longest) {
+            longest = len[3+i%3];
+          }
+          return INT2NUM(longest);
+        }
+SRC
+    end
+
     # finds longest orf in a sequence
     def orf_length sequence
-      longest=0
-      (1..6).each do |frame|
-        translated = Bio::Sequence::NA.new(sequence).translate(frame)
-        translated.split('*').each do |orf|
-          if orf.length > longest
-            longest=orf.length
-          end
-        end
-      end
+      longest = longest_orf(sequence)
       return longest
     end
 
@@ -250,7 +314,7 @@ module Transrate
     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.join('\n')
     end
 
   end # Assembly

data/lib/transrate/comparative_metrics.rb

@@ -7,7 +7,6 @@ module Transrate
     attr_reader :rbh_per_contig
     attr_reader :rbh_per_reference
     attr_reader :reciprocal_hits
-    attr_reader :reference_coverage
     attr_reader :has_run
 
     def initialize assembly, reference
@@ -17,12 +16,12 @@ module Transrate
     end
 
     def run
-      rbu = self.reciprocal_best_ublast
-      @ortholog_hit_ratio = self.ortholog_hit_ratio rbu
-      @collapse_factor = self.collapse_factor @ra.r2l_hits
+      rbu = reciprocal_best_ublast
+      @ortholog_hit_ratio = ortholog_hit_ratio rbu
+      @collapse_factor = collapse_factor @ra.r2l_hits
       @reciprocal_hits = rbu.size
       @rbh_per_reference = @reciprocal_hits.to_f / @reference.size.to_f
-      @reference_coverage = @rbh_per_reference * @collapse_factor
+      @reference_coverage = @ortholog_hit_ratio * @rbh_per_reference
       @rbh_per_contig = @reciprocal_hits.to_f / @assembly.assembly.size.to_f
       @has_run = true
     end
@@ -32,6 +31,7 @@ module Transrate
         :reciprocal_hits => @reciprocal_hits,
         :rbh_per_contig => @rbh_per_contig,
         :rbh_per_reference => @rbh_per_reference,
+        :reference_coverage => @reference_coverage,
         :ortholog_hit_ratio => @ortholog_hit_ratio,
         :collapse_factor => @collapse_factor
       }
@@ -43,8 +43,9 @@ module Transrate
     end
 
     def ortholog_hit_ratio rbu=nil
-      return @ortholog_hit_ratio unless @ortholog_hit_ratio.nil? 
-      rbu.reduce(0.0){ |sum, hit| sum += hit.last.tcov.to_f } / rbu.size
+      return @ortholog_hit_ratio unless @ortholog_hit_ratio.nil?
+      divisor = (rbu.size * 100).to_f 
+      rbu.reduce(0){ |sum, hit| sum += hit.last.target_coverage } / divisor
     end
 
     def collapse_factor hits=nil

data/lib/transrate/log.rb

@@ -0,0 +1,16 @@
+require 'logger'
+
+module Transrate
+
+  class Log < Logger
+
+    def dump_process?(status, output, msg)
+      unless status.exitstatus == 0
+        fatal(msg)
+        fatal(output)
+      end
+    end
+    
+  end # Log
+
+end # Transrate

data/lib/transrate/rb_hit.rb

@@ -6,7 +6,7 @@ module Transrate
     # gap opens, q. start, q. end, s. start, s. end, evalue, bit score
     attr_accessor :query, :target, :id, :alnlen, :mismatches
     attr_accessor :gaps, :qstart, :qend, :tstart, :tend, :evalue
-    attr_accessor :bitscore, :tcov
+    attr_accessor :bitscore, :target_coverage
     
     def initialize(list)
       @query      = list[0].scan(/[^|]+/).first.split.first # extract only identifier
@@ -21,7 +21,7 @@ module Transrate
       @tend       = list[9]
       @evalue     = list[10]
       @bitscore   = list[11]
-      @tcov       = list[12]
+      @target_coverage       = list[12].to_i
     end
 
     def to_s

data/lib/transrate/reciprocal_annotation.rb

@@ -59,16 +59,28 @@ module Transrate
         next if best.nil?
         tbest = @r2l_hits[best.target]
         next if tbest.nil?
-        @results[query] = best if query == tbest.target
+        if query == tbest.target
+        	@results[query] = best 
+        end
       end
     end
 
