miga-base 1.2.15.2 → 1.2.15.4

data/utils/enveomics/Scripts/ogs.annotate.rb

@@ -1,88 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R
-# @update: Mar-23-2015
-# @license: artistic license 2.0
-#
-
-$:.push File.expand_path(File.dirname(__FILE__) + '/lib')
-require 'enveomics_rb/og'
-require 'optparse'
-
-o = {:q=>FALSE, :f=>"(\\S+)\\.txt", :consolidate=>TRUE, :pre=>[]}
-ARGV << '-h' if ARGV.size==0
-OptionParser.new do |opts|
-   opts.banner = "
-Annotates Orthology Groups (OGs) using one or more reference genomes.
-
-Usage: #{$0} [options]"
-   opts.separator ""
-   opts.separator "Mandatory"
-   opts.on("-i", "--in FILE", "Input file containing the OGs (as generated by ogs.rb)."){ |v| o[:in]=v }
-   opts.on("-o", "--out FILE", "Output file containing the annotated OGs."){ |v| o[:out]=v }
-   opts.on("-a FILE1,FILE2,...", Array, "Input file(s) containing the annotations.One or more tab-delimited files",
-   		"with the gene names in the first column and the annotation in the second."){ |v| o[:annotations]=v }
-   opts.separator ""
-   opts.separator "Other Options"
-   opts.on("-f","--format STRING", "Format of the filenames for the annotation files, using regex syntax.",
-   		"By default: '#{o[:f]}'."){ |v| o[:f]=v }
-   opts.on("-q", "--quiet", "Run quietly (no STDERR output)."){ o[:q] = TRUE }
-   opts.on("-h", "--help", "Display this screen.") do
-      puts opts
-      exit
-   end
-   opts.separator ""
-end.parse!
-abort "-i is mandatory" if o[:in].nil?
-abort "-o is mandatory" if o[:out].nil?
-abort "-a is mandatory" if o[:annotations].nil?
-
-##### MAIN:
-begin
-   # Read the pre-computed OGs
-   collection = OGCollection.new
-   $stderr.puts "Reading pre-computed OGs in '#{o[:in]}'." unless o[:q]
-   f = File.open(o[:in], 'r')
-   h = f.gets.chomp.split /\t/
-   while ln = f.gets
-      collection << OG.new(h, ln.chomp.split(/\t/))
-   end
-   f.close
-   $stderr.puts " Loaded OGs: #{collection.ogs.length}." unless o[:q]
-
-   # Read annotations
-   o[:annotations].each do |annot|
-      m = /#{o[:f]}/.match(annot)
-      if m.nil? or m[1].nil?
-	 warn "Cannot parse filename: #{rbm_file} (doesn't match /#{o[:f]}/)."
-	 next
-      end
-      f = File.open(annot, 'r')
-      no_og = 0
-      collection.add_note_src m[1]+' annotation'
-      while ln=f.gets
-	 r = ln.chomp.split /\t/
-	 g = Gene.new m[1], r[0]
-	 og = collection.get_og g
-	 if og.nil?
-	    no_og += 1
-	 else
-	    og.add_note g.id + ': ' + r[1], collection.note_srcs.length-1
-	 end
-      end
-      warn "Warning: Cannot find #{no_og} genes from #{m[1]} in OG collection." if no_og>0
-   end 
-   # Save the output matrix
-   $stderr.puts "Saving annotated OGs into '#{o[:out]}'." unless o[:q]
-   f = File.open(o[:out], "w")
-   f.puts collection.to_s
-   f.close
-   $stderr.puts "Done.\n" unless o[:q] 
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts l + "\n" }
-   err
-end
-
-

data/utils/enveomics/Scripts/ogs.core-pan.rb

@@ -1,160 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R
-# @license: artistic-2.0
-#
-
-$:.push File.expand_path("../lib", __FILE__)
-require "optparse"
-require "json"
-require "tmpdir"
-
-o = {q:false, n:100, thr:2}
-ARGV << "-h" if ARGV.size==0
-OptionParser.new do |opts|
-  opts.banner = "
-Subsamples the genomes in a set of Orthology Groups (OGs) and estimates the
-trend of core genome and pangenome sizes.
-
-Usage: #{$0} [options]"
-  opts.separator ""
-  opts.separator "Mandatory"
-  opts.on("-o", "--ogs FILE",
-    "Input file containing the precomputed OGs."){ |v| o[:ogs]=v }
-  opts.separator ""
-  opts.separator "Output Options"
-  opts.on("-s", "--summary FILE",
-    "Output file in tabular format with summary statistics."){ |v| o[:summ]=v }
-  opts.on("-t", "--tab FILE","Output file in tabular format."){ |v| o[:tab]=v }
-  opts.on("-j", "--json FILE", "Output file in JSON format."){ |v| o[:json]=v }
-  opts.separator ""
-  opts.separator "Other Options"
-  opts.on("-n", "--replicates INT",
-    "Number of replicates to estimate. By default: #{o[:n]}."
-    ){ |v| o[:n]=v.to_i }
-  opts.on("--threads INT",
-    "Children threads to spawn. By default: #{o[:thr]}."){ |v| o[:thr]=v.to_i}
-  opts.on("-q", "--quiet", "Run quietly (no STDERR output)."){ o[:q] = true }
-  opts.on("-h", "--help", "Display this screen.") do
-    puts opts
-    exit
-  end
-  opts.separator ""
-end.parse!
-abort "-o is mandatory" if o[:ogs].nil?
-
-##### MAIN:
-begin
-  # Read the pre-computed OGs
-  $stderr.puts "Reading pre-computed OGs in '#{o[:ogs]}'." unless o[:q]
-  bool_a = []
-  genomes_n = nil
-  File.open(o[:ogs], "r") do |f|
-    h = f.gets.chomp.split "\t"
-    genomes_n = h.size
-    while ln = f.gets
-      bool_a << ln.chomp.split("\t").map{ |g| g!="-" }
-    end
-  end
-  $stderr.puts " Loaded OGs: #{bool_a.size}." unless o[:q]
-  bool_a_b = bool_a.map{ |og| og.map{ |g| g ? "1" : "0" }.join("").to_i(2) }
-
-  # Generate subsamples
-  size = {core:[], pan:[]}
-  Dir.mktmpdir do |dir|
-    children = 0
-    (0 .. o[:n]-1).each do |i|
-      fork do
-        # Generate trajectory
-        genomes = (0 .. genomes_n-1).to_a.shuffle
-        genomes_b = (2 ** genomes_n) - 1
-        core = []
-        pan = []
-        while not genomes.empty?
-          core.unshift 0
-          pan.unshift 0
-          bool_a_b.map! do |og|
-            r_og = og & genomes_b
-            if r_og>0
-              core[0] += 1 if r_og==genomes_b
-              pan[0]  += 1
-              og
-            else
-              nil
-            end
-          end
-          bool_a_b.compact!
-          genomes_b ^= 2 ** genomes.pop
-        end
-        abort "UNEXPECTED ERROR: Final genomes_b=#{genomes_b}." if genomes_b>0
-        # Store trajectory
-        File.open("#{dir}/#{i}", "w") do |tfh|
-          tfh.puts JSON.generate({core:core, pan:pan})
-        end
-      end # fork
-      children += 1
-      if children >= o[:thr]
-        Process.wait
-        children -= 1
-      end
-    end
-    Process.waitall
-    # Recover trajectories
-    (0 .. o[:n]-1).each do |i|
-      s = JSON.parse(File.read("#{dir}/#{i}"), {:symbolize_names=>true})
-      size[:core][i] = s[:core]
-      size[:pan][i] = s[:pan]
-    end
-  end # Dir.mktmpdir
-
-  # Show result
-  $stderr.puts "Generating reports." unless o[:q]
-
-  # Save results in JSON
-  unless o[:json].nil?
-    ofh = File.open(o[:json], "w")
-    ofh.puts JSON.pretty_generate(size)
-    ofh.close
-  end
-
-  # Save results in tab
-  unless o[:tab].nil?
-    ofh = File.open(o[:tab], "w")
-    ofh.puts (%w{replicate metric}+(1 .. genomes_n).to_a).join("\t")
-    (0 .. o[:n]-1).each do |i|
-      ofh.puts ([i+1,"core"] + size[:core][i]).join("\t")
-      ofh.puts ([i+1,"pan"] + size[:pan][i]).join("\t")
-    end
-    ofh.close
-  end
-
-  # Save summary results in tab
-  unless o[:summ].nil?
-    ofh = File.open(o[:summ], "w")
-    ofh.puts %w{genomes core_avg core_sd core_q1 core_q2 core_q3
-      pan_avg pan_sd pan_q1 pan_q2 pan_q3}.join("\t")
-    (0 .. genomes_n-1).each do |i|
-      res = [ i+1 ]
-      [:core, :pan].each do |met|
-        a = size[met].map{ |r| r[i] }.sort
-        avg = a.inject(0,:+).to_f / a.size
-        var = a.map{ |v| v**2 }.inject(0,:+).to_f/a.size - avg**2
-        sd = Math.sqrt(var)
-        q1 = a[ a.size*1/4 ]
-        q2 = a[ a.size*2/4 ]
-        q3 = a[ a.size*3/4 ]
-        res += [avg,sd,q1,q2,q3]
-      end
-      ofh.puts res.join("\t")
-    end
-    ofh.close
-  end
-
-  $stderr.puts "Done.\n" unless o[:q] 
-rescue => err
-  $stderr.puts "Exception: #{err}\n\n"
-  err.backtrace.each { |l| $stderr.puts l + "\n" }
-  err
-end
-

data/utils/enveomics/Scripts/ogs.extract.rb

@@ -1,125 +0,0 @@
-#!/usr/bin/env ruby
-#
-# @author Luis M. Rodriguez-R
-# @license artistic license 2.0
-#
-
-$:.push File.expand_path("lib", File.dirname(__FILE__))
-require "enveomics_rb/enveomics"
-require "enveomics_rb/og"
-
-o = {q:false, pergenome:false, prefix:false, first:false, rand:false,
-   core:0.0, dups:0}
-OptionParser.new do |opts|
-   opts.banner = "
-Extracts sequences of Orthology Groups (OGs) from genomes (proteomes).
-
-Usage: #{$0} [options]"
-   opts.separator ""
-   opts.separator "Mandatory"
-   opts.on("-i", "--in FILE",
-      "Input file containing the OGs (as generated by ogs.rb)."){ |v| o[:in]=v }
-   opts.on("-o", "--out FILE",
-      "Output directory where to place extracted sequences."){ |v| o[:out]=v }
-   opts.on("-s", "--seqs STRING",
-      "Path to the proteomes in FastA format, using '%s' to denote the genome.",
-      "For example: /path/to/seqs/%s.faa."){ |v| o[:seqs]=v }
-   opts.separator ""
-   opts.separator "Other Options"
-   opts.on("-c", "--core FLOAT",
-      "Use only OGs present in at least this fraction of the genomes.",
-      "To use only the strict core genome*, use -c 1."){ |v| o[:core]=v.to_f }
-   opts.on("-d", "--duplicates INT",
-      "Use only OGs with less than this number of in-paralogs in a genome.",
-      "To use only genes without in-paralogs*, use -d 1."
-      ){ |v| o[:dups]=v.to_i }
-   opts.on("-g", "--per-genome",
-      "If set, the output is generated per genome.",
-      "By default, the output is per OG."){ |v| o[:pergenome]=v }
-   opts.on("-p", "--prefix",
-      "If set, each sequence is prefixed with the genome name",
-      "(or OG number, if --per-genome) and a dash."){ |v| o[:prefix]=v }
-   opts.on("-r", "--rand",
-      "Get only one gene per genome per OG (random) regardless of in-paralogs.",
-      "By default all genes are extracted."){ |v| o[:rand]=v }
-   opts.on("-f", "--first",
-      "Get only one gene per genome per OG (first) regardless of in-paralogs.",
-      "By default all genes are extracted. Takes precendece over --rand."
