transrate 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -4,6 +4,7 @@
 .config
 Gemfile.lock
 coverage
+test_data
 InstalledFiles
 lib/bundler/man
 pkg
@@ -13,6 +14,8 @@ test/tmp
 test/version_tmp
 tmp
 *~
+.#*
+\#*
 
 # YARD artifacts
 .yardoc
@@ -21,4 +24,16 @@ doc/
 .ruby-version
 
 # large test files not for repo
-dryrun
+dryrun
+*.blast
+*.phr
+*.pin
+*.psq
+*.nhr
+*.nin
+*.nsq
+*.bt2
+*.fai
+*.bam
+*.csv
+*.coverage

data/.travis.yml

@@ -0,0 +1,8 @@
+language: ruby
+rvm:
+  - "2.0.0"
+  - "2.1.0"
+before_script:
+  - gem install bindeps
+  - bundle install
+  - bundle exec bin/transrate --install-deps

data/README.md

@@ -3,6 +3,18 @@ Transrate
 
 Quality analysis and comparison of transcriptome assemblies.
 
+[![Gem Version](https://badge.fury.io/rb/transrate.png)][gem]
+[![Build Status](https://secure.travis-ci.org/Blahah/transrate.png?branch=master)][travis]
+[![Dependency Status](https://gemnasium.com/Blahah/transrate.png?travis)][gemnasium]
+[![Code Climate](https://codeclimate.com/github/Blahah/transrate.png)][codeclimate]
+[![Coverage Status](https://coveralls.io/repos/Blahah/transrate/badge.png?branch=master)][coveralls]
+
+[gem]: https://badge.fury.io/rb/transrate
+[travis]: https://travis-ci.org/Blahah/transrate
+[gemnasium]: https://gemnasium.com/Blahah/transrate
+[codeclimate]: https://codeclimate.com/github/Blahah/transrate
+[coveralls]: https://coveralls.io/r/Blahah/transrate
+
 ## Contents
 
 1. [Development status](https://github.com/Blahah/transrate#development-status)
@@ -15,24 +27,12 @@ Quality analysis and comparison of transcriptome assemblies.
 5. [Requirements](https://github.com/Blahah/transrate#requirements)
     - [Ruby](https://github.com/Blahah/transrate#ruby)
     - [RubyGems](https://github.com/Blahah/transrate#rubygems)
-    - [USEARCH, Bowtie 2, and eXpress](https://github.com/Blahah/transrate#usearch-bowtie2-and-express)
+    - [Blast+, Bowtie 2](https://github.com/Blahah/transrate#blast+-and-bowtie2)
 6. [Getting help](https://github.com/Blahah/transrate#getting-help)
 
 ## Development status
 
-This software is in early development. Users should be aware that until the first release is made, features may change faster than the documentation is updated. Nevertheless, we welcome bug reports.
-
-[![Gem Version](https://badge.fury.io/rb/transrate.png)][gem]
-[![Build Status](https://secure.travis-ci.org/Blahah/transrate.png?branch=master)][travis]
-[![Dependency Status](https://gemnasium.com/Blahah/transrate.png?travis)][gemnasium]
-[![Code Climate](https://codeclimate.com/github/Blahah/transrate.png)][codeclimate]
-[![Coverage Status](https://coveralls.io/repos/Blahah/transrate/badge.png?branch=master)][coveralls]
-
-[gem]: https://badge.fury.io/rb/transrate
-[travis]: https://travis-ci.org/Blahah/transrate
-[gemnasium]: https://gemnasium.com/Blahah/transrate
-[codeclimate]: https://codeclimate.com/github/Blahah/transrate
-[coveralls]: https://coveralls.io/r/Blahah/transrate
+This software is being actively developed. Please be aware that they may be bugs. If you find any, please report them on the [issue tracker](https://github.com/Blahah/transrate/issues).
 
 ## Transcriptome assembly quality metrics
 
@@ -40,57 +40,59 @@ This software is in early development. Users should be aware that until the firs
 
 ## Installation
 
-Assuming all the requirements are met (see below), you can install transrate very easily. Just run at the terminal:
+Assuming you've got a recent version of Ruby installed (see below), you can install transrate very easily. Just run at the terminal:
 
 `gem install transrate`
 
-If you're new to linux/unix, there's a detailed tutorial for installing transrate with all the dependencies [on my blog](http://blahah.net/bioinformatics/2013/10/19/installing-transrate/).
+Next all the software Transrate depends on needs to be installed. Luckily, transrate is clever enough to do this itself. Simply run
+
+`transrate --install-deps`
+
+Transrate will check whether its dependencies are installed, and if not will download and install them for you.
 