+    # what is this method trying to do? :/
     def results_to_hits results
       hits = {}
+      puts "<results_to_hits> results.size = #{results.size}"
       results.each do |hit|
         if hits.has_key? hit.query
           old_hit = hits[hit.query]
           old_eval, old_bits = old_hit.evalue, old_hit.bitscore
+          if hit.bitscore == nil
+            p hit
+            abort "oh noes"
+          end
+          if old_bits == nil
+            p old_hit
+            raise 'hell'
+          end
           if hit.bitscore > old_bits
             hits[hit.query] = hit 
           elsif hit.bitscore == old_bits && hit.evalue < old_eval

data/lib/transrate/transrater.rb

@@ -1,11 +1,27 @@
 module Transrate
 
+  # A transrater runs all types of metrics on an assembly.
+  #
+  # @!attribute [r] assembly
+  #   @return [Assembly, String] an Assembly or the path to an assembly
+  # @!attribute [r] read_metrics
+  #   @return [Hash] the read metrics if they have been calculated
+  # @!attribute [r] comparative_metrics
+  #   @return [hash] the comparative metrics if they have been calculated
   class Transrater
 
     attr_reader :assembly
     attr_reader :read_metrics
-    attr_reader :comparative_metrics
 
+    # A new Transrater
+    #
+    # @param assembly [Assembly, String] the Assembly or path to the FASTA
+    # @param reference [Assembly, String] the reference Assembly or
+    #   path to the FASTA
+    # @param left [String] path to the left reads
+    # @param right [String] path to the right reads
+    # @param insertsize [Integer] mean insert size of the read pairs
+    # @param insertsd [Integer] standard deviation of the read pair insert size
     def initialize assembly, reference, left=nil, right=nil, insertsize=nil, insertsd=nil
       @assembly  = assembly.is_a?(Assembly)  ? assembly  : Assembly.new(assembly)
       @reference = reference.is_a?(Assembly) ? reference : Assembly.new(reference)
@@ -13,6 +29,12 @@ module Transrate
       @comparative_metrics = ComparativeMetrics.new(@assembly, @reference)
     end
 
+    # Run all analyses
+    #
+    # @param left [String] path to the left reads
+    # @param right [String] path to the right reads
+    # @param insertsize [Integer] mean insert size of the read pairs
+    # @param insertsd [Integer] standard deviation of the read pair insert size
     def run left=nil, right=nil, insertsize=nil, insertsd=nil
       assembly_metrics
       if left && right
@@ -21,6 +43,11 @@ module Transrate
       comparative_metrics
     end
 
+    # Reduce all metrics for the assembly to a single quality score.
+    #
+    # 
+    #
+    # @return [Integer] the assembly score
     def assembly_score
       @score, pg, rc = nil
       if @read_metrics.has_run
@@ -47,7 +74,7 @@ module Transrate
     end
 
     def comparative_metrics
-      @comparative_metrics.run unless @comparative_metrics.has_run
+      @comparative_metrics.run #unless @comparative_metrics.has_run
       @comparative_metrics
     end
 

data/lib/transrate/version.rb

@@ -1,12 +1,19 @@
 # encoding: utf-8
 
 module Transrate
+
+  # Defines the version of this codebase.
+  #
+  # This module is used in help messages and in generating
+  # the Gem. Versions must be incremented in accordance with
+  # Semantic Versioning 2.0 (http://semver.org/).
   module VERSION
     MAJOR = 0
     MINOR = 0
-    PATCH = 12
+    PATCH = 13
     BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
   end
+
 end # Transrate

