bio-rocker 1.1.10 → 1.1.11
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- checksums.yaml +4 -4
- data/bin/ROCker +19 -9
- data/lib/rocker.rb +1 -1
- metadata +14 -14
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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4
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data.tar.gz:
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3
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metadata.gz: 85c453e6a8e2ced8f03b930ea696682b11a90c5c
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4
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data.tar.gz: 64e2894fdb38450bd3849168825d2a75cdac960f
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SHA512:
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6
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metadata.gz:
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7
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data.tar.gz:
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6
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metadata.gz: db06cca064320b559290ac7ecb5aad40e89bc4bab30cd69510e4f537b834d863ab4b7fbe64885790d181246a033fabfd6184667b2bb10841a00b5908c8addd91
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7
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data.tar.gz: 574a1ab17ec2fc44a7993eba843c193db2c8acb7ed56e52429436d2b9a03162f6c0f540d715eff73de2e145a85e7c76c6a1bd424d1d1e9a759d465eacea23a41
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data/bin/ROCker
CHANGED
@@ -1,10 +1,9 @@
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1
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#!/usr/bin/env ruby
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-
# @author
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4
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# @author
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+
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# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
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# @author Luis (Coto) Orellana
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# @license artistic license 2.0
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-
# @update
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7
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-
#
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6
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# @update Mar-28-2016
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lib = File.expand_path("../lib", File.dirname(__FILE__))
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$:.push lib if Dir.exist? lib
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@@ -26,8 +25,13 @@ $t = {
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"thresholds, and the hits.",
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"info" => "Display additional information about ROCker."
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}
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-
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-
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28
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+
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if %w[-V --version].include? ARGV.first
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task = "info"
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else
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task = (ARGV.empty? ? "" : ARGV.shift).downcase
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ARGV << "-h" if ARGV.empty? and task != "info"
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end
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o = {}
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opts = OptionParser.new do |opt|
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@@ -324,10 +328,14 @@ opts = OptionParser.new do |opt|
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opt.on("-q", "--quiet", "Run quietly."){ |v| o[:q]=true }
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opt.on("-d", "--debug",
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"Display debugging information."){ |v| o[:debug]=true }
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327
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-
opt.on("-h", "--help", "Display this screen") do
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331
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+
opt.on("-h", "--help", "Display this screen.") do
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puts opt
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exit
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end
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335
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+
opt.on("-V", "--version","Display version.") do
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puts "ROCker v" + ROCker.VERSION
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exit
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end
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opt.separator ""
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unless $t.include? task
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puts opt
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@@ -336,6 +344,8 @@ opts = OptionParser.new do |opt|
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end
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opts.parse!
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p ARGV
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348
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#================================[ Main ]
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rocker = ROCker.new(o)
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@@ -363,7 +373,7 @@ begin
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puts "For additional information and documentation, visit:"
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puts "http://enve-omics.ce.gatech.edu/rocker/"
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puts ""
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-
puts "For our list of curated models,
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puts "For our list of curated models, visit:"
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puts "http://enve-omics.ce.gatech.edu/rocker/models"
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end
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rescue => err
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data/lib/rocker.rb
CHANGED
@@ -10,7 +10,7 @@ require "rocker/rocdata"
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class ROCker
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#================================[ Class ]
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-
@@VERSION = "1.1.
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+
@@VERSION = "1.1.11"
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@@CITATION = [
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"Orellana, Rodriguez-R, & Konstantinidis. Under review.",
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"Detecting and quantifying functional genes in short-read",
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: bio-rocker
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version: !ruby/object:Gem::Version
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version: 1.1.
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version: 1.1.11
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platform: ruby
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authors:
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- Luis (Coto) Orellana
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@@ -15,28 +15,28 @@ dependencies:
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name: rest-client
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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+
- - ~>
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- !ruby/object:Gem::Version
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version: '1.7'
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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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+
- - ~>
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- !ruby/object:Gem::Version
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version: '1.7'
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- !ruby/object:Gem::Dependency
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name: json
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requirement: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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- - ~>
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- !ruby/object:Gem::Version
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version: '1.8'
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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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- - ~>
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- !ruby/object:Gem::Version
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version: '1.8'
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description: Detecting and quantifying functional genes in short-read metagenomic
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@@ -47,21 +47,21 @@ executables:
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extensions: []
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extra_rdoc_files: []
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files:
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-
- bin/ROCker
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- lib/rocker.rb
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51
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+
- lib/rocker/sequence.rb
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- lib/rocker/alignment.rb
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- lib/rocker/blasthit.rb
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- lib/rocker/rocwindow.rb
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- lib/rocker/rocdata.rb
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- lib/rocker/rinterface.rb
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- lib/rocker/genome-set.rb
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- lib/rocker/protein-set.rb
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- lib/rocker/rinterface.rb
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- lib/rocker/rocdata.rb
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- lib/rocker/rocwindow.rb
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- lib/rocker/sequence.rb
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- lib/rocker/step/build.rb
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- lib/rocker/step/compile.rb
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- lib/rocker/step/search.rb
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- lib/rocker/step/filter.rb
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- lib/rocker/step/plot.rb
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-
-
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- bin/ROCker
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homepage: http://enve-omics.ce.gatech.edu/rocker
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licenses:
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- artistic 2.0
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@@ -72,17 +72,17 @@ require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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- - '>='
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- !ruby/object:Gem::Version
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version: '2.0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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-
- -
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+
- - '>='
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.
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rubygems_version: 2.0.14
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signing_key:
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specification_version: 4
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summary: ROCker
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