bio-rocker 1.3.1 → 1.4.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e1d57ddce91458189a74b7d7f104b2b663396f0df6a2ab7077d4bea45028d982
-  data.tar.gz: 2625bbba04cec1435ae82518cdee6848d6c1fa3775e8030e6bcd6b754db54409
+  metadata.gz: 7cf59c3a66eb06806a91fd768c0ec6202149b7b4b16090bc7be19e96b073fcd3
+  data.tar.gz: 513a5c4de89965d9a852b87ce5b0d7d3da9fb9246471e919fe337dc571cdbe3a
 SHA512:
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-  data.tar.gz: fb260962739d7b8c0e65629786154ff295c1a46b243a7502697cb497bf56f6390147731823a0c390c8e7855e4402c5ce4fdfa3a66ef86d044ed7ba08ed3b3ed0
+  metadata.gz: 95cd32ec66b65516c6253ea5396354b621ac05a945f4a743fefafb9eb9b9b6df67eb0badc93a8dd7329643a7ecadc32a15c3aedd3ef683ef57cfe51a6ddbe304
+  data.tar.gz: 8528c3c5f10b4b5a8a895c51de9368aeafef413edf2931ab9ac5d5f4d92f211f2289636a9b6efbb98573ac305afacf1a127ed27482639f1e3a14496699eb9578

data/bin/ROCker

@@ -238,6 +238,9 @@ opts = OptionParser.new do |opt|
 	 "kept."){ |v| o[:qblast]=v }
       opt.on('-L', '--length-correction',
          'Apply read-length correction to bit scores.'){ |v| o[:lencorr] = v }
+      opt.on('-M', '--max-length-correction FLOAT',
+         'Maximum length correction, as a read length fraction.'
+         ){ |v| o[:lencorr_max] = v.to_f }
       
       opt.separator ""
       opt.separator "+ EXTERNAL SOFTWARE OPTIONS"
@@ -276,6 +279,9 @@ opts = OptionParser.new do |opt|
       opt.on('-L', '--length-correction PATH',
          'Path to the query reads, used to apply read-length correction to ' +
          'bit scores.'){ |v| o[:lencorr] = v }
+      opt.on('-M', '--max-length-correction FLOAT',
+         'Maximum length correction, as a read length fraction.'
+         ){ |v| o[:lencorr_max] = v.to_f }
    when "plot"
       opt.separator "+ PLOTTING ARGUMENTS"
       opt.on("-k", "--rocker PATH",

data/lib/rocker.rb

@@ -4,83 +4,83 @@
 # @license Artistic-2.0
 #
 
-require "rocker/blasthit"
-require "rocker/rocdata"
+require 'rocker/blasthit'
+require 'rocker/rocdata'
 
 class ROCker
-   #================================[ Class ]
-   @@VERSION = "1.3.1"
-   @@CITATION = [
-      "Orellana, Rodriguez-R & Konstantinidis, 2016. DOI:10.1093/nar/gkw900.",
-      "ROCker: accurate detection and quantification of target genes in",
-      "short-read metagenomic data sets by modeling sliding-window bitscores.",
-      "Nucleic Acids Research 45(3):e14."]
-   @@DATE = "2019-06-02"
-   @@DEFAULTS = {
-      # General
-      q: false, r: "R", nucl: false, debug: false, thr: 2, search: :blast,
-      # External software
-      searchbins: "",
-      searchcmd: {
-	 blast: '%1$s%2$s -query "%3$s" -db "%4$s" -out "%5$s" ' +
-	    '-num_threads %6$d -outfmt 6 -max_target_seqs 1',
-	 diamond: '%1$sdiamond %2$s -q "%3$s" -d "%4$s" -a "%5$s.daa" -p %6$d' +
-	    ' -k 1 --min-score 20 --sensitive && %1$sdiamond view -a "%5$s"' +
-	    ' -o "%5$s"'},
-      makedbcmd: {
-	 blast: '%1$smakeblastdb -dbtype %2$s -in "%3$s" -out "%4$s"',
-	 diamond: '%1$sdiamond makedb --in "%3$s" -d "%4$s"'}
-   }
-   def self.defaults() @@DEFAULTS ; end
-   def self.default(k) @@DEFAULTS[k] ; end
-   def self.VERSION; @@VERSION ; end
-   def self.DATE; @@DATE ; end
-   def self.CITATION(j=" ") @@CITATION.join(j) ; end
+  #================================[ Class ]
+  @@VERSION = '1.4.0'
+  @@CITATION = [
+    'Orellana, Rodriguez-R & Konstantinidis, 2016. DOI:10.1093/nar/gkw900.',
+    'ROCker: accurate detection and quantification of target genes in',
+    'short-read metagenomic data sets by modeling sliding-window bitscores.',
+    'Nucleic Acids Research 45(3):e14.']
+  @@DATE = '2019-07-20'
+  @@DEFAULTS = {
+    # General
+    q: false, r: 'R', nucl: false, debug: false, thr: 2, search: :blast,
+    # External software
+    searchbins: '',
+    searchcmd: {
+      blast: '%1$s%2$s -query "%3$s" -db "%4$s" -out "%5$s" ' +
+        '-num_threads %6$d -outfmt 6 -max_target_seqs 1',
+      diamond: '%1$sdiamond %2$s -q "%3$s" -d "%4$s" -a "%5$s.daa" -p %6$d' +
+        ' -k 1 --min-score 20 --sensitive && %1$sdiamond view -a "%5$s"' +
+        ' -o "%5$s"'},
+    makedbcmd: {
+      blast: '%1$smakeblastdb -dbtype %2$s -in "%3$s" -out "%4$s"',
+      diamond: '%1$sdiamond makedb --in "%3$s" -d "%4$s"'}
+  }
+  def self.defaults() @@DEFAULTS ; end
+  def self.default(k) @@DEFAULTS[k] ; end
+  def self.VERSION; @@VERSION ; end
+  def self.DATE; @@DATE ; end
+  def self.CITATION(j = ' ') @@CITATION.join(j) ; end
 
-   #================================[ Instance ]
-   attr_reader :o
-   def initialize(opts)
-      @o = ROCker.defaults
-      opts.each{ |k,v| @o[k] = v }
-      RInterface.R_BIN = opts[:r] unless opts[:r].nil?
-   end
+  #================================[ Instance ]
+  attr_reader :o
+  def initialize(opts)
+    @o = ROCker.defaults
+    opts.each{ |k,v| @o[k] = v }
+    RInterface.R_BIN = opts[:r] unless opts[:r].nil?
+  end
    
-   #================================[ Utilities ]
-   def blast2table(blast_f, table_f, aln, minscore)
-      ifh = File.open(blast_f, "r")
-      ofh = File.open(table_f, "w")
-      while ln = ifh.gets
-	 bh = BlastHit.new(ln, aln)
-	 ofh.print bh.to_s if bh.bits >= minscore
-      end
-      ifh.close
-      ofh.close
-   end
-   def bash(cmd, err_msg=nil)
-      o = `#{cmd} 2>&1 && echo '{'`
-      raise (err_msg.nil? ? "Error executing: #{cmd}\n\n#{o}" : err_msg) unless
-	 o[-2]=="{"
-      true
-   end
+  #================================[ Utilities ]
+  def blast2table(blast_f, table_f, aln, minscore)
+    ifh = File.open(blast_f, 'r')
+    ofh = File.open(table_f, 'w')
+    while ln = ifh.gets
+      bh = BlastHit.new(ln, aln)
+      ofh.print bh.to_s if bh.bits >= minscore
+    end
+    ifh.close
+    ofh.close
+  end
+  def bash(cmd, err_msg=nil)
+    o = `#{cmd} 2>&1 && echo '{'`
+    raise (err_msg.nil? ? "Error executing: #{cmd}\n\n#{o}" : err_msg) unless
+      o[-2]=="{"
+    true
+  end
 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
-   def ordinalize
+  def ordinalize
       n= self.to_s
-      s= n[-2]=='1' ? "th" :
-	 n[-1]=='1' ? "st" :
-	 n[-1]=='2' ? "nd" :
-	 n[-1]=='3' ? "rd" : "th"
+      s= n[-2]=='1' ? 'th' :
+	 n[-1]=='1' ? 'st' :
+	 n[-1]=='2' ? 'nd' :
+	 n[-1]=='3' ? 'rd' : 'th'
       n + s
-   end
+  end
 end
 

data/lib/rocker/step/filter.rb

@@ -20,20 +20,21 @@ class ROCker
       puts "Loading ROCker file: #{@o[:rocker]}." unless @o[:q]
       data = ROCData.new @o[:rocker]
     end
-    corr = {}
-    readlen = 0
+    readlengths = {}
+    exp_readlen = 0
     unless @o[:lencorr].nil?
+      @o[:lencorr_max] ||= 0.4
       raise "Unsigned length in model, please re-compile model to use -L" if
         data.signatures[:l].nil?
-      readlen = data.signatures[:l].to_i
+      exp_readlen = data.signatures[:l].to_i
       File.open(@o[:lencorr], 'r') do |fh|
         k = nil
         fh.each_line do |ln|
           if ln =~ /^>(\S+)/
             k = $1
-            corr[k] = 0
+            readlengths[k] = 0
           else
-            corr[k] += ln.chomp.size
+            readlengths[k] += ln.chomp.size
           end
         end
       end
@@ -45,16 +46,26 @@ class ROCker
     File.open(@o[:qblast], 'r') do |ih|
       ih.each_line do |ln|
         bh = BlastHit.new(ln, data.aln)
-        bs = bh.bits
-        unless @o[:lencorr].nil?
-          corrlen = [corr[bh.qry].to_i, 0.6 * readlen].max
-          bs = bs * readlen / corrlen if corrlen < readlen
-        end
-        oh.print ln if
-          not(bh.sfrom.nil?) and bs >= data.win_at_col(bh.midpoint).thr
+        next if bh.sbj.nil? # <- When the hit is not against a known target
+        bs = @o[:lencorr].nil? ? bh.bits :
+          correct_bs(bh, readlengths[bh.qry], exp_readlen, @o[:lencorr_max])
+        oh.print ln if not(bh.sfrom.nil?) and
+          bs >= data.win_at_col(bh.midpoint).thr
       end
     end
     oh.close
   end # filter!
+
+  def correct_bs(bh, readlen, exp_readlen, max_corr)
+    bs = bh.bits
+    return bs if @o[:lencorr].nil? or readlen.nil? or readlen >= exp_readlen
+    bits_per_aa = bs.to_f / readlen
+    miss = exp_readlen - readlen
+    max_tri = max_corr * readlen * bits_per_aa / 2
+    extra = [0.0, readlen * (max_corr + 1.0) - exp_readlen].max
+    tanTheta = max_corr > 0.0 ? bits_per_aa / (max_corr * readlen) : 0.0
+    extra_tri = extra * extra * tanTheta / 2
+    bs + (max_tri - extra_tri)
+  end
 end # ROCker
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 1.3.1
+  version: 1.4.0
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-06-02 00:00:00.000000000 Z
+date: 2019-07-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client