transrate 0.1.0 → 0.2.0

data/lib/transrate/express.rb

@@ -1,37 +0,0 @@
-module Transrate
-
-  require 'which'
-  
-  class Express
-
-    # return an Express object
-    def initialize
-      express_path = Which::which('express')
-      raise "could not find eXpress in the path" if express_path.empty?
-      @express = express_path.first
-    end
-
-    # return hash of expression for each sequenceID
-    # in the assembly fastafile
-    def quantify_expression assembly, samfile
-      assembly = assembly.file if assembly.is_a? Assembly
-      cmd = "#{@express} --no-bias-correct #{File.expand_path assembly} #{File.expand_path samfile}"
-      ex_output = 'results.xprs'
-      fin_output = "#{assembly}_#{ex_output}"
-      unless File.exists? fin_output
-        `#{cmd} 2>&1`.split(/\n/)[1..30].join("\n")
-        File.rename(ex_output, fin_output)
-      end
-      expression = {}
-      File.open(fin_output).each do |line|
-        line = line.chomp.split("\t")
-        target = line[1]
-        effective_count = line[7]
-        expression[target] = effective_count
-      end
-      expression
-    end
-    
-  end # Express
-
- end # Transrate

data/lib/transrate/log.rb

@@ -1,16 +0,0 @@
-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

@@ -1,33 +0,0 @@
-module Transrate
-
-  class RBHit
-
-    # Fields: query id, subject id, % identity, alignment length, mismatches,
-    # 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, :target_coverage
-    
-    def initialize(list)
-      @query      = list[0].scan(/[^|]+/).first.split.first # extract only identifier
-      @target     = list[1].scan(/[^|]+/).first.split.first
-      @id         = list[2]
-      @alnlen     = list[3]
-      @mismatches = list[4]
-      @gaps       = list[5]
-      @qstart     = list[6]
-      @qend       = list[7]
-      @tstart     = list[8]
-      @tend       = list[9]
-      @evalue     = list[10]
-      @bitscore   = list[11]
-      @target_coverage       = list[12].to_i
-    end
-
-    def to_s
-      @query + " => " + @target
-    end
-
-  end # RBHit
-
-end # Transrate

data/lib/transrate/reciprocal_annotation.rb

@@ -1,105 +0,0 @@
-module Transrate
-
-  class ReciprocalAnnotation
-
-    attr_reader :l2r_hits
-    attr_reader :r2l_hits
-    attr_reader :results
-
-    def initialize assembly, reference
-      @assembly = assembly
-      @reference = reference
-      @usearch = Usearch.new
-    end
-
-    def run
-      self.make_assembly_db
-      self.make_reference_db
-      left2right, right2left = self.reciprocal_align
-      self.parse_results left2right, right2left
-      @results
-    end
-
-    def make_assembly_db
-      unless @assembly.orfs_ublast_db
-        assembly_dir = File.dirname(@assembly.file)
-        assembly_base = File.basename(@assembly.file, ".*")
-        assembly_orfs = assembly_base + ".orfs"
-        @usearch.findorfs @assembly.file, assembly_orfs
-        assembly_db = File.join(assembly_dir, assembly_base + ".udb")
-        @usearch.makeudb_ublast assembly_orfs, assembly_db
-        @assembly.orfs_ublast_db = assembly_db
-      end
-    end
-
-    def make_reference_db
-      unless @reference.ublast_db
-        reference_dir = File.dirname(@reference.file)
-        reference_base = File.basename(@reference.file, ".*")
-        reference_db = File.join(reference_dir, reference_base + ".udb")
-        @usearch.makeudb_ublast @reference.file, reference_db
-        @reference.ublast_db = reference_db
-        return reference_db
-      end
-    end
-
-    def reciprocal_align
-      left2right = @usearch.ublast @assembly.file, @reference.ublast_db
-      right2left = @usearch.ublast @reference.file, @assembly.orfs_ublast_db
-      [left2right, right2left]
-    end
-
-    def parse_results left2right, right2left
-      l2r_results = self.load_results_file left2right
-      r2l_results = self.load_results_file right2left
-      @l2r_hits = self.results_to_hits l2r_results
-      @r2l_hits = self.results_to_hits r2l_results
-      @results = {}
-      @l2r_hits.each_pair do |query, best|
-        next if best.nil?
-        tbest = @r2l_hits[best.target]
-        next if tbest.nil?
-        if query == tbest.target
-        	@results[query] = best 
-        end
-      end
-    end
-
-    # what is this method trying to do? :/
-    def results_to_hits results
-      hits = {}
-      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
-            hits[hit.query] = hit
-          end
-        else
-          hits[hit.query] = hit
-        end
-      end
-      hits
-    end
-
-    def load_results_file file
-      results = []
-      File.open(file).each_line do |line|
-        results << RBHit.new(line.chomp.split("\t"))
-      end
-      results
-    end
-
-  end # ReciprocalAnnotation
-
-end # Transrate

data/lib/transrate/usearch.rb

@@ -1,66 +0,0 @@
-module Transrate
-
-  class Usearch
-
-    require 'which'
-    include Which
-
-    def initialize threads=8
-      @threads = threads
-      paths = which('usearch')
-      if paths.empty?
-        raise "usearch not found in path. Please ensure usearch is installed and aliased as 'usearch' in your path."
-      end
-      @cmd = paths.first
-    end
-
-    def custom_output_fields
-      " -userfields query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits+tcov"
-    end
-
-    def ublast query, target, evalue="1e-5"
-      blast6outfile = "#{File.basename(query)}_#{File.basename(target)}.b6"
-      unless File.exists? blast6outfile
-      subcmd = " -ublast #{query}"
-        subcmd += " -db #{target}"
-        subcmd += " -evalue #{evalue}"
-        subcmd += " -userout #{blast6outfile}"
-        subcmd += self.custom_output_fields
-        subcmd += " -strand both"
-        subcmd += " -threads #{@threads}"
-        self.run subcmd
-      end
-      blast6outfile
-    end
-
-    def makeudb_ublast filepath, output
-      unless File.exists? output
-        subcmd = " -makeudb_ublast #{filepath}"
-        subcmd += " -output #{output}"
-        self.run subcmd
-      end
-    end
-
-    def findorfs filepath, output
-      if File.exists? output
-        puts "skipping ORF finding: ORF file already exists at #{output}"
-      else
-        subcmd = " -findorfs #{filepath}"
-        subcmd += " -output #{output}"
-        subcmd += " -xlat"
-        subcmd += " -orfstyle 7"
-        self.run subcmd
-      end
-    end
-
-    def run subcmd
-      subcmd += " -quiet"
-      ret = `#{@cmd}#{subcmd} 2>&1`
-      unless $?.exitstatus == 0
-        puts "usearch command failed: #{subcmd}\noutput:\n#{ret}"
-      end
-    end
-
-  end # Usearch
-
-end # Transrate

data/test/test_test.rb

@@ -1,41 +0,0 @@
-#!/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