data/test/assembly.fasta

@@ -0,0 +1,8 @@
+>scaffold1
+TTTCAGTTGATGAAGAAAAAACTAGAGTGTGTGGATTGCATGAAATGAGCTGGGGCTTGTTGAAATTTTGCTATTGAAACTAATGTTTACTTCAAATTGATAGGAATTCAGTTGGTTTTCTGGTGGTNTCTCTTTCTTCTTCACAATTGAATTTTGATTCCAAACACCATCTCTTAGGAATTCAGTTGGTTTTCTGGTGATAAACACTTCAATTTGACTATGGACTCTGTGTATTGTAAAGAACATGATGACAGAATTGCTTCGAATCCGGTGGGTTTACAGTCATCCGGGTCGGGTCCTTGGTGGGGTGGGCTCGTGACTCAATCGGGTTTTGAAGAATCCATGGGGAGATTGAAGAATTCATCAATGGAACCACTCGTGCGAATAGCCCCTAAACTGTCGATTTCTGCTGCAGATCAATCAATGGCAAAAGGGGATACGACTTCTTTTGATATCTTTCATGGTGACTCCAAGAGTTCGTCAAATGGTCAAAAACCAGTGCTATTGCAAGCTGTTTCCACCTTGCAATCTGCTCCACAAGTGTTTGGAGGTCATCTTGAGCTTGGGTTTGGTCAGCCGGCTGTGGCATGTGGCGTGTATCCTTATGGCGACCAATCTTATCGCGTGCTCTCTGCTTATGGACCTCAAACCGTGGGTCGTGTTATGCTGCCTTTGAACTTGAGCACTGATGATGGACCTATATTTGTGAATGCAAAGCAGTATCATGGAATAATCAGGCGCAGACGATCAAGAGCTAAAGCAGAAATGGCAAAAAAGTTTACAAAAAGTCGAAAGCCATATCTGCACTTGTCGCGTCATCTTCATGCAAAACGTCGACCAAGAGGCTGTGGGGGCCGCTTCCTAAACACTAAAGAAATGGACAAGGGCAAAGTTGGAAACTTGGATTCAAAACCAACCAATAATCCAACCACTTCTCAGAGATCCGAGGTCTTACAATGTGATCATGAATCGAATGGTAGCAAGTCCTACACACTAGGGTCAGAGGTAACAAGCGTTTTCTCCATGGGAGACCTCAATCAATTCCCCATGGGAGATATTTCTGTTATTTCTCATTATGGCATGATGGCGTCTGGCAATGCCATTCTTAGTCTTGGCATGCAGAACGATTGGGTTGCAGTGGGTGCAGGTGGGGGTATCTGCTGCAACCTGACAGTCTGATGGTACATGGGGTCTGATGTGCCTGCACGACAGACCCCATTCTTAGATAGTCAAACGGGACGGGGTTGTTTTCCGTTGTTTGGCTATGGCAAATCATCCTTGGCTATGACGTGTGAAGGTTGTGTCTCTAACTTCAATTCCCCTGACAAATGCAGACTAGGAATTGTTTTAAAGATGCTGATAACCTCAATACATATGATGGGCAATCATTTATTCTAGATGTGTTTGTTTCATCCTATGTTAATACTTTGTTGTTGTTTGAAATAAACTAAACCTTAGAACTCTATTTTCAAGGTATGTATCATGTGAATCTTGACTTCCAAACATTTAGGAGATGCCATATATTGTGTTTGATATTTTCTTGATAGTTATGCGCATGTTGGTAATTAAGAAATTCCTTTGGGATAATCTTGTAAATTAACATGAATGGTGGATGTTTATGCTTACAATA
+>scaffold2
+AAAAGGCATATATGACAAATCCTCCTTTCAAGTCGAACAACATTAGAGTTTTGTACAGATTTAAGACCAAAGCATTACTCGTTTCTATTCTCTCTTTAAATGTGAAATTTACCATCATAGTATTACATAATCTTATACGCGATATCATTTTAAAAAGATTATTGTTTTCATCGTCTTAACAGATTGTATGCTGGTAACTCTTTCACACATGTGACATCTTCGATCGCAAGCTCCCTCTCTAGCTGCATTCTTGTGGATTTTATAACCTCATTGAATTCCATATATGAAGCACGCCTCGCAAGCCAATGAGCATCCATGAGTTTGAAAGCAACACAATATAGCTCATCAAAAGCCGATTCATCATTACTAAGAAATTGCAAGAACCGCACCCCTGACGAAGACGTTGGTAATCCTGACTGAATATCCAACATCTGCACCAACATGAAAGAAATATTGATGCCAGCTACAGCAAAAGGATATTCCCATTCAGCTCTAATTCCTTCTTTTTTGTTTAAAAGGTTTTGAAAAGCTTCCGGATATGTGCGGGCAAAGAAGATAAGATTCTCTAGAGATATGAATCCTCCACCTCTAAAGTCTGTTGAAGGATCATTTCCTTGCCACCCCATATCTTTCCAAACCTCTGATTTAAGTCCTGGGAGTTCTCTATTTGGATAAGCTGACCTCCATAATTTTCTAAGTGCATCTTGATGCTCCAAACAAGTACCATCGAAAGGGACCTCCAATCGTTTCTGCAGATTTCTGAGTCTTGATTCCTGTAATGGAGTAAGTATAGGTGGAAGAAACTTCTTCGTGGGTCCACTTCCTATTGTTGAAGGCAACGTCAAGAACCGTATAATAAACGATCCAGATCCAAGTAGAACATTTGCTAGCCACTGTGCCCATTCTGAAATTAAATGAGAGAATAGAAACGTCCAGTGGAGGTGTTCTTTTCTTTTTTCATCATACAAAATATCTTCGAGCCTTGGTACCTCCGACTGTTTAAGTTTATACTCGTCATTATTCCCTAGTAAAGGTTCACTTAGGTCATTTAAATCTGCACCAACTAAATGCTCGTGCTTTTTACCATCAACATCCCCATGGTGAAGTCTTCTCCTCATTGTTTGTGATGTCATTAATCCTTCAATGCCCGAACTTCTTTCTGAAGCCTTGAGGGATAGGGTGAGAAGAAGATTGATTGATGGATGAAACCCTAATGAAGGGAGTAGAGAAAGAGTAAGAAAGAAAGCCCTTTCTTTTTGTTCTTCTTCTAATCTCTTTCTCTACCCTAATGAAGCACCACAAAGTAGGAATGAAGGAAGAAAGGAACCCTCTCTTTCTCACATCTACATTTACATCTGCATCTGCTTTACGTTTTCAGGAAGAAACATCACACCGTCAATTAAGCGGATCTGGTAACGCCTGCGCGGGCAAACGGGTCGGATCTTGATCTATTAAAACCACTTCATTTTTTTTTTTTTTTTTTT
+>scaffold3
+AAAAGGCATATATGACAAATCCTCCTTTCAAGTCGAACAACATTAGAGTTTTGTACAGATTTAAGACCAAAGCATTACTCGTTTCTATTCTCTCTTTAAATGTGAAATTTACCATCATAGTATTACATAATCTTATACGCGATATCATTTTAAAAAGATTATTGTTTTCATCGTCTTAACAGATTGTATGCTGGTAACTCTTTCACACATGTGACATCTTCGATCGCAAGCTCCCTCTCTAGCTGCATTCTTGTGGATTTTATAACCTCATTGAATTCCATATATGAAGCACGCCTCGCAAGCCAATGAGCATCCATGAGTTTGAAAGCAACACAATATAGCTCATCAAAAGCCGATTCATCATTACTAAGAAATTGCAAGAACCGCACCCCTGACGAAGACGTTGGTAATCCTGACTGAATATCCAACATCTGCACCAACATGAAAGAAATATTGATGCCAGCTACAGCAAAAGGATATTCCCATTCAGCTCTAATTCCTTCTTTTTTGTTTAAAAGGTTTTGAAAAGCTTCCGGATATGTGCGGGCAAAGAAGATNTGTTTTCAACAAAATAGCAATTAAAATACACTTTCCAACCTTTTACATATATGCAAATTATGGAACTTGTACAAAAGTTTCAATTTGAACAATAGGAGTTCAAAAATGTTTCAGCAGTACAACCGAAGTACAAAAGGTGTCATTTGCATGGTAAATGATGGCCAAATGGCCAAAATTGCCACCTTCAGATTCAACCTTTATTTTCTTCATTAACTTTAGTTTCATCAAGAACTCATTGAACACCAAAATGACACCTAATTTGAAATCAAATAAAAACCCAAACTTGATACACAAATTGCATGATTTGCCCAAATGTTACAGTTTGAAAAAACGGTATAAAAGTATGTTTCATTTGTTAAAACAAGTGTGAAGATATCATGTGTGAGGAATGTGATGACATAACGACCAAAACTACTCTCTCCGCCTTCAACCTCTCTTTACTTCTCAAGTATTTATTCTTAATATATCAGAATTCACGACATAAAGAACACCAAAATCAAACCCAATGTTCAAACTATCTCAAAATATCTGCAAAGGCACGTGATGGGCAAATAACAATCTTCCACTTCAACCTCTATTTTCTCTTTAAAACTTACTTTCTTACAGAAACCAAAATACCAAAATCCAAAATAACTCAAAAACCAAGATATTTGCAAAGGCAATAGAAGAATCTATCAATCTCGAAAAAACAAACCGGATATGTGCGGGCAAAGAAGATAAGATTCTCTAGAGATATGAATCCTCCACCTCTGCAAATAATACTCAATGCTTGAAATAACCAATTTGAATAAACTTCATTTGGTTAACTATAACAAGTAACTAAGTTACCTAAAGTCTGTTGAAGGATCATT
+>scaffold5
+CATCGATTTCATTTAGTGGCTAACCAGACCAGTCCTTCCGGTTCGATACGTGTGGAGATGAGAAGAACCCAACAGGAGTTCTGGAGGAAATTTGCCTGATTAAACAGACTCTACAGTTGATTTGGAGAGGTTGAAGATGGATGGAATTGAAGAACATGGAGATTGCACTTCTAGGTGCTGCTAGACAAGCTCAGAGAAAATCAAATGCTGATATATATTGAGTCTCTACTGGAAGTCTGGAAGAGTATCATCTAAGGGTATCGGCCCTCGAAAGAAAGACTTATCCTAATCCATTGCGTTCCAATCCTGCATATTCGGTTGTGAAGTAAGTTACATTTGAGTGACTGCATCTACTTTTCTTCAAGAACTACTTCTAATTTTTTTTATTAAGTGAACTAATCAGATCAGAAACTGTATCCAAACTTAAAAGGTTAAAACTTGATTATTACATTTTAAAACAACTTCAAGATTGAAGAGAACAATTTGGTGAGTTTAAGAATAGACAAAGCAGCCTTGGAGAAGCTGCTGGAAGAAAAACAAATGCTGATATCAAGTCTCTACAGGAGAAGTATCAGCAAAGAGTGTCGGCCCTCGAAAGAAAGTTAAATGGTTTGCATATTTGTAGAAGCTTAGTTTAACACCTCTGTTTTAAAAACACTGCAGGGAAGTATTTGAAGAAAGTTTTATGGTCCGTACTTTGAAAATTTTGTCACCAAAGACTTTTGCTGATTTATCTCAACTTATAAAACTGAACAAAAAGGTCCTTATAAATTTTATGGATTTGATTATGCAAAAAATAAAGAACTTTTAGTTGAACTTTTATAAGTTTAAGCACTTTTTCTAAATCTGACATTTTGTTTAAATCTGACTTTTTGTTAAAAATGAAGTCCATGGGGCATTTTTGGTGAGTGTTTATTAGTTAAAGGATATAGTTATGCAAAAATGAAGTCCAGGTTTGTGAACAAGCACAAAGTCTATAGGCTTTTTTTTCCCTTTTATATTATTTTTGGCAACTACACATAACTAAAATGAATTTAAAGGTTGTATGTGCTAAAAATGCACTTTGGGTGACTTTATCAACCAATTTCACCTATTTTTGTTTAGCTAGATATGTTGGTTTGATCATTTGACATGCTTGGGTTAAAAACATATTCTAAACTGACCCAATTGTAAGTGAACGGGTCGGCTTTAACATCTGTTCTCAGGTAAGTGAATGTAGATGTGACGAACTGGTTATGCAAGATCCTAAATGTATCAGGCCTCTTTTGAGGCAGATTGAGGCTATGCAGGCATTCTTTGGTTTGACATGGCACCATGAGCTTTATGGTTTGAACACTTGTACTAGGAACGATCTGCTAGAAAGGCAGAAGCTTTGCTGTGAGGAATCACTAAACATGCGGCTTCAGGTTTGATAAATGGTATATGTGTGTAGTTTCTTTGAAGTATAAATTATCTCAAGCCCAGTGATATTTTTTGTTTTGTATGAATCTTCGAGGCATTTGAAGGAGGG

data/test/test_inline.rb

@@ -0,0 +1,30 @@
+#!/usr/bin/env  ruby
+
+require 'helper'
+
+class TestInline < Test::Unit::TestCase
+
+  context 'transrate' do
+
+    setup do
+      @a = Transrate::Assembly.new('test/assembly.fasta')
+      @seq1 = 'ATGCCCCTAGGGTAG'
+    end
+
+    should 'find longest orf in file' do
+      orfs = []
+      @a.assembly.each do |entry|
+        l = @a.orf_length entry.seq
+        orfs << l
+      end
+      assert_equal orfs.length, 4
+      assert_equal orfs, [333, 370, 131, 84]
+    end
+
+    should 'find longest orf in sequence' do
+      l = @a.orf_length(@seq1)
+      assert_equal l, 4
+    end
+
+  end
+end

data/test/test_test.rb

@@ -0,0 +1,41 @@
+#!/usr/bin/env	ruby
+
+require 'helper'
+
+class TestTransrate < Test::Unit::TestCase
+
+  context "transrate" do
+
+    setup do
+      @a = Transrate::Assembly.new("test/assembly.fasta")
+      @seq1 = "ATGCCCGGGTAG"
+    end
+
+    should "run metrics on assembly" do
+      ans = @a.run(2) # using 2 threads
+      assert_equal ans, true, "should run but returned #{ans}"
+    end
+
+    should "find longest orf" do
+      len = @a.orf_length("ATGCCCGGGTAG")
+      assert_equal len, 3, "expected 4 but got #{len}"
+    end
+
+    should "find longest orf in file" do
+      orfs = []
+      @a.assembly.each do |entry|
+        l = @a.orf_length entry.seq
+        orfs << l
+      end
+      assert_equal orfs.length, 4
+      assert_equal orfs, [333, 370, 131, 84]
+    end
+
+    should "find the mean length" do
+      ans = @a.run(2)
+      mean = @a.mean_len
+      assert_equal mean, 1508.25
+    end
+
+  end
+end

data/transrate.gemspec

@@ -21,6 +21,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'which'
   gem.add_dependency 'bio'
   gem.add_dependency 'bettersam'
+  gem.add_dependency 'RubyInline', '~> 3.12'
 
   gem.add_development_dependency 'turn'
   gem.add_development_dependency 'simplecov'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 0.0.12
+  version: 0.0.13
 platform: ruby
 authors:
 - Richard Smith
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-14 00:00:00.000000000 Z
+date: 2014-04-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -80,6 +80,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: RubyInline
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: turn
   requirement: !ruby/object:Gem::Requirement
@@ -156,6 +170,7 @@ files:
 - lib/transrate/comparative_metrics.rb
 - lib/transrate/dimension_reduce.rb
 - lib/transrate/express.rb
+- lib/transrate/log.rb
 - lib/transrate/metric.rb
 - lib/transrate/rb_hit.rb
 - lib/transrate/read_metrics.rb
@@ -164,7 +179,11 @@ files:
 - lib/transrate/usearch.rb
 - lib/transrate/version.rb
 - lib/transrate/writer.rb
+- test/assembly.fasta
 - test/helper.rb
+- test/test_inline.rb
+- test/test_test.rb
+- test/test_test.rb~
 - transrate.gemspec
 homepage: https://github.com/Blahah/transrate
 licenses: