dirseq 0.0.2

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 84e91d3823af5395053c2104197b68223d3e4d96
+  data.tar.gz: 7488e7557cd4005dcfc8b6f3c504d4e250434e5b
+SHA512:
+  metadata.gz: f21a59e7fc5bf7e9cf77721ed50935a85a3123cb4fcc74a0a556666721d13449de00c93464e3defb8f3552f1872b7c2df49ea2168810354dd89946eaa5035205
+  data.tar.gz: e202cb7e0f00eb15b76cb91ccafb55b00fbe1269b617088f8d601b7f94d55b56fd900ecef578584fbaebacebaffe3c5e999e56a069b9a5c672921435e9bfb7b7

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,18 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "bio-commandeer", "~>0.1"
+gem "bio-logger", "~>1.0"
+gem "bio", "~>1.4", ">=1.4.2"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", "~> 3.5"
+  gem "rdoc", "~> 3.12"
+  gem "simplecov", "~> 0.8"
+  gem "jeweler", "~> 2.0"
+  gem "bundler", "~> 1.6"
+  gem "rspec", "~> 2.99"
+end

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2014 Ben J. Woodcroft
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

@@ -0,0 +1,67 @@
+# dirseq
+
+[![Build Status](https://secure.travis-ci.org/wwood/dirseq.png)](http://travis-ci.org/wwood/dirseq)
+
+DirSeq work out whether RNAseq reads from metatranscriptomes are generally in the same direction as the ORF predicted, and provide gene-wise coverages using DNAseq mappings.
+
+Note: this software is under active development!
+
+## Installation
+
+Won't work just yet:
+```sh
+gem install dirseq
+```
+Requires:
+* samtools (tested with 0.1.19)
+* bedtools (tested with 2.20.1)
+* Ruby (tested with 2.1.1)
+
+## Usage
+
+Only the script is available at the moment
+```sh
+$ dirseq -h
+
+    Usage: dirseq <arguments>
+
+    Reports the coverage of a mapping in against each gene given in a GFF file
+
+        --bam FILE                   path to mapping file [required]
+        --gff FILE                   path to GFF3 file [required]
+
+Optional parameters:
+
+        --ignore-directions          ignore directionality, give overall coverage [default: false i.e. differentiate between directions]
+
+Verbosity:
+
+    -q, --quiet                      Run quietly, set logging to ERROR level [default INFO]
+        --logger filename            Log to file [default stderr]
+        --trace options              Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG
+```
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/wwood/dirseq
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-rnaseq_transcription_directionality)
+
+## Copyright
+
+Copyright (c) 2014 Ben J. Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "dirseq"
+  gem.homepage = "http://github.com/wwood/dirseq"
+  gem.license = "MIT"
+  gem.summary = %Q{FPKG calculator for metatranscriptomics}
+  gem.description = %Q{FPKG (gene expression metric) calculator for metatranscriptomics}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "rnaseq_transcription_directionality #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.2

