bio-rocker 1.4.1 → 1.5.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 4ff6be0bd286c94666f81e5f7177acfcbcc62f0fd4f855e980a52d42b8c15cdc
-  data.tar.gz: 6d22ef33999ab9177020fdef6db4d3ef5fb38c2f1a5a66de3818ce78f8723c2b
+  metadata.gz: 8b4564c29d3e69957f820b74d06c5203d20e3ee5bf204f869ff4cf33ac5d88b6
+  data.tar.gz: 6c2b445e7af8c2375947f15833cf96cc7543870cc9661b737b7b110c3d260da6
 SHA512:
-  metadata.gz: 49a8ac3c4f628d949deeb5c440b188c7f1d47554f4d99a4762a4742386045de4997dd521255a44bbcdd4208f3321fe0afc1a3c233fa968a41532bae7c8c70afc
-  data.tar.gz: 7dc2d0b151c2e5db7ecdc4180be2fb887c1da1a07f8adb8894332f47a4917600de3fe143378f0ffd7f6d23f6af18e8af50e52f78763df5a537cd523b0094571b
+  metadata.gz: 03000a1b229e95178c63ea726048eefaac48f7adacd47ee7d72aef8e09c0dc7899fc40a1c1b850c98c8fad2536616292aa9e65944a6dcfd95ad53db8c0f896ae
+  data.tar.gz: 2751ba9bda4f54adf351ee4998782c2bde98a775ad3726e997f84e78d22ae0ff2ce29dfe705df60ddff9c656636c584fb30ce8485fadc2abab316eea7f3b0785

data/bin/ROCker

@@ -241,7 +241,10 @@ opts = OptionParser.new do |opt|
       opt.on('-M', '--max-length-correction FLOAT',
          'Maximum length correction, as a read length fraction.',
          'By default: 0.4.'){ |v| o[:lencorr_max] = v.to_f }
-      
+      opt.on('-P', '--length-correction-penalty FLOAT',
+         'Penalty for length correction. By default uses the triangle method.',
+         'Recommended value: 0.5.'){ |v| o[:lencorr_pen] = v.to_f }
+
       opt.separator ""
       opt.separator "+ EXTERNAL SOFTWARE OPTIONS"
       opt.on("--search STR",
@@ -266,6 +269,7 @@ opts = OptionParser.new do |opt|
 	    ["By default if --search #{k}:",
                "'" + ROCker.default(:makedbcmd)[k] + "'" ]
 	 end.flatten ){ |v| o[:makedbcmd]=v }
+
    when "filter"
       opt.separator "+ FILTERING ARGUMENTS"
       opt.on("-k", "--rocker PATH",
@@ -282,6 +286,10 @@ opts = OptionParser.new do |opt|
       opt.on('-M', '--max-length-correction FLOAT',
          'Maximum length correction, as a read length fraction.',
          'By default: 0.4.'){ |v| o[:lencorr_max] = v.to_f }
+      opt.on('-P', '--length-correction-penalty FLOAT',
+         'Penalty for length correction. By default uses the triangle method.',
+         'Recommended value: 0.5.'){ |v| o[:lencorr_pen] = v.to_f }
+
    when "plot"
       opt.separator "+ PLOTTING ARGUMENTS"
       opt.on("-k", "--rocker PATH",
@@ -327,6 +335,7 @@ opts = OptionParser.new do |opt|
 	 "Height of the plot in inches. By default: " +
 	 ROCker.default(:height).to_s +
 	 "."){ |v| o[:width]=v.to_f }
+
    else
       opt.banner = "Usage: ROCker.rb [task] [options]"
       opt.separator ""

data/lib/rocker.rb

@@ -9,13 +9,13 @@ require 'rocker/rocdata'
 
 class ROCker
   #================================[ Class ]
-  @@VERSION = '1.4.1'
+  @@VERSION = '1.5.0'
   @@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'
+  @@DATE = '2019-08-01'
   @@DEFAULTS = {
     # General
     q: false, r: 'R', nucl: false, debug: false, thr: 2, search: :blast,

data/lib/rocker/step/filter.rb

@@ -48,7 +48,8 @@ class ROCker
         bh = BlastHit.new(ln, data.aln)
         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])
+          correct_bs(bh, readlengths[bh.qry], exp_readlen,
+            @o[:lencorr_max], @o[:lencorr_pen])
         oh.print ln if not(bh.sfrom.nil?) and
           bs >= data.win_at_col(bh.midpoint).thr
       end
@@ -56,16 +57,20 @@ class ROCker
     oh.close
   end # filter!
 
-  def correct_bs(bh, readlen, exp_readlen, max_corr)
+  def correct_bs(bh, readlen, exp_readlen, max_corr, penalty)
     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)
+    if penalty.nil? or penalty > 1.0
+      miss = [exp_readlen - readlen, max_corr * readlen].min
+      return bs + (bits_per_aa * miss * penalty)
+    else
+      extra = [0.0, readlen * (max_corr + 1.0) - exp_readlen].max
+      max_tri = max_corr * readlen * bits_per_aa / 2
+      tanTheta = max_corr > 0.0 ? bits_per_aa / (max_corr * readlen) : 0.0
+      extra_tri = extra * extra * tanTheta / 2
+      return bs + (max_tri - extra_tri)
+    end
   end
 end # ROCker
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 1.4.1
+  version: 1.5.0
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-20 00:00:00.000000000 Z
+date: 2019-08-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -81,7 +81,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubyforge_project: 
+rubygems_version: 2.7.6
 signing_key: 
 specification_version: 4
 summary: ROCker