-      ){ |v| o[:first]=v }
-   opts.on("-q", "--quiet", "Run quietly (no STDERR output)."){ o[:q] = TRUE }
-   opts.on("-h", "--help", "Display this screen.") do
-      puts opts
-      exit
-   end
-   opts.separator ""
-   opts.separator "    * To use only the unus genome (OGs with exactly one " +
-      "gene per genome), use: -c 1 -d 1."
-   opts.separator ""
-end.parse!
-abort "-i is mandatory" if o[:in].nil?
-abort "-o is mandatory" if o[:out].nil?
-abort "-s is mandatory" if o[:seqs].nil?
-
-##### MAIN:
-begin
-   # Read the pre-computed OGs
-   collection = OGCollection.new
-   $stderr.puts "Reading pre-computed OGs in '#{o[:in]}'." unless o[:q]
-   f = File.open(o[:in], "r")
-   h = f.gets.chomp.split /\t/
-   while ln = f.gets
-      collection << OG.new(h, ln.chomp.split(/\t/))
-   end
-   f.close
-   $stderr.puts " Loaded OGs: #{collection.ogs.size}." unless o[:q]
-   $stderr.puts " Reported Genomes: #{Gene.genomes.size}." unless o[:q]
-
-   # Filter core/in-paralog genes
-   collection.filter_core! o[:core] unless o[:core]==0.0
-   collection.remove_inparalogs! o[:dups] unless o[:dups]==0
-   $stderr.puts " Filtered OGs: #{collection.ogs.size}." unless
-      o[:q] or o[:core]==0.0
-
-   # Open outputs
-   $stderr.puts "Initializing output files." unless o[:q]
-   Dir.mkdir(o[:out]) unless Dir.exist? o[:out]
-   ofhs = o[:pergenome] ?
-      Gene.genomes.map{|g| File.open("#{o[:out]}/#{g}.fa", "w")} :
-      ( (1 .. collection.ogs.size).map do |og|
-	 File.open("#{o[:out]}/OG#{og}.fa", "w")
-      end )
-   $stderr.puts " Created files: #{ofhs.size}." unless o[:q]
-   
-   # Read genomes
-   $stderr.puts "Filtering genes." unless o[:q]
-   genome_i = -1
-   Gene.genomes.each do |genome|
-      genome_i = Gene.genomes.index(genome)
-      $stderr.print "  Genome #{genome_i+1}.   \r" unless o[:q]
-      genes = ( collection.get_genome_genes(genome).map do |og|
-	    o[:first] ? [og.first] : (o[:rand] ? [og.sample] : og)
-	 end )
-      hand = nil
-      File.open(sprintf(o[:seqs], genome), "r").each do |ln|
-	 if ln =~ /^>(\S+)/
-	    og = genes.index{|g| g.include? $1}
-	    hand = og.nil? ? nil : ( o[:pergenome] ? genome_i : og )
-	    ln.sub!(/^>/, ">#{o[:pergenome] ? "OG#{og}" : genome}-") if
-	       o[:prefix] and not hand.nil?
-	 end
-	 ofhs[hand].puts(ln) unless hand.nil?
-      end
-   end
-   $stderr.puts "  #{genome_i+1} genomes processed." unless o[:q]
-
-   # Close outputs
-   $stderr.puts "Closing output files." unless o[:q]
-   ofhs.each{|h| h.close}
-   $stderr.puts "Done.\n" unless o[:q] 
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts l + "\n" }
-   err
-end
-
-

data/utils/enveomics/Scripts/ogs.mcl.rb

@@ -1,186 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R
-# @update: Sep-11-2015
-# @license: artistic license 2.0
-#
-
-$:.push File.expand_path(File.dirname(__FILE__) + "/lib")
-require 'enveomics_rb/og'
-require 'optparse'
-require 'tmpdir'
-
-o = {q:false, f:"(\\S+)-(\\S+)\\.rbm", mcl:"", inflation:1.5, blind:false,
-   evalue:false, thr:2, identity:false, bestmatch:false}
-ARGV << "-h" if ARGV.size==0
-OptionParser.new do |opts|
-   opts.banner = "
-Identifies Orthology Groups (OGs) in Reciprocal Best Matches (RBM)
-between all pairs in a collection of genomes, using the Markov Cluster
-Algorithm.
