bio-rocker 1.2.0 → 1.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: d4f32b4736d380d7e8b0ff7b6ef46b221b9a0651
-  data.tar.gz: cfbff18723f9b2d95d45350aba30a9b75cb32d5d
+SHA256:
+  metadata.gz: 0ecb36031d65a56ae6a7e4144d7102f171d30bebcadfdf5a132622b3a743b901
+  data.tar.gz: 5f8251402d40ddbba6097014e1f93a1bce0245e4cc2b3fac4a3d849c5a009c18
 SHA512:
-  metadata.gz: 1a6d9fd0c94338415f334e50c928174ee595690c3c093b1478251d169b11265843eafccdec645d9997acd2ccff0cabcb7db67e77960e43a10d5bbc90298592ff
-  data.tar.gz: bd711c0f3a87f221b60014633130b73a581b5b5f6dd60eee5a948d5740f87bee68714f0b71b9b27412cf36ade84aac314ab20b267ae134e32a5d998e3855c056
+  metadata.gz: 5eac28f2473d7b8357d127741c54aab97403872fe9ef3a2185268b049bb4eb32cc3ea0216f56d6d955de66ea7172962a81a76b90a3b229fbad631365c3eb0a40
+  data.tar.gz: 8c23e1ad05edc88aa364b4f54ca594897cf971a98b3f98332a165d0a268b65985bba84eb020e509b3a5ae414099bcd79878d025ee2cb164f6c25d8e225ace685

data/bin/ROCker

@@ -139,14 +139,14 @@ opts = OptionParser.new do |opt|
 	 *ROCker.default(:searchcmd).keys.map do |k|
 	    ["By default if --search #{k}:", "'" +
 	       ROCker.default(:searchcmd)[k] + "'"]
-	 end.reduce([],:+) ){ |v| o[:searchcmd]=v }
+	 end.flatten ){ |v| o[:searchcmd]=v }
       opt.on("--makedb-cmd STR",
 	 "Command calling database formater for similarity search, where",
 	 "%1$s: binaries, %2$s: dbtype, %3$s: input, %4$s: database.",
 	 *ROCker.default(:makedbcmd).keys.map do |k|
 	    ["By default if --search #{k}:", "'" +
 	       ROCker.default(:makedbcmd)[k] + "'"]
-	 end.reduce([],:+) ){ |v| o[:makedbcmd]=v }
+	 end.flatten ){ |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$s: output file, " +
@@ -154,7 +154,7 @@ opts = OptionParser.new do |opt|
 	 *ROCker.default(:simulatorcmd).keys.map do |k|
 	    ["By default if --simulator #{k}:", "'" +
 	       ROCker.default(:simulatorcmd)[k] + "'"]
-	 end.reduce([],:+) ){ |v| o[:simulatorcmd]=v }
+	 end.flatten ){ |v| o[:simulatorcmd]=v }
       opt.on("--aligner-cmd STR",
 	 "Command calling aligner, where %1$s: binary, %2$s: input,",
 	 "%3$s: output, %4$d: threads.",
@@ -164,6 +164,9 @@ opts = OptionParser.new do |opt|
 	 end.reduce([],:+) ){ |v| o[:alignercmd]=v }
    when "compile"
       opt.separator "+ COMPILATION ARGUMENTS"
+      opt.on("-l", "--readlen INTEGER",
+	 "Average read length used in the compile step (Mandatory)."
+	 ){ |v| o[:readlen] = v.to_i }
       opt.on("-a", "--alignment PATH",
 	 "Protein alignment of the reference sequences. Required."
 	 ){ |v| o[:aln]=v }
@@ -233,6 +236,9 @@ opts = OptionParser.new do |opt|
       opt.on("-x", "--query-blast PATH",
 	 "Unfiltered tabular BLAST. By default, this file is not " +
 	 "kept."){ |v| o[:qblast]=v }
+      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.separator ""
       opt.separator "+ EXTERNAL SOFTWARE OPTIONS"
@@ -248,16 +254,16 @@ opts = OptionParser.new do |opt|
 	 "Command calling similarity search, where %1$s: binaries, %2$s: " +
 	 "program, %3$s: input, %4$s: database, %5$s: output, %6$d: threads.",
 	 *ROCker.default(:searchcmd).keys.map do |k|
-	    "By default if --search #{k}: '" + ROCker.default(:searchcmd)[k] +
-	       "'."
-	 end ){ |v| o[:searchcmd]=v }
+	    ["By default if --search #{k}:",
+               "'" + ROCker.default(:searchcmd)[k] + "'"]
+	 end.flatten ){ |v| o[:searchcmd]=v }
       opt.on("--makedb-cmd STR",
 	 "Command calling database format for similarity search, where %1$s: " +
 	 "binaries, %2$s: dbtype, %3$s: input, %4$s: database.",
 	 *ROCker.default(:makedbcmd).keys.map do |k|
-	    "By default if --search #{k}: '" + ROCker.default(:makedbcmd)[k] +
-	       "'."
-	 end ){ |v| o[:makedbcmd]=v }
+	    ["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",
@@ -268,6 +274,9 @@ opts = OptionParser.new do |opt|
 	 "dataset. Required."){ |v| o[:qblast]=v }
       opt.on("-o", "--out-blast PATH",
 	 "Filtered tabular BLAST to be created. Required."){ |v| o[:oblast]=v }
+      opt.on('-L', '--length-correction PATH',
+         'Path to the query reads, used to apply read-length correction to ' +
+         'bit scores.'){ |v| o[:lencorr] = v }
    when "plot"
       opt.separator "+ PLOTTING ARGUMENTS"
       opt.on("-k", "--rocker PATH",

