transrate 1.0.0.beta4 → 1.0.0.beta5

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 2863b7bc2b0f63af4c43dc31c77f43324dafccfc
+  metadata.gz: 6010a898aadeb76441e40dc958a2985c3df1d444
+  data.tar.gz: 3c908a057b696e778cb4d369d50798ee8887d271
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data/README.md

@@ -28,7 +28,7 @@ This software is being actively developed. Please be aware that there may be bug
 
 ## Citation
 
-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).
+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).
 
 ## Documentation
 

data/bin/transrate

@@ -4,6 +4,7 @@ require 'trollop'
 require 'transrate'
 require 'csv'
 require 'bindeps'
+require 'colorize'
 
 include Transrate
 
@@ -27,9 +28,19 @@ module Kernel
   end
 end
 
+txp = '░▓▓▓^▓▓▓░'
+toptxp = txp.green
+midtxp = txp.yellow
+bottxp = txp.red
+
 opts = Trollop::options do
   version Transrate::VERSION::STRING.dup
   banner <<-EOS
+           _                                        _
+          | |_  _ __  __ _  _ __   ___  _ __  __ _ | |_  ___
+#{toptxp} | __|| '__|/ _` || '_ \\ / __|| '__|/ _` || __|/ _ \\ #{toptxp}
+#{midtxp} | |_ | |  | (_| || | | |\\__ \\| |  | (_| || |_|  __/ #{midtxp}
+#{bottxp}  \\__||_|   \\__,_||_| |_||___/|_|   \\__,_| \\__|\\___| #{bottxp}
 
   Transrate v#{Transrate::VERSION::STRING.dup}
   by Richard Smith-Unna, Chris Boursnell, Rob Patro,
@@ -38,28 +49,15 @@ opts = Trollop::options do
   DESCRIPTION:
   Analyse a de-novo transcriptome assembly using three kinds of metrics:
 
-  1. sequence-based (basic)
-  2. read-mapping-based (if --left and --right are provided)
-  3. reference-based (if --reference is provided)
+  1. sequence based (if --assembly is given)
+  2. read mapping based (if --left and --right are given)
+  3. reference based (if --reference is given)
 
-  Bug reports and feature requests at:
-  http://github.com/blahah/transrate
+  Documentation at http://hibberdlab.com/transrate
 
   USAGE:
   transrate <options>
 
-  EXAMPLES:
-  # check dependencies and install any that are missing
-  transrate --install-deps
-  # get the transrate score for the assembly and each contig
-  transrate --assembly contigs.fa --left left.fq --right right.fq
-  # basic assembly metrics only
-  transrate --assembly contigs.fa
-  # basic and reference-based metrics with 8 threads
-  transrate --assembly contigs.fa --reference Athaliana_transcripts.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
@@ -69,22 +67,47 @@ opts = Trollop::options do
       :type => String
   opt :right, "Right reads file in FASTQ format",
       :type => String
-  opt :reference, "Reference proteome file in FASTA format",
+  opt :reference, "Reference proteome or transcriptome file in FASTA format",
       :type => String
   opt :threads, "Number of threads to use",
       :default => 8,
       :type => Integer
-  opt :merge_assemblies, "Merge multiple assemblies into file",
+  opt :merge_assemblies, "Merge best contigs from multiple assemblies into file",
       :type => String
   opt :outfile, "Prefix filename to use for CSV output",
       :default => 'transrate'
-  opt :loglevel, "The amount of information to print. " +
+  opt :loglevel, "Log level. " +
                  "One of [error, info, warn, debug]",
       :default => 'info'
   opt :install_deps, "Install any missing dependencies. One of [all, read, ref]",
       :type => String, :default => nil
-  # opt :install_read_deps, "install missing dependencies for read metrics only"
-  # opt :install_ref_deps, "install missing dependencies for reference metrics only"
+  opt :examples, "Show some example commands with explanations"
+end
+
+if opts.examples
+  puts <<-EOS
+
+  Transrate v#{Transrate::VERSION::STRING.dup}
+
+  EXAMPLE COMMANDS:
+
+  # check dependencies and install any that are missing
+  transrate --install-deps
+
+  # get the transrate score for the assembly and each contig
+  transrate --assembly contigs.fa --left left.fq --right right.fq
+
+  # basic assembly metrics only
+  transrate --assembly contigs.fa
+
+  # basic and reference-based metrics with 8 threads
+  transrate --assembly contigs.fa --reference ref.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
+
+  EOS
+  exit(0)
 end
 
 # Check dependencies if they are relevant to the command issued,

data/lib/transrate.rb

@@ -37,4 +37,3 @@ require 'transrate/read_metrics'
 require 'transrate/comparative_metrics'
 require 'transrate/contig_metrics'
 require 'transrate/cmd'
-require 'transrate/transrate.so'

data/lib/transrate/version.rb

@@ -11,7 +11,7 @@ module Transrate
     MAJOR = 1
     MINOR = 0
     PATCH = 0
-    BUILD = 'beta4'
+    BUILD = 'beta5'
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
   end

data/transrate.gemspec

@@ -23,6 +23,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
   gem.add_dependency 'crb-blast', '~> 0.6', '>= 0.6.4'
   gem.add_dependency 'fix-trinity-output', '~> 1.0', '>= 1.0'
+  gem.add_dependency 'colorize', '~> 0.7', '>= 0.7.7'
 
   gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
   gem.add_development_dependency 'rake-compiler', '~> 0.9', '>= 0.9.2'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 1.0.0.beta4
+  version: 1.0.0.beta5
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-05 00:00:00.000000000 Z
+date: 2015-06-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell
@@ -131,6 +131,26 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: colorize
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.7.7
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.7.7
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement