refactor as gem, abstract bowtie and readmappings as classes

Author: blahah

Gemfile

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+source "https://rubygems.org"
+
+gemspec

Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    transrate (0.0.1)
+      bettersam
+      bio
+      rake (~> 10.1.0)
+      trollop (~> 2.0)
+      which
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ansi (1.4.3)
+    bettersam (0.0.1.alpha)
+    bio (1.4.3)
+    colorize (0.5.8)
+    coveralls (0.6.7)
+      colorize
+      multi_json (~> 1.3)
+      rest-client
+      simplecov (>= 0.7)
+      thor
+    facade (1.0.5)
+    mime-types (1.23)
+    multi_json (1.7.7)
+    pathname2 (1.6.5)
+      facade
+    rake (10.1.0)
+    rest-client (1.6.7)
+      mime-types (>= 1.16)
+    shoulda-context (1.1.5)
+    simplecov (0.7.1)
+      multi_json (~> 1.0)
+      simplecov-html (~> 0.7.1)
+    simplecov-html (0.7.1)
+    thor (0.16.0)
+    trollop (2.0)
+    turn (0.9.6)
+      ansi
+    which (0.0.2)
+      pathname2 (>= 1.4.4)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  coveralls (~> 0.6.7)
+  shoulda-context
+  simplecov
+  transrate!
+  turn

assembly.rb

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+#! /usr/bin/env ruby
+
+require 'trollop'
+require 'transrate'
+
+opts = Trollop::options do
+  version "v0.0.1a"
+  banner <<-EOS
+
+Transrate v0.0.1a by Richard Smith <[email protected]>
+
+DESCRIPTION:
+Analyse a de-novo transcriptome
+assembly using three kinds of metrics:
+
+1. contig-based
+2. read-mapping
+3. reference-based
+
+Please make sure USEARCH and bowtie2 are both installed
+and in the PATH.
+
+Bug reports and feature requests at:
+https://github.com/blahah/transrate
+
+USAGE:
+transrate <options>
+
+OPTIONS:
+
+EOS
+  opt :assembly, "assembly file in FASTA format", :required => true, :type => String
+  opt :reference, "reference proteome file in FASTA format", :required => true, :type => String
+  opt :left, "left reads file in FASTQ format", :type => String
+  opt :right, "right reads file in FASTQ format", :type => String
+  opt :insertsize, "mean insert size",  :default => 200, :type => Integer
+  opt :insertsd, "insert size standard deviation", :default => 50, :type => Integer
+  opt :threads, "number of threads to use", :default => 8, :type => Integer
+end
+
+def pretty_print_hash hash, width
+  hash.map{ |k, v| "#{k.to_s}#{" " * (width - (k.length + v.to_i.to_s.length))}#{v.to_i}" }.join("\n")
+end
+
+include Transrate
+
+a = Assembly.new opts.assembly
+r = Assembly.new opts.reference
+
+puts "\n\nAnalysing assembly: #{opts.assembly}\n\n"
+
+puts "calculating contig stats..."
+t0 = Time.now
+contig_results = a.basic_stats
+puts "...done in #{Time.now - t0} seconds"
+
+read_results = nil
+if (opts.left && opts.right)
+  puts "\ncalculating read diagnostics..."
+  t0 = Time.now
+  read_metrics = ReadMetrics.new a
+  read_results = read_metrics.run(opts.left, opts.right)
+  puts "...done in #{Time.now - t0} seconds"
+else
+  puts "\nno reads provided, skipping read diagnostics"
+end
+
+puts "\ncalculating comparative metrics..."
+t0 = Time.now
+comparative_metrics = ComparativeMetrics.new(a, r)
+comparative_results = comparative_metrics.run
+puts "...done in #{Time.now - t0} seconds"
+
+report_width = 30
+
+if contig_results
+  puts "\n\n"
+  puts "Contig metrics:"
+  puts "-" *  report_width
+  puts pretty_print_hash(contig_results, report_width)
+end
+
+if read_results
+  puts "\n\n"
+  puts "Read mapping metrics:"
+  puts "-" *  report_width
+  puts pretty_print_hash(read_results, report_width)
+end
+
+if comparative_results
+  puts "\n\n"
+  puts "Comparative metrics:"
+  puts "-" *  report_width
+  puts pretty_print_hash(comparative_results, report_width)
+end