 ## Usage
 
 ### Command line
 
-`transrate --help` will give you...
+`transrate --help` will display basic usage instructions.
 
 ```
-Transrate v0.0.10 by Richard Smith <rds45@cam.ac.uk>
+  Transrate v0.2.0 by Richard Smith-Unna <rds45@cam.ac.uk>
 
-DESCRIPTION:
-Analyse a de-novo transcriptome
-assembly using three kinds of metrics:
+  DESCRIPTION:
+  Analyse a de-novo transcriptome
+  assembly using three kinds of metrics:
 
-1. contig-based
-2. read-mapping
-3. reference-based
+  1. contig-based
+  2. read-mapping (if --left and --right are provided)
+  3. reference-based (if --reference is provided)
 
-Please make sure USEARCH, bowtie 2 and eXpress are installed
-and in the PATH.
+  Bug reports and feature requests at:
+  http://github.com/blahah/transrate
 
-Bug reports and feature requests at:
-http://github.com/blahah/transrate
+  USAGE:
+  transrate <options>
 
-USAGE:
-transrate <options>
+  EXAMPLES:
+  transrate --assembly contigs.fa --reference Athaliana_protein.fa --threads 8
 
-OPTIONS:
-    --assembly, -a <s>:   assembly file in FASTA format
+  OPTIONS:
+    --assembly, -a <s>:   assembly file(s) in FASTA format, comma-separated
    --reference, -r <s>:   reference proteome file in FASTA format
         --left, -l <s>:   left reads file in FASTQ format
        --right, -i <s>:   right reads file in FASTQ format
   --insertsize, -n <i>:   mean insert size (default: 200)
     --insertsd, -s <i>:   insert size standard deviation (default: 50)
      --threads, -t <i>:   number of threads to use (default: 8)
+     --outfile, -o <s>:   filename to use for CSV output (default: transate_results.csv)
+    --loglevel, -g <s>:   the amount of information to print. one of [error, info, warn, debug] (default: info)
+    --install-deps, -d:   install any missing dependencies
+         --profile, -p:   debug option: profile the code as it runs
          --version, -v:   Print version and exit
             --help, -h:   Show this message
 ```
 
-If you don't include --left and --right read files, the read-mapping based analysis will be skipped. I recommend that you don't align all your reads - just a subset of 500,000 will give you a very good idea of the quality. You can get a subset by running (on a linux system):
-
-`head -2000000 left.fastq > left_500k.fastq`
-
-`head -2000000 right.fastq > right_500k.fastq`
-
-FASTQ records are 4 lines long, so make sure you multiply the number of reads you want by 4, and be sure to run the same command on both the left and right read files.
+See the [getting started guide] on the website for more instructions, and see the [command-line options] part of the manual for details.
 
 #### Example
 
@@ -123,13 +125,13 @@ puts t.assembly_score
 
 ### Ruby
 
-First, you'll need Ruby v1.9.3 or greater installed. You can check with:
+First, you'll need Ruby v2.0.0 or greater installed. You can check with:
 
 `ruby --version`
 
 If you don't have Ruby installed, or you need a higher version, I recommend using [RVM](http://rvm.io/) as your Ruby Version Manager. To install RVM along with the latest Ruby, just run:
 
-`\curl -L https://get.rvm.io | bash -s stable`
+`\curl -L https://get.rvm.io | bash -s stable --ruby`
 
 ### Rubygems
 
@@ -139,9 +141,9 @@ Your Ruby installation *should* come with RubyGems, the package manager for Ruby
 
 If you don't have it installed, I recommend installing the latest version of Ruby and RubyGems using the RVM instructions above (in the [Requirements:Ruby](https://github.com/Blahah/transrate#ruby) section).
 
-### Usearch, Bowtie2 and eXpress
+## Other software
 
-Usearch (http://drive5.com/usearch), Bowtie2 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2) and eXpress (http://bio.math.berkeley.edu/eXpress/) must be installed and in your PATH. Additionally, the Usearch binary executable should be named `usearch`.
+Transrate uses a variety of other software including NCBI BLAST+, Bowtie2 and Samtools. But you don't need to worry about installing those yourself - Transrate does that automatically using the [bindeps](https://github.com/Blahah/bindeps) gem.
 
 ## Getting help
 

data/Rakefile

@@ -4,5 +4,41 @@ Rake::TestTask.new do |t|
   t.libs << 'test'
 end
 
+Rake::TestTask.new do |t|
+  t.name = :recip
+  t.libs << 'test'
+  t.test_files = ['test/test_reciprocal.rb']
+end
+
+Rake::TestTask.new do |t|
+  t.name = :comp
+  t.libs << 'test'
+  t.test_files = ['test/test_comp_metrics.rb']
+end
+
+Rake::TestTask.new do |t|
+  t.name = :contig
+  t.libs << 'test'
+  t.test_files = ['test/test_contig_metrics.rb']
+end
+
+Rake::TestTask.new do |t|
+  t.name = :read
+  t.libs << 'test'
+  t.test_files = ['test/test_read_metrics.rb']
+end
+
+Rake::TestTask.new do |t|
+  t.name = :bowtie
+  t.libs << 'test'
+  t.test_files = ['test/test_bowtie.rb']
+end
+
+Rake::TestTask.new do |t|
+  t.name = :rater
+  t.libs << 'test'
+  t.test_files = ['test/test_transrater.rb']
+end
+
 desc "Run tests"
 task :default => :test

data/bin/transrate

@@ -3,16 +3,17 @@
 require 'trollop'
 require 'transrate'
 require 'csv'
+require 'bindeps'
+require 'ruby-prof'
 
 opts = Trollop::options do
   version Transrate::VERSION::STRING.dup
   banner <<-EOS
 
-  Transrate v#{Transrate::VERSION::STRING.dup} by Richard Smith <rds45@cam.ac.uk>
+  Transrate v#{Transrate::VERSION::STRING.dup} by Richard Smith-Unna <rds45@cam.ac.uk>
 
   DESCRIPTION:
-  Analyse a de-novo transcriptome
-  assembly using three kinds of metrics:
+  Analyse a de-novo transcriptome assembly using three kinds of metrics:
 
   1. contig-based
   2. read-mapping (if --left and --right are provided)
@@ -25,13 +26,19 @@ opts = Trollop::options do
   transrate <options>
 
   EXAMPLES:
+  # just check dependencies and install any that are missing
+  transrate --install-deps
+  # contig metrics only
+  transrate --assembly contigs.fa
+  # contig and reference-based metrics with 8 threads
   transrate --assembly contigs.fa --reference Athaliana_protein.fa --threads 8
+  # contig and read-based metrics for two assemblies with 32 threads
+  transrate --assembly one.fa,two.fa --left l.fq --right r.fq --threads 32
 
   OPTIONS:
 
   EOS
   opt :assembly, "assembly file(s) in FASTA format, comma-separated",
-      :required => true, 
       :type => String
   opt :reference, "reference proteome file in FASTA format",
       :type => String
@@ -48,7 +55,36 @@ opts = Trollop::options do
   opt :threads, "number of threads to use",
       :default => 8,
       :type => Integer
-  opt :quiet, "don't print results - only save to file"
+  opt :outfile, "filename to use for CSV output",
+      :default => 'transate_results.csv'
+  opt :loglevel, "the amount of information to print. " +
+                 "one of [error, info, warn, debug]",
+      :default => 'info'
+  opt :install_deps, "install any missing dependencies"
+  opt :profile, "debug option: profile the code as it runs"
+end
+
+if opts.install_deps
+  puts "Checking dependencies"
+  gem_dir = Gem.loaded_specs['transrate'].full_gem_path
+  gem_deps = File.join(gem_dir, 'deps', 'deps.yaml')
+  Bindeps.require gem_deps
+  puts "All dependencies installed"
+  exit
+end
+
+unless opts.assembly
+  raise ArgumentError.new "Option --assembly must be specified. " +
+                          "Try --help for help."
+end
+
+if opts.reference && !File.exist?(opts.reference)
+  raise IOError.new "Reference fasta file does not exist: #{opts.reference}"
+end
+
+if opts.profile
+  logger.info "Starting profiler"
+  RubyProf.start
 end
 
 def pretty_print_hash hash, width
@@ -57,101 +93,105 @@ def pretty_print_hash hash, width
     if v.to_f.round(2).to_s.split('.').last.to_i > 0
       v = v.to_f.round(2)
     end
+    if v.is_a? Float
+      v = v.round(2)
+    end
     pad = (width - (k.to_s.length + v.to_s.length))
-    "#{k.to_s.split('_').join(' ')}" + 
+    pad = [pad, 0].max
+    logger.info "#{k.to_s.split('_').join(' ')}" +
     "#{" " * pad}" +
     "#{v}"
-  end.join("\n")
-end
-
-# don't log if --quiet is set
-$quiet = opts.quiet
-def log msg
-  unless $quiet
-    puts msg
   end
 end
 
 include Transrate
 
-r = opts.reference ? Assembly.new(opts.reference) : nil 
-report_width = 30
+unless %w[error info warn debug].include? opts.loglevel
+  raise "Loglevel #{opts.loglevel} is not valid. " +
+        "It must be one of: error, info, warn, debug."
+end
+
+logger.level = Yell::Level.new opts.loglevel.to_sym
+
+logger.info "Loading reference dataset"
+
+r = opts.reference ? Assembly.new(opts.reference) : nil
+report_width = 35
 