data/bin/dirseq

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+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'bio-logger'
+require 'bio'
+require 'bio-commandeer'
+#require 'pry'
+require 'set'
+require 'tempfile'
+
+SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
+
+# Parse command line options into the options hash
+options = {
+  :ignore_directions => false,
+  :logger => 'stderr',
+  :log_level => 'info',
+}
+o = OptionParser.new do |opts|
+  opts.banner = "
+    Usage: #{SCRIPT_NAME} <arguments>
+
+    Reports the coverage of a mapping in against each gene given in a GFF file\n\n"
+
+  opts.on("--bam FILE", "path to mapping file [required]") do |arg|
+    options[:bam] = arg
+  end
+  opts.on("--gff FILE", "path to GFF3 file [required]") do |arg|
+    options[:gff] = arg
+  end
+  opts.separator "\nOptional parameters:\n\n"
+  opts.on("--ignore-directions", "ignore directionality, give overall coverage [default: false i.e. differentiate between directions]") do |arg|
+    options[:ignore_directions] = true
+  end
+
+  # logger options
+  opts.separator "\nVerbosity:\n\n"
+  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
+  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
+  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
+end; o.parse!
+if ARGV.length != 0 or options[:bam].nil? or options[:gff].nil?
+  $stderr.puts o
+  exit 1
+end
+# Setup logging
+Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME); log.outputters[0].formatter = Log4r::PatternFormatter.new(:pattern => "%5l %c %d: %m", :date_pattern => '%d/%m %T')
+
+gff_file = options[:gff]
+bam_file = options[:bam]
+
+
+calculate_cov = lambda do |covs, num_covs|
+  covs.reduce(:+).to_f / num_covs
+end
+
+get_covs = lambda do |cov_lines|
+  feature_to_covs = {}
+  previous_feature = nil
+  covs = []
+  num_covs = 0
+  cov_lines.each_line do |line|
+    splits = line.split("\t")
+    break if splits[0] == 'all'
+
+    #gi|169887498|gb|CP000948.1|
+    #Prodigal_v2.6.1
+    #CDS
+    #1047994
+    #1049139
+    #157.2
+    #-
+    #0
+    #ID=1_972;partial=00;start_type=ATG;rbs_motif=AGGA;rbs_spacer=5-10bp;gc_cont=0.568;conf=100.00;score=157.25;cscore=141.04;sscore=16.20;rscore=10.98;uscore=-0.89;tscore=3.93;
+    #70 #coverage
+    #2 #num reads with coverage 70
+    #96 #coverage
+    #0.0208333
+    feat = splits[0..8]
+    if feat != previous_feature
+      feature_to_covs[previous_feature] = calculate_cov.call(covs, num_covs) unless previous_feature.nil?
+      covs = []
+      num_covs = 0
+    end
+    num = splits[10].to_i
+    covs.push num*splits[9].to_i
+    num_covs += num
+    previous_feature = feat
+  end
+  feature_to_covs[previous_feature] = calculate_cov.call(covs, num_covs)
+
+  feature_to_covs
+end
+
+# Remove the ##FASTA and afterwards from the GFF file as this makes bedtools <2.25 fail
+# https://github.com/arq5x/bedtools2/issues/235#issuecomment-103776618
+no_fasta_gff = Tempfile.new('dirseq')
+Bio::Commandeer.run "sed '/^##FASTA$/,$d' #{gff_file.inspect} > #{no_fasta_gff.path}"
+gff_file = no_fasta_gff.path
+
+covs_fwd = nil
+if options[:ignore_directions]
+  cmd1 = "bedtools coverage -abam #{bam_file.inspect} -b #{gff_file.inspect} -hist"
+  cov_lines_fwd = Bio::Commandeer.run cmd1, :log => log
+  log.info "Parsing coverage profiles"
+  covs_fwd = get_covs.call(cov_lines_fwd)
+
+else
+  # fwd read 1
+  read1_flag = '-F128' #account for read1 in pair, as well as single reads mapping
+  read2_flag = '-f128'
+  cmdf1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -s"
+  cmdf2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -s"
+  cmdr1 = "samtools view -u #{read1_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -S"
+  cmdr2 = "samtools view -u #{read2_flag} #{bam_file.inspect} |bedtools coverage -abam /dev/stdin -b #{gff_file.inspect} -hist -S"
+
+  command_to_parsed = lambda do |cmds, name|
+    covs_lines_initial = cmds.collect do |cmd|
+      Bio::Commandeer.run cmd, :log => log
+    end
+    covs_initial = covs_lines_initial.collect do |lines|
+      log.info "Parsing #{name}"
+      get_covs.call(lines)
+    end
+    #binding.pry
+    covs = covs_initial[0]
+    covs_initial[1].each do |cov_key, cov|
+      covs[cov_key] += cov
+    end
+    covs #'return' from lambda
+  end
+
+  # Agreeing reads (those whose template are fwd along the reference sequence) are either first and fwd, or second and rev
+  covs_fwd = command_to_parsed.call([cmdf1,cmdr2], 'reads with same direction as their reference')
+  covs_rev = command_to_parsed.call([cmdf2,cmdr1], 'reads with opposing direction as their reference')
+end
+
+headers = [
+  'contig',
+  'type',
+  'start',
+  'end',
+  'strand',
+]
+if options[:ignore_directions]
+  headers.push 'average_coverage'
+else
+  headers.push 'forward_average_coverage'
+  headers.push 'reverse_average_coverage'
+end
+headers.push 'annotation'
+puts headers.join("\t")
+
+covs_fwd.each do |feature, cov_fwd|
+  cov_rev = covs_rev[feature] unless options[:ignore_directions]
+  record = Bio::GFF::GFF3::Record.new(feature.join("\t"))
+
+  products = record.attributes.select{|a| a[0] == 'product'}
+  product = 'unannotated'
+  if products.length == 1
+    product = products[0][1]
+  end
+
+  to_print = [
+    record.seqname,
+    record.feature,
+    record.start,
+    record.end,
+    record.strand,
+    cov_fwd,
+  ]
+  to_print.push cov_rev unless options[:ignore_directions]
+  to_print.push product
+  puts to_print.join("\t")
+end

data/lib/bio-rnaseq_transcription_directionality/rnaseq_transcription_directionality.rb