-
-Requires MCL (see http://www.micans.org/mcl).
-
-Usage: #{$0} [options]"
-   opts.separator ""
-   opts.separator "Mandatory"
-   opts.on("-o", "--out FILE",
-      "Output file containing the detected OGs."){ |v| o[:out]=v }
-   opts.on("-d", "--dir DIR",
-      "Directory containing the RBM files.",
-      "Becomes optional iff --abc is set to a non-empty file."){ |v| o[:dir]=v }
-   opts.separator ""
-   opts.separator "Other Options"
-   opts.on("-f", "--format STRING",
-      "Format of the filenames for the RBM files (within -d), using regex " +
-      "syntax.", "By default: '#{o[:f]}'."){ |v| o[:f]=v }
-   opts.on("-I", "--inflation FLOAT",
-      "Inflation parameter for MCL clustering. By default: #{o[:inflation]}."
-      ){ |v| o[:inflation]=v.to_f }
-   opts.on("-b", "--blind",
-      "If set, computes clusters without taking bitscore into account."
-      ){ |v| o[:blind]=v }
-   opts.on("-e", "--evalue",
-      "If set, uses the e-value to weight edges, instead of the default " +
-      "Bit-Score."){ |v| o[:evalue]=v }
-   opts.on("-i", "--identity",
-      "If set, uses the identity to weight edges, instead of the default " +
-      "Bit-Score."){ |v| o[:identity]=v }
-   opts.on("-B", "--best-match",
-      "If set, it assumes best-matches instead reciprocal best matches."
-      ){ |v| o[:bestmatch]=v }
-   opts.on("-m", "--mcl-bin DIR",
-      "Path to the directory containing the mcl binaries.",
-      "By default, assumed to be in the PATH."){ |v| o[:mcl]=v+"/" }
-   opts.on("--abc FILE",
-      "Use this abc file instead of a temporal file."){ |v| o[:abc] = v }
-   opts.on("-t", "--threads INT",
-      "Number of threads to use. By default: #{o[:thr]}."){ |v| o[:thr]=v.to_i }
-   opts.on("-q", "--quiet", "Run quietly (no STDERR output)."){ o[:q] = true }
-   opts.on("-h", "--help", "Display this screen.") do
-      puts opts
-      exit
-   end
-   opts.separator ""
-end.parse!
-abort "-o is mandatory" if o[:out].nil?
-o[:evalue] = false if o[:identity]
-o[:evalue] = false if o[:blind]
-o[:identity] = false if o[:blind]
-
-##### MAIN:
-begin
-   Dir.mktmpdir do |dir|
-      o[:abc] = "#{dir}/rbms.abc" if o[:abc].nil?
-      abort "-d must exist and be a directory" unless
-	 File.size?(o[:abc]) or
-	 (!o[:dir].nil? and File.exists?(o[:dir]) and File.directory?(o[:dir]))
-      # Traverse the whole directory
-      if File.size? o[:abc]
-	 $stderr.puts "Reusing existing abc file '#{o[:abc]}'." unless o[:q]
-      else
-	 file_i = 0
-	 ln_i = 0
-	 $stderr.puts "Reading RBM files within '#{o[:dir]}'." unless o[:q]
-	 abc = File.open(o[:abc] + ".tmp", "w")
-	 Dir.entries(o[:dir]).each do |rbm_file|
-	    next unless File.file?(o[:dir]+"/"+rbm_file)
-	    # Parse the filename to identify the genomes
-	    m = /#{o[:f]}/.match(rbm_file)
-	    if m.nil? or m[2].nil?
-	       warn "Ignoring #{rbm_file}: doesn't match /#{o[:f]}/."