data/lib/rocker.rb

@@ -9,13 +9,13 @@ require "rocker/rocdata"
 
 class ROCker
    #================================[ Class ]
-   @@VERSION = "1.2.0"
+   @@VERSION = "1.3.0"
    @@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 = "2018-06-28"
+   @@DATE = "2019-06-02"
    @@DEFAULTS = {
       # General
       q: false, r: "R", nucl: false, debug: false, thr: 2, search: :blast,

data/lib/rocker/blasthit.rb

@@ -6,7 +6,7 @@
 #
 
 class BlastHit
-   attr_reader :sbj, :sfrom, :sto, :bits, :istrue, :isfalse, :midpoint
+   attr_reader :qry, :sbj, :sfrom, :sto, :bits, :istrue, :isfalse, :midpoint
    # Initialize from BLAST using new(ln,aln),
    # initialize from TABLE using new(ln)
    def initialize(ln, aln=nil)
@@ -20,6 +20,7 @@ class BlastHit
 	 @istrue = l[4]=='-1'
 	 @midpoint = l[5].to_i
       else
+         @qry   = l[0]
 	 s = aln.seq(l[1])
 	 return nil if s.nil?
 	 @sbj	= s.id

data/lib/rocker/rocdata.rb

@@ -11,24 +11,30 @@ require 'rocker/alignment'
 require 'tmpdir'
 
 class ROCData
-   attr_reader :aln, :windows, :r, :refined
+   attr_reader :aln, :windows, :r, :refined, :signatures
    # Use ROCData.new(table,aln,window) to re-compute from table, use
    # ROCData.new(data) to load
-   def initialize(val, aln=nil, window=nil)
+   def initialize(val, aln = nil, window = nil)
       @r = RInterface.new
       @nucl = false
       @refined = false
       if not aln.nil?
 	 @aln = aln
+         @signatures = { v: "ROCker #{ROCker.VERSION}", d: Time.now.to_s }
 	 self.rrun "library('pROC');"
 	 self.rrun "x <- read.table('#{val}', sep='\\t', h=F);"
 	 self.init_windows! window
       else
 	 f = File.open(val, "r")
 	 @windows = []
+         @signatures = {}
 	 while ln = f.gets
-	    break unless /^#:/.match(ln).nil?
-	    @windows << ROCWindow.new(self, ln)
+            break unless /^#:/.match(ln).nil?
+            if ln =~ /^#(\S+) (.*)/
+               @signatures[$1.to_sym] = $2
+            else
+               @windows << ROCWindow.new(self, ln)
+            end
 	 end
 	 f.close
 	 @aln = Alignment.new
@@ -126,16 +132,15 @@ class ROCData
       end
    end
    def rrun(cmd, type=nil) self.r.run cmd, type end
-   def save(file)
-      f = File.open(file, "w")
-      f.print self.to_s
-      f.close
+   def save(file, sign = {})
+     @signatures.merge! sign
+     File.open(file, 'w') { |fh| fh.print self.to_s }
    end
    def to_s
-      o = "#v ROCker " + ROCker.VERSION + "\n"
-      self.windows.each{|w| o += w.to_s}
-      o += self.aln.to_s
-      return o
+     o = signatures.map{ |k,v| "##{k} #{v}\n" }.join
+     self.windows.each{ |w| o += w.to_s }
+     o += self.aln.to_s
+     return o
    end
 end
 

