bio-rocker 1.1.9 → 1.1.10

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: d3780e512d02ef04c60696a01f8c736b61703707
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data/bin/ROCker

@@ -3,13 +3,13 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Sep-07-2015
+# @update Nov-25-2015
 #
 
-lib = File.expand_path(File.dirname(__FILE__) + '/../lib')
+lib = File.expand_path("../lib", File.dirname(__FILE__))
 $:.push lib if Dir.exist? lib
-require 'rocker'
-require 'optparse'
+require "rocker"
+require "optparse"
 
 
 #================================[ Options parsing ]
@@ -355,13 +355,14 @@ begin
       puts "ROCker v" + ROCker.VERSION
       puts ""
       puts "If you use ROCker in your research, please cite:"
-      puts ROCker.CITATION
+      puts ROCker.CITATION("\n")
       puts ""
       puts "ROCker can be freely used and distributed under the "
       puts "terms of the Artistic License 2.0. See LICENSE.txt."
       puts ""
       puts "For additional information and documentation, visit:"
       puts "http://enve-omics.ce.gatech.edu/rocker/"
+      puts ""
       puts "For our list of curated models, visits:"
       puts "http://enve-omics.ce.gatech.edu/rocker/models"
    end

data/lib/rocker.rb

@@ -1,20 +1,22 @@
 #
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @author Luis (Coto) Orellana
+# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
+# @author  Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Sep-07-2015
+# @update  Dec-01-2015
 #
 
-require 'rocker/blasthit'
-require 'rocker/rocdata'
+require "rocker/blasthit"
+require "rocker/rocdata"
 
 class ROCker
    #================================[ Class ]
-   @@VERSION = "1.1.9"
-   @@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."
+   @@VERSION = "1.1.10"
+   @@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"
    @@DEFAULTS = {
       # General
       q: false, r: "R", nucl: false, debug: false, thr: 2, search: :blast,
@@ -33,7 +35,8 @@ class ROCker
    def self.defaults() @@DEFAULTS ; end
    def self.default(k) @@DEFAULTS[k] ; end
    def self.VERSION; @@VERSION ; end
-   def self.CITATION; @@CITATION ; end
+   def self.DATE; @@DATE ; end
+   def self.CITATION(j=" ") @@CITATION.join(j) ; end
 
    #================================[ Instance ]
    attr_reader :o
@@ -64,11 +67,11 @@ end
 
 #================================[ Extensions ]
 # To ROCker
-require 'rocker/step/build'
-require 'rocker/step/compile'
-require 'rocker/step/search'
-require 'rocker/step/filter'
-require 'rocker/step/plot'
+require "rocker/step/build"
+require "rocker/step/compile"
+require "rocker/step/search"
+require "rocker/step/filter"
+require "rocker/step/plot"
 
 # To other
 class Numeric

data/lib/rocker/genome-set.rb

@@ -2,7 +2,7 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Jun-23-2015
+# @update Dec-01-2015
 #
 
 class GenomeSet
@@ -46,10 +46,10 @@ class GenomeSet
    def empty?() self.ids.empty? end
 
    #================================[ Utilities ]
-   def genome2taxon(genome_id, rank='species')
+   def genome2taxon(genome_id, rank="species")
       v = genome2taxid(genome_id)
       unless v.nil?
-	 xml = rocker.ebiFetch('taxonomy', [v], 'enataxonomyxml').gsub(/\s*\n\s*/,'')
+	 xml = rocker.ebiFetch(:taxonomy, [v], :enataxonomyxml).gsub(/\s*\n\s*/,"")
 	 v = xml.scan(/<taxon [^>]+>/).grep(/rank="#{rank}"/).first
 	 v.sub!(/.* taxId="(\d+)".*/,"\\1") unless v.nil?
       end
@@ -57,7 +57,7 @@ class GenomeSet
       v
    end
    def genome2taxid(genome_id)
-      doc = rocker.ebiFetch('embl', [genome_id], 'annot').split(/[\n\r]/)
+      doc = rocker.ebiFetch(:embl, [genome_id], :annot).split(/[\n\r]/)
       ln = doc.grep(/^FT\s+\/db_xref="taxon:/).first
       ln = doc.grep(/^OX\s+NCBI_TaxID=/).first if ln.nil?
       return nil if ln.nil?

data/lib/rocker/protein-set.rb

@@ -2,10 +2,10 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Jul-20-2015
+# @update Dec-01-2015
 #
 
-require 'rocker/alignment'
+require "rocker/alignment"
 
 class ProteinSet
    attr_reader :rocker, :ids, :aln
@@ -43,7 +43,7 @@ class ProteinSet
       self.ids.each do |id|
 	 doc = self.rocker.ebiFetch(:uniprotkb, [id], :annot).split("\n")
 	 doc.grep( /^DR\s+EMBL;/ ).map do |ln|
-	    r=ln.split('; ')
+	    r=ln.split("; ")
 	    self.link_genome(id, r[1])
 	    self.link_tranid(id, r[2])
 	 end
@@ -67,16 +67,20 @@ class ProteinSet
       return [] if @tranids.empty?
       @tranids.values.reduce(:+).uniq
    end
+   def tranids_dump
+      @tranids.map{|k,v| "{#{k}: #{v}}"}.join(", ")
+   end
    def in_coords(coords)
       coords.keys.map do |genome|
 	 locations = coords[ genome ]
 	 locations.map do |loc|
-	    if not loc[:prot_id].nil?
-	       loc[:prot_id] if self.include? loc[:prot_id]
-	    elsif not loc[:tran_id].nil? and not @tranids.rassoc(loc[:tran_id]).nil?
-	       @tranids.rassoc(loc[:tran_id]).first
+	    if not loc[:prot_id].nil? 
+	       loc[:prot_id] if include? loc[:prot_id]
+	    elsif not loc[:tran_id].nil?
+	       @tranids.map{ |k,v| v.include?(loc[:tran_id]) ? k : nil }.compact.first
 	    else
-	       warn "Warning: Impossible to resolve protein located in '#{genome}' at: #{loc}."
+	       warn "Warning: Impossible to resolve protein located " +
+		  "in '#{genome}' at: #{loc}."
 	       nil
 	    end
 	 end

data/lib/rocker/step/build.rb

@@ -2,12 +2,12 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Sep-11-2015
+# @update Dec-01-2015
 #
 
-require 'json'
-require 'rocker/protein-set'
-require 'rocker/genome-set'
+require "json"
+require "rocker/protein-set"
+require "rocker/genome-set"
 
 class ROCker
    #================================[ Class ]
@@ -30,8 +30,8 @@ class ROCker
       return @@HAS_BUILD_GEMS unless @@HAS_BUILD_GEMS.nil?
       @@HAS_BUILD_GEMS = TRUE
       begin
-	 require 'rubygems'
-	 require 'restclient'
+	 require "rubygems"
+	 require "restclient"
       rescue LoadError
 	 @@HAS_BUILD_GEMS = FALSE
       end
@@ -41,8 +41,8 @@ class ROCker
    #================================[ Utilities ]
    def restcall(url, outfile=nil)
       $stderr.puts "   # Calling: #{url}" if @o[:debug]
-      response = RestClient::Request.execute(:method=>:get, :url=>url,
-	 :timeout=>600)
+      response = RestClient::Request.execute(method: :get, url: url,
+	 timeout: 600)
       raise "Unable to reach EBI REST client, error code " +
 	 response.code.to_s + "." unless response.code == 200
       unless outfile.nil?
@@ -73,6 +73,10 @@ class ROCker
 	    genome_file=nil unless @o[:noclean]
 	    doc = ebiFetch(:embl, [genome_id], :gff3,
 	       genome_file).split("\n").grep(/^[^#]/)
+	    if doc.first =~ /ERROR 12 No entries found/
+	       doc = ebiFetch(:emblconexp, [genome_id], :gff3,
+		  genome_file).split("\n").grep(/^[^#]/)
+	    end
 	 end
 	 doc.each do |ln|
 	    next if ln =~ /^#/
@@ -80,7 +84,7 @@ class ROCker
 	    next if r.size < 9
 	    prots = r[8].split(/;/).grep(
 	       /^db_xref=UniProtKB[\/A-Za-z-]*:/){ |xref| xref.split(/:/)[1] }
-	    p = prots.select{ |id| pset.ids.include? id }.first
+	    p = prots.compact.select{ |id| pset.ids.include? id }.first
 	    trans = r[8].split(/;/).grep(
 	       /^protein_id=/){ |pid| pid.split(/=/)[1] }
 	    t = trans.select{ |id| pset.tranids.include? id }.first
@@ -191,7 +195,7 @@ class ROCker
 	    puts "  * downloading and parsing #{genome_set[set_type].size} " +
 	       "GFF3 document(s) in #{thrs} threads." unless @o[:q]
 	    $stderr.puts "   # Looking for translations: " +
-	       "#{protein_set[set_type].tranids}" if @o[:debug]
+	       "#{protein_set[set_type].tranids_dump}" if @o[:debug]
 	    $stderr.puts "   # Looking into: #{genome_set[set_type].ids}" if
 	       @o[:debug]
 	    # Launch threads

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 1.1.9
+  version: 1.1.10
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -9,36 +9,36 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-02 00:00:00.000000000 Z
+date: 2015-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.7.3
+        version: '1.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.7.3
+        version: '1.7'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.1
+        version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.8.1
+        version: '1.8'
 description: Detecting and quantifying functional genes in short-read metagenomic
   datasets
 email: lhorellana@gatech.edu