 # loop through the assemblies, storing their outputs in an array of hashes
 all = []
 opts.assembly.split(',').each do |assembly|
 
+  logger.info "Loading assembly: #{assembly}"
+
   a = Assembly.new assembly
+  transrater = Transrater.new(a, r,
+                              left: opts.left,
+                              right: opts.right,
+                              insertsize: opts.insertsize,
+                              insertsd: opts.insertsd,
+                              threads: opts.threads)
 
-  transrater = Transrater.new(a, r, 
-    opts.left, 
-    opts.right,
-    opts.insertsize,
-    opts.insertsd)
 
-  log "\nAnalysing assembly: #{assembly}\n\n"
+  logger.info "Analysing assembly: #{assembly}"
 
   contig_results = {}
 
-  log "Calculating contig metrics..."
+  logger.info "Calculating contig metrics..."
   t0 = Time.now
   contig_results = transrater.assembly_metrics.basic_stats
-
+  contig_results.merge! transrater.assembly.contig_metrics.results
   if contig_results
-    log "\n"
-    log "Contig metrics:"
-    log "-" *  report_width
-    log pretty_print_hash(contig_results, report_width)
+    logger.info "Contig metrics:"
+    logger.info "-" *  report_width
+    pretty_print_hash(contig_results, report_width)
   end
 
-  log "Contig metrics done in #{Time.now - t0} seconds"
+  logger.info "Contig metrics done in #{Time.now - t0} seconds"
 
   read_results = {}
 
   if (opts.left && opts.right)
-    log "\ncalculating read diagnostics..."
+    logger.info "Calculating read diagnostics..."
     t0 = Time.now
-    read_results = transrater.read_metrics(opts.left, opts.right).read_stats
+    read_results = transrater.read_metrics(opts.left,
+                                           opts.right).read_stats
 
     if read_results
-      log "\n"
-      log "Read mapping metrics:"
-      log "-" *  report_width
-      log pretty_print_hash(read_results, report_width)
+      logger.info "Read mapping metrics:"
+      logger.info "-" *  report_width
+      pretty_print_hash(read_results, report_width)
     end
 
-    log "Read metrics done in #{Time.now - t0} seconds"
+    logger.info "Read metrics done in #{Time.now - t0} seconds"
   else
-    log "\nNo reads provided, skipping read diagnostics"
+    logger.info "No reads provided, skipping read diagnostics"
   end
 
   comparative_results={}
 
   if opts.reference
-    log "\nCalculating comparative metrics..."
+    logger.info "Calculating comparative metrics..."
     t0 = Time.now
     comparative_metrics = transrater.comparative_metrics
     comparative_results = comparative_metrics.comp_stats
 
     if comparative_results
-      log "\n"
-      log "Comparative metrics:"
-      log "-" *  report_width
-      log pretty_print_hash(comparative_results, report_width)
+      logger.info "Comparative metrics:"
+      logger.info "-" *  report_width
+      pretty_print_hash(comparative_results, report_width)
     end
 
-    log "Comparative metrics done in #{Time.now - t0} seconds"
-
+    logger.info "Comparative metrics done in #{Time.now - t0} seconds"
 
-    log "\n"
-    log "-" * report_width
+    logger.info "-" * report_width
     score = transrater.assembly_score
     unless score.nil?
-      log "OVERALL SCORE: #{score.to_f.round(2) * 100}%"
-      log "-" * report_width
+      logger.info "OVERALL SCORE: #{score.to_f.round(2) * 100}%"
+      logger.info "-" * report_width
     end
   else
-    log "\nNo reference provided, skipping comparative diagnostics"
+    logger.info "No reference provided, skipping comparative diagnostics"
   end
 
   all << contig_results.
@@ -163,6 +203,7 @@ end
 
 # write out all resuls to .csv
 outfile = opts.out || 'transrate.csv'
+logger.info "Writing analysis results to #{outfile}"
 CSV.open(outfile, 'wb') do |file|
   keys = all[0].keys
   keys.delete(:assembly)
@@ -171,4 +212,11 @@ CSV.open(outfile, 'wb') do |file|
   all.each do |row|
     file << head.map { |x| row[x] }
   end
-end
+end
+
+if opts.profile
+  logger.info "Writing profiling results to transrate_profile.txt"
+  result = RubyProf.stop
+  printer = RubyProf::FlatPrinter.new(result)
+  printer.print(File.open('transrate_profile.txt', 'w'))
+end