@@ -0,0 +1,3 @@
+
+module BioRnaseqTranscriptionDirectionality
+end

data/lib/bio-rnaseq_transcription_directionality.rb

@@ -0,0 +1,12 @@
+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-rnaseq_transcription_directionality/rnaseq_transcription_directionality.rb'
+

data/spec/data/eg.gff

@@ -0,0 +1 @@
+contig_100	Prodigal_v2.60	CDS	2	127	0.5	+	0	ID=40_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.230;conf=52.95;score=0.51;cscore=-2.21;sscore=2.72;rscore=0.00;uscore=0.00;tscore=3.22;

data/spec/data/eg_with_fasta.gff

@@ -0,0 +1,9 @@
+contig_100	Prodigal_v2.60	CDS	2	127	0.5	+	0	ID=40_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.230;conf=52.95;score=0.51;cscore=-2.21;sscore=2.72;rscore=0.00;uscore=0.00;tscore=3.22;
+##FASTA
+>contig_1015388
+TCCGGGCCGATCACGAACACGTTGCGCACCGTCTGGTTATCGGCCGGCGTACGGGTCGCC
+GGGTCACCCTCCGTGCCCGCGGGCAGCATGCCGTAAAGCTTCGAAACATTGAAGTCGGAG
+TCACCGATGATCGGGTAGTTCGGCGCCGTCCCCTGGGTCTCCTCGATGTCCTTGGCCCAA
+CCTGAATGCTTATCAACCGGATCGACCGACAGCCCGATCACCTTCACACCACGGCGATCA
+AACTCCGGCTTAATCGAAGCCAGGTAGCCAAGTTCAGTCGTGCACACCGGCGTGAAGTCC
+TTCGGATGCGAAAACAACACCGCCCATGAATCGCCGATCCAATCATGGAAATGGATCCGG

data/spec/script_spec.rb

@@ -0,0 +1,42 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe 'script' do
+  path_to_script = File.join(File.dirname(__FILE__),'..','bin','dirseq')
+  data_dir = File.absolute_path(File.join(File.dirname(__FILE__),'data'))
+
+  it "should regular mode" do
+    answer = %w(
+    contig	type	start	end	strand	forward_average_coverage	reverse_average_coverage	annotation
+    ).join("\t")+"\n"+%w(
+    contig_100	CDS	2	127	+	0.0	1.1428571428571428	unannotated
+    ).join("\t")+"\n"
+
+    found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/eg.gff -q"
+
+    found.should == answer
+  end
+
+  it "should ignore directions mode" do
+    found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/eg.gff -q --ignore-direction"
+
+    answer = %w(
+    contig	type	start	end	strand	average_coverage	annotation
+    ).join("\t")+"\n"+%w(
+    contig_100	CDS	2	127	+	1.1428571428571428	unannotated
+    ).join("\t")+"\n"
+
+    found.should == answer
+  end
+
+  it 'should not fail when the GFF has a FASTA section' do
+    answer = %w(
+    contig	type	start	end	strand	forward_average_coverage	reverse_average_coverage	annotation
+    ).join("\t")+"\n"+%w(
+    contig_100	CDS	2	127	+	0.0	1.1428571428571428	unannotated
+    ).join("\t")+"\n"
+
+    found = Bio::Commandeer.run "#{path_to_script} --bam #{data_dir}/eg.bam --gff #{data_dir}/eg_with_fasta.gff -q"
+
+    found.should == answer
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,12 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-commandeer'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,193 @@
+--- !ruby/object:Gem::Specification
+name: dirseq
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-06-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-commandeer
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.99'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.99'
+description: FPKG (gene expression metric) calculator for metatranscriptomics
+email: donttrustben near gmail.com
+executables:
+- dirseq
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- bin/dirseq
+- lib/bio-rnaseq_transcription_directionality.rb
+- lib/bio-rnaseq_transcription_directionality/rnaseq_transcription_directionality.rb
+- spec/data/eg.bam
+- spec/data/eg.gff
+- spec/data/eg_with_fasta.gff
+- spec/script_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/dirseq
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: FPKG calculator for metatranscriptomics
+test_files: []