-	       next
-	    end
-	    file_i += 1
-	    # Read the RBMs list
-	    f = File.open(o[:dir]+"/"+rbm_file, "r")
-	    while ln = f.gets
-	       # Add the RBM to the abc file
-	       row = ln.split(/\t/)
-	       abc.puts [m[1]+">"+row[0], m[2]+">"+row[1],
-		  (o[:blind] ? "1" :
-		  (o[:evalue] ? row[10] :
-		  (o[:identity] ? row[2] : row[11])))].join("\t")
-	       ln_i += 1
-	    end
-	    f.close
-	    $stderr.print " Scanned files: #{file_i}. " +
-	       "Found RBMs: #{ln_i}.   \r" unless o[:q]
-	 end
-	 abc.close
-	 File.rename(o[:abc] + ".tmp", o[:abc])
-	 $stderr.print "\n" unless o[:q]
-      end # if File.size? o[:abc] ... else
-
-      # Build .mci file (mcxload) and compute .mccl file (mcl)
-      $stderr.puts "Markov-Clustering" unless o[:q]
-      `'#{o[:mcl]}mcxload' #{"--stream-mirror" unless o[:bestmatch]} \
-	 -abc '#{o[:abc]}' -o '#{dir}/rbms.mci' --write-binary \
-	 -write-tab '#{dir}/genes.tab' #{"--stream-neg-log10" if o[:evalue]} \
-	 &>/dev/null`
-      `'#{o[:mcl]}mcl' '#{dir}/rbms.mci' -V all -I #{o[:inflation].to_s} \
-	 -o '#{dir}/ogs.mcl' -te #{o[:thr].to_s}`
-
-      # Load .tab as Gene objects
-      $stderr.puts "Loading gene table from '#{dir}/genes.tab'." unless o[:q]
-      genes = []
-      tab = File.open("#{dir}/genes.tab", "r")
-      while ln = tab.gets
-	 ln.chomp!
-	 r = ln.split /\t|>/
-	 genes[ r[0].to_i ] = Gene.new(r[1], r[2])
-      end
-      tab.close
-      $stderr.puts " Got " + genes.size.to_s + " genes in " +
-	 Gene.genomes.size.to_s + " genomes." unless o[:q]
-      
-      # Load .mcl file as OGCollection
-      $stderr.puts "Loading clusters from '#{dir}/ogs.mcl'." unless o[:q]
-      collection = OGCollection.new
-      mcl = File.open("#{dir}/ogs.mcl", "r")
-      in_matrix = false
-      my_genes = nil
-      while ln = mcl.gets
-         ln.chomp!
-	 if ln =~ /^\(mclmatrix$/
-	    in_matrix = true
-	    next
-	 end
-	 next if ln =~ /^begin$/
-	 if in_matrix
-	    break if ln =~ /^\)$/
-	    if ln =~ /^\d+\s+/
-	       ln.sub!(/^\d+\s+/, "")
-	       my_genes = []
-	    end
-	    ln.sub!(/^\s+/, "")
-	    raise "Incomplete mcl matrix, offending line: #{$.}: #{ln}" if
-	       my_genes.nil?
-	    my_genes += ln.split(/\s/)
-	    if my_genes.last == "$"
-	       my_genes.pop
-	       og = OG.new
-	       my_genes.each{|i| og << genes[ i.to_i ]}
-	       collection << og
-	       my_genes = nil
-	    end
-	 end
-      end
-      mcl.close
-      $stderr.puts " Got #{collection.ogs.size} clusters." unless o[:q]
-      
-      # Save the output matrix
-      $stderr.puts "Saving matrix into '#{o[:out]}'." unless o[:q]
-      f = File.open(o[:out], "w")
-      f.puts collection.to_s
-      f.close
-      $stderr.puts "Done.\n" unless o[:q] 
-   end
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts l + "\n" }
-   err
-end
-
-

data/utils/enveomics/Scripts/ogs.rb

@@ -1,104 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R
-# @update: Apr-29-2015
-# @license: artistic license 2.0
-#
-
-$:.push File.expand_path(File.dirname(__FILE__) + '/lib')
-require 'enveomics_rb/og'
-require 'optparse'
-
-o = {:q=>FALSE, :f=>"(\\S+)-(\\S+)\\.rbm", :consolidate=>TRUE, :pre=>[]}
-ARGV << '-h' if ARGV.size==0
-OptionParser.new do |opts|
-   opts.banner = "
-***IMPORTANT NOTE***
-This script suffers from chaining effect and is very sensitive to spurious connections,
-because it applies a greedy clustering algorithm. For most practical purposes, the use
-of this script is discouraged and `ogs.mcl.rb` should be preferred. [ Apr-29-2015 ]
-
-Identifies Orthology Groups (OGs) in Reciprocal Best Matches (RBM)
-between all pairs in a collection of genomes.
