transrate 1.0.0.beta4 → 1.0.0.beta5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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data/README.md CHANGED
@@ -28,7 +28,7 @@ This software is being actively developed. Please be aware that there may be bug
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  ## Citation
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- Transrate is pre-publication academic software. If you use it, please cite the github repository and the DOI: [![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.13161.svg)](http://dx.doi.org/10.5281/zenodo.13161).
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+ Transrate is pre-publication academic software. If you use it, please cite the github repository and the DOI: [![DOI](https://zenodo.org/badge/3687/Blahah/transrate.svg)](http://dx.doi.org/10.5281/zenodo.18325).
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  ## Documentation
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data/bin/transrate CHANGED
@@ -4,6 +4,7 @@ require 'trollop'
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  require 'transrate'
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  require 'csv'
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  require 'bindeps'
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+ require 'colorize'
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  include Transrate
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@@ -27,9 +28,19 @@ module Kernel
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  end
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  end
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+ txp = '░▓▓▓^▓▓▓░'
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+ toptxp = txp.green
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+ midtxp = txp.yellow
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+ bottxp = txp.red
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+
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  opts = Trollop::options do
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  version Transrate::VERSION::STRING.dup
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  banner <<-EOS
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+ _ _
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+ | |_ _ __ __ _ _ __ ___ _ __ __ _ | |_ ___
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+ #{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp}
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+ #{midtxp} | |_ | | | (_| || | | |\\__ \\| | | (_| || |_| __/ #{midtxp}
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+ #{bottxp} \\__||_| \\__,_||_| |_||___/|_| \\__,_| \\__|\\___| #{bottxp}
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  Transrate v#{Transrate::VERSION::STRING.dup}
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  by Richard Smith-Unna, Chris Boursnell, Rob Patro,
@@ -38,28 +49,15 @@ opts = Trollop::options do
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  DESCRIPTION:
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  Analyse a de-novo transcriptome assembly using three kinds of metrics:
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- 1. sequence-based (basic)
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- 2. read-mapping-based (if --left and --right are provided)
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- 3. reference-based (if --reference is provided)
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+ 1. sequence based (if --assembly is given)
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+ 2. read mapping based (if --left and --right are given)
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+ 3. reference based (if --reference is given)
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- Bug reports and feature requests at:
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- http://github.com/blahah/transrate
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+ Documentation at http://hibberdlab.com/transrate
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  USAGE:
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  transrate <options>
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- EXAMPLES:
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- # check dependencies and install any that are missing
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- transrate --install-deps
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- # get the transrate score for the assembly and each contig
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- transrate --assembly contigs.fa --left left.fq --right right.fq
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- # basic assembly metrics only
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- transrate --assembly contigs.fa
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- # basic and reference-based metrics with 8 threads
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- transrate --assembly contigs.fa --reference Athaliana_transcripts.fa --threads 8
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- # contig and read-based metrics for two assemblies with 32 threads
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- transrate --assembly one.fa,two.fa --left l.fq --right r.fq --threads 32
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-
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  OPTIONS:
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  EOS
@@ -69,22 +67,47 @@ opts = Trollop::options do
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  :type => String
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  opt :right, "Right reads file in FASTQ format",
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  :type => String
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- opt :reference, "Reference proteome file in FASTA format",
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+ opt :reference, "Reference proteome or transcriptome file in FASTA format",
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  :type => String
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  opt :threads, "Number of threads to use",
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  :default => 8,
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  :type => Integer
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- opt :merge_assemblies, "Merge multiple assemblies into file",
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+ opt :merge_assemblies, "Merge best contigs from multiple assemblies into file",
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  :type => String
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  opt :outfile, "Prefix filename to use for CSV output",
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  :default => 'transrate'
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- opt :loglevel, "The amount of information to print. " +
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+ opt :loglevel, "Log level. " +
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  "One of [error, info, warn, debug]",
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  :default => 'info'
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  opt :install_deps, "Install any missing dependencies. One of [all, read, ref]",
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  :type => String, :default => nil
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- # opt :install_read_deps, "install missing dependencies for read metrics only"
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- # opt :install_ref_deps, "install missing dependencies for reference metrics only"
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+ opt :examples, "Show some example commands with explanations"
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+ end
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+
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+ if opts.examples
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+ puts <<-EOS
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+
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+ Transrate v#{Transrate::VERSION::STRING.dup}
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+
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+ EXAMPLE COMMANDS:
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+
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+ # check dependencies and install any that are missing
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+ transrate --install-deps
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+
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+ # get the transrate score for the assembly and each contig
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+ transrate --assembly contigs.fa --left left.fq --right right.fq
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+
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+ # basic assembly metrics only
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+ transrate --assembly contigs.fa
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+
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+ # basic and reference-based metrics with 8 threads
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+ transrate --assembly contigs.fa --reference ref.fa --threads 8
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+
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+ # contig and read-based metrics for two assemblies with 32 threads
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+ transrate --assembly one.fa,two.fa --left l.fq --right r.fq --threads 32
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+
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+ EOS
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+ exit(0)
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  end
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  # Check dependencies if they are relevant to the command issued,
data/lib/transrate.rb CHANGED
@@ -37,4 +37,3 @@ require 'transrate/read_metrics'
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  require 'transrate/comparative_metrics'
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  require 'transrate/contig_metrics'
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  require 'transrate/cmd'
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- require 'transrate/transrate.so'
@@ -11,7 +11,7 @@ module Transrate
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  MAJOR = 1
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  MINOR = 0
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  PATCH = 0
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- BUILD = 'beta4'
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+ BUILD = 'beta5'
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  STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
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  end
data/transrate.gemspec CHANGED
@@ -23,6 +23,7 @@ Gem::Specification.new do |gem|
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  gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
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  gem.add_dependency 'crb-blast', '~> 0.6', '>= 0.6.4'
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  gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
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+ gem.add_dependency 'colorize', '~> 0.7', '>= 0.7.7'
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  gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
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  gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: transrate
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  version: !ruby/object:Gem::Version
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- version: 1.0.0.beta4
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+ version: 1.0.0.beta5
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  platform: ruby
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  authors:
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  - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2015-06-05 00:00:00.000000000 Z
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+ date: 2015-06-11 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: yell
@@ -131,6 +131,26 @@ dependencies:
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  - - ">="
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  - !ruby/object:Gem::Version
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  version: '1.0'
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+ - !ruby/object:Gem::Dependency
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+ name: colorize
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '0.7'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.7.7
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '0.7'
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: 0.7.7
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  - !ruby/object:Gem::Dependency
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  name: rake
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  requirement: !ruby/object:Gem::Requirement