bio-rocker 1.1.11 → 1.1.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 85c453e6a8e2ced8f03b930ea696682b11a90c5c
-  data.tar.gz: 64e2894fdb38450bd3849168825d2a75cdac960f
+  metadata.gz: 77c08046b7d0b8f4528e38726c4b0681ce55a5c1
+  data.tar.gz: 8335d7484f0227f768a1cebdf0937bd8e7ef0513
 SHA512:
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-  data.tar.gz: 574a1ab17ec2fc44a7993eba843c193db2c8acb7ed56e52429436d2b9a03162f6c0f540d715eff73de2e145a85e7c76c6a1bd424d1d1e9a759d465eacea23a41
+  metadata.gz: 1a359c796f73a44fb008032786df546e640079d186751429c100e06b09cbc9141ecbe19d7937dc15ae7a3e1a2a02885fa6f08c42c22c97a131d48c471275f96e
+  data.tar.gz: 38ca17ae7f4cd04f85ea799851e23cb6f095a17a3475dfb298b8863f1be8dcc3701e2d9dac08e2f3f8bc5b5f88726904488c411b99d03d277b4ef11f6b5a3a05

data/bin/ROCker

@@ -2,8 +2,7 @@
 
 # @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author  Luis (Coto) Orellana
-# @license artistic license 2.0
-# @update  Mar-28-2016
+# @license Artistic-2.0
 
 lib = File.expand_path("../lib", File.dirname(__FILE__))
 $:.push lib if Dir.exist? lib
@@ -147,7 +146,8 @@ opts = OptionParser.new do |opt|
 	 end.reduce([],:+) ){ |v| o[:makedbcmd]=v }
       opt.on("--simulator-cmd STR",
 	 "Command calling simulator, where %1$s: binary, %2$s: input,",
-	 "%3$s: seq. depth (X), %4$d: read len., %5$s: output.",
+	 "%3$s: seq. depth (X), %4$d: read len., %5$s: output file, " +
+         "%6$s: output dir.",
 	 *ROCker.default(:simulatorcmd).keys.map do |k|
 	    ["By default if --simulator #{k}:", "'" +
 	       ROCker.default(:simulatorcmd)[k] + "'"]

data/lib/rocker.rb

@@ -1,8 +1,7 @@
 #
 # @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author  Luis (Coto) Orellana
-# @license artistic license 2.0
-# @update  Dec-01-2015
+# @license Artistic-2.0
 #
 
 require "rocker/blasthit"
@@ -10,13 +9,13 @@ require "rocker/rocdata"
 
 class ROCker
    #================================[ Class ]
-   @@VERSION = "1.1.11"
+   @@VERSION = "1.1.12"
    @@CITATION = [
       "Orellana, Rodriguez-R, & Konstantinidis. Under review.",
       "Detecting and quantifying functional genes in short-read",
       "metagenomic datasets: method development and application",
       "to the nitrogen cycle genes."]
-   @@DATE = "2015-12-01"
+   @@DATE = "2016-05-17"
    @@DEFAULTS = {
       # General
       q: false, r: "R", nucl: false, debug: false, thr: 2, search: :blast,

data/lib/rocker/step/build.rb

@@ -1,8 +1,7 @@
 #
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @author Luis (Coto) Orellana
-# @license artistic license 2.0
-# @update Dec-01-2015
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author  Luis (Coto) Orellana
+# @license Artistic-2.0
 #
 
 require "json"
@@ -19,7 +18,7 @@ class ROCker
       simulatorbin:{grinder:"grinder"},
       simulatorcmd:{grinder:"%1$s -reference_file \"%2$s\" -cf \"%3$f\" " +
 	 "-dc '-~*NnKkMmRrYySsWwBbVvHhDdXx' -md uniform 0.1 -mr 95 5 " +
-	 "-rd %4$d uniform 5 -base_name \"%5$s\""},
+	 "-rd %4$d uniform 5 -base_name \"%5$s\" -output_dir \"%6$s\""},
       alignerbin:{muscle:"muscle", clustalo:"clustalo"},
       alignercmd:{muscle:"%1$s -in \"%2$s\" -out \"%3$s\" -quiet",
 	 clustalo:"%1$s -i \"%2$s\" -o \"%3$s\" --threads=%4$d --force"}
@@ -303,10 +302,11 @@ class ROCker
 
 		  # Run simulator (except if the temporal file is already
 		  # there and can be reused)
+                  ofile = "#{@o[:baseout]}.mg.tmp.#{thr_i.to_s}"
 		  bash sprintf(@o[:simulatorcmd], @o[:simulatorbin],
 		     "#{@o[:baseout]}.src.fasta.#{thr_i.to_s}",
 		     @o[:seqdepth]*@o[:readlen].to_f, @o[:readlen],
-		     "#{@o[:baseout]}.mg.tmp.#{thr_i.to_s}") unless
+		     File.basename(ofile), File.dirname(ofile)) unless
 			@o[:reuse] and
 			File.size? @o[:baseout] +
 			".mg.tmp.#{thr_i.to_s}-reads.fa"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 1.1.11
+  version: 1.1.12
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -9,34 +9,34 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-01 00:00:00.000000000 Z
+date: 2016-05-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.7'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.8'
 description: Detecting and quantifying functional genes in short-read metagenomic
@@ -47,21 +47,21 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- bin/ROCker
 - lib/rocker.rb
-- lib/rocker/sequence.rb
 - lib/rocker/alignment.rb
 - lib/rocker/blasthit.rb
-- lib/rocker/rocwindow.rb
-- lib/rocker/rocdata.rb
-- lib/rocker/rinterface.rb
 - lib/rocker/genome-set.rb
 - lib/rocker/protein-set.rb
+- lib/rocker/rinterface.rb
+- lib/rocker/rocdata.rb
+- lib/rocker/rocwindow.rb
+- lib/rocker/sequence.rb
 - lib/rocker/step/build.rb
 - lib/rocker/step/compile.rb
-- lib/rocker/step/search.rb
 - lib/rocker/step/filter.rb
 - lib/rocker/step/plot.rb
-- bin/ROCker
+- lib/rocker/step/search.rb
 homepage: http://enve-omics.ce.gatech.edu/rocker
 licenses:
 - artistic 2.0
@@ -72,17 +72,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '2.0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.14
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: ROCker