-
-Usage: #{$0} [options]"
-   opts.separator ""
-   opts.separator "Mandatory"
-   opts.on("-o", "--out FILE", "Output file containing the detected OGs."){ |v| o[:out]=v }
-   opts.separator ""
-   opts.separator "Other Options"
-   opts.on("-d", "--dir DIR", "Directory containing the RBM files."){ |v| o[:dir]=v }
-   opts.on("-p", "--pre-ogs FILE1,FILE2,...", Array, "Pre-computed OGs file(s), separated by commas."){ |v| o[:pre]=v }
-   opts.on("-n", "--unchecked", "Do not check internal redundancy in OGs."){ o[:consolidate]=FALSE }
-   opts.on("-f","--format STRING", "Format of the filenames for the RBM files (within -d), using regex syntax. By default: '#{o[:f]}'."){ |v| o[:f]=v }
-   opts.on("-q", "--quiet", "Run quietly (no STDERR output)."){ o[:q] = TRUE }
-   opts.on("-h", "--help", "Display this screen.") do
-      puts opts
-      exit
-   end
-   opts.separator ""
-end.parse!
-abort "-o is mandatory" if o[:out].nil?
-
-##### MAIN:
-begin
-   # Initialize the collection of OGs.
-   collection = OGCollection.new
-   # Read the pre-computed OGs (if -p is passed).
-   o[:pre].each do |pre|
-      $stderr.puts "Reading pre-computed OGs in '#{pre}'." unless o[:q]
-      f = File.open(pre, 'r')
-      h = f.gets.chomp.split /\t/
-      while ln = f.gets
-	 collection << OG.new(h, ln.chomp.split(/\t/))
-      end
-      f.close
-      $stderr.puts " Loaded OGs: #{collection.ogs.length}." unless o[:q]
-   end
-   # Read the RBM files in the directory (if -d is passed).
-   unless o[:dir].nil?
-      abort "-d must exist and be a directory" unless File.exists?(o[:dir]) and File.directory?(o[:dir])
-      # Traverse the whole directory.
-      file_i = 0
-      $stderr.puts "Reading RBM files within '#{o[:dir]}'." unless o[:q] 
-      Dir.entries(o[:dir]).each do |rbm_file|
-	 next unless File.file?(o[:dir]+"/"+rbm_file)
-	 # Parse the filename to identify the genomes.
-	 m = /#{o[:f]}/.match(rbm_file)
-	 if m.nil? or m[2].nil?
-	    warn "Cannot parse filename: #{rbm_file} (doesn't match /#{o[:f]}/)."
-	    next
-	 end
-	 file_i += 1
-	 # Read the RBMs list
-	 f = File.open(o[:dir]+"/"+rbm_file, "r")
-	 while ln = f.gets
-	    # Add the RBM to the collection of OGs. Only the first two columns are used.
-	    row = ln.split(/\t/)
-	    collection.add_rbm( Gene.new(m[1],row[0]), Gene.new(m[2],row[1]) )
-	 end
-	 f.close
-	 $stderr.print " Scanned files: #{file_i}. Found OGs: #{collection.ogs.length}.   \r" unless o[:q]
-      end
-      $stderr.print "\n" unless o[:q]
-   end
-   # Evaluate internal consistency merging linked OGs (unless -n is passed).
-   if o[:consolidate]
-      $stderr.puts "Evaluating internal consistency." unless o[:q] 
-      collection.consolidate!
-      $stderr.puts " Final OGs: #{collection.ogs.length}." unless o[:q]
-   end
-   # Save the output matrix
-   $stderr.puts "Saving matrix into '#{o[:out]}'." unless o[:q]
-   f = File.open(o[:out], "w")
-   f.puts collection.to_s
-   f.close
-   $stderr.puts "Done.\n" unless o[:q] 
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts l + "\n" }
-   err
-end
-
-