data/lib/rocker/step/compile.rb

@@ -13,6 +13,7 @@ class ROCker
    def compile!
       raise "-a/--alignment is mandatory." if @o[:aln].nil?
       raise "-a/--alignment must exist." unless File.exist? @o[:aln]
+      raise "-l/--readlen is mandatory." if @o[:readlen].nil?
       if @o[:table].nil?
 	 raise "-T/--table is mandatory unless -b is provided." if
 	    @o[:blast].nil? or not File.exist? @o[:blast]
@@ -52,7 +53,7 @@ class ROCker
 	    data.refine! @o[:table]
       end
       puts "  * saving ROCker file: #{@o[:rocker]}." unless @o[:q]
-      data.save @o[:rocker]
+      data.save(@o[:rocker], l: @o[:readlen])
    end # compile!
 end # ROCker
 

data/lib/rocker/step/filter.rb

@@ -6,31 +6,55 @@
 #
 
 class ROCker
-   #================================[ Class ]
-   #@@DEFAULTS.merge!({  })
-   
-   #================================[ Filter ]
-   def filter!(data=nil)
-      raise "-k/--rocker is mandatory." if @o[:rocker].nil?
-      raise "-x/--query-blast is mandatory." if @o[:qblast].nil?
-      raise "-o/--out-blast is mandatory." if @o[:oblast].nil?
-      
-      # Read ROCker file
-      if data.nil?
-	 puts "Loading ROCker file: #{@o[:rocker]}." unless @o[:q]
-	 data = ROCData.new @o[:rocker]
+  #================================[ Class ]
+  #@@DEFAULTS.merge!({  })
+
+  #================================[ Filter ]
+  def filter!(data=nil)
+    raise "-k/--rocker is mandatory." if @o[:rocker].nil?
+    raise "-x/--query-blast is mandatory." if @o[:qblast].nil?
+    raise "-o/--out-blast is mandatory." if @o[:oblast].nil?
+    
+    # Read ROCker file
+    if data.nil?
+      puts "Loading ROCker file: #{@o[:rocker]}." unless @o[:q]
+      data = ROCData.new @o[:rocker]
+    end
+    corr = {}
+    readlen = 0
+    unless @o[:lencorr].nil?
+      raise "Unsigned length in model, please re-compile model to use -L" if
+        data.signatures[:l].nil?
+      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
+          else
+            corr[k] += ln.chomp.size
+          end
+        end
       end
+    end
 
-      # Filter similarity search
-      puts "Filtering similarity search: #{@o[:qblast]}." unless @o[:q]
-      ih = File.open(@o[:qblast], "r")
-      oh = File.open(@o[:oblast], "w")
-      while ln = ih.gets
-	 bh = BlastHit.new(ln, data.aln)
-	 oh.print ln if not(bh.sfrom.nil?) and bh.bits >= data.win_at_col(bh.midpoint).thr
+    # Filter similarity search
+    puts "Filtering similarity search: #{@o[:qblast]}." unless @o[:q]
+    oh = File.open(@o[:oblast], 'w')
+    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
       end
-      ih.close
-      oh.close
-   end # filter!
+    end
+    oh.close
+  end # filter!
 end # ROCker
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 1.2.0
+  version: 1.3.0
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-06-28 00:00:00.000000000 Z
+date: 2019-06-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -81,8 +81,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.13
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: ROCker