miga-base 1.2.15.1 → 1.2.15.3

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

@@ -1,131 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R
-# @license: Artistic-2.0
-#
-
-$:.push File.expand_path(File.dirname(__FILE__) + '/lib')
-require 'enveomics_rb/og'
-require 'optparse'
-require 'json'
-
-o = {q:false, a:false}
-ARGV << '-h' if ARGV.size==0
-OptionParser.new do |opts|
-  opts.banner = "
-Estimates some descriptive statistics on a set of Orthology Groups (OGs).
-
-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 "Other Options"
-  opts.on("-j", "--json FILE", "Output file in JSON format."){ |v| o[:json]=v }
-  opts.on("-t", "--tab FILE","Output file in tabular format."){ |v| o[:tab]=v }
-  opts.on("-T", "--transposed-tab FILE",
-    "Output file in transposed tabular format."){ |v| o[:ttab]=v }
-  opts.on("-a", "--auto", "Run completely quietly (no STDERR or STDOUT)") do
-    o[:q] = true
-    o[:a] = true
-  end
-  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
-  # Initialize the collection of OGs.
-  collection = OGCollection.new
-   
-  # Read the pre-computed OGs
-  $stderr.puts "Reading pre-computed OGs in '#{o[:ogs]}'." unless o[:q]
-  f = File.open(o[:ogs], "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]
-   
-  # Estimate descriptive stats
-  stat_name = {
-    genomes: "Number of genomes",
-    pan: "Pangenome (OGs)",
-    core: "Core genome (OGs)",
-    core90pc: "OGs in 90% of the genomes",
-    core80pc: "OGs in 80% of the genomes",
-    unus: "Unus genome, core genome discarding paralogs (OGs)",
-    avg: "Average number of OGs in a genome",
-    avg_pan: "Average genome (OGs) / Pangenome (OGs)",
-    core_avg: "Core genome (OGs) / Average genome (OGs)",
-    core_pan: "Core genome (OGs) / Pangenome (OGs)",
-    ogs_shannon: "Entropy of the OG frequencies (bits)"
-  }
-  stats = {}
-  stats[:genomes] = Gene.genomes.length
-  stats[:pan] = collection.ogs.length
-  stats[:core] = collection.ogs.map do |og|
-    (og.genomes.length == Gene.genomes.length) ? 1 : 0
-  end.inject(0,:+)
-  stats[:core90pc] = collection.ogs.map do |og|
-    (og.genomes.length >= 0.9*Gene.genomes.length) ? 1 : 0
-  end.inject(0,:+)
-  stats[:core80pc] = collection.ogs.map do |og|
-    (og.genomes.length >= 0.8*Gene.genomes.length) ? 1 : 0
-  end.inject(0,:+)
-  stats[:unus] = collection.ogs.map do |og|
-    (og.genomes.length != Gene.genomes.length) ? 0 :
-      (og.genes.all?{ |i| i.size==1 }) ? 1 : 0
-  end.inject(0,:+)
-  og_genomes = collection.ogs.map{ |og| og.genomes.length }.inject(0,:+)
-  stats[:avg] = og_genomes.to_f/Gene.genomes.length
-  stats[:avg_pan] = stats[:avg]/stats[:pan]
-  stats[:core_avg] = stats[:core].to_f/stats[:avg]
-  stats[:core_pan] = stats[:core].to_f/stats[:pan]
-  stats[:ogs_shannon] = -1 * collection.ogs.map do |og|
-    pi = og.genomes.length.to_f/Gene.genomes.length
-    pi * Math.log(pi)
-  end.inject(0.0,:+)
-
-  # Show result
-  $stderr.puts "Generating reports." unless o[:q]
-  stats.each_pair{ |k,v| puts " #{stat_name[k]}: #{v}" } unless o[:a]
-
-  # Save results in JSON
-  unless o[:json].nil?
-    ohf = File.open(o[:json], "w")
-    ohf.puts JSON.pretty_generate(stats)
-    ohf.close
-  end
-
-  # Save results in tab
-  unless o[:tab].nil?
-    ohf = File.open(o[:tab], "w")
-    stats.each_pair{ |k,v| ohf.puts "#{k}\t#{v}" }
-    ohf.close
-  end
-
-  # Save results in T(tab)
-  unless o[:ttab].nil?
-    ohf = File.open(o[:ttab], "w")
-    ohf.puts stats.keys.join("\t")
-    ohf.puts stats.values.join("\t")
-    ohf.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/rbm-legacy.rb

@@ -1,172 +0,0 @@
-#!/usr/bin/env ruby
-
-# frozen_string_literal: true
-
-$VERSION = 0.1
-$:.push File.expand_path('../lib', __FILE__)
-require 'enveomics_rb/enveomics'
-require 'tmpdir'
-
-o = {
-  q: false, thr: 1,
-  len: 0, id: 0.0, fract: 0.0, score: 0.0,
-  bin: '', program: :'blast+', nucl: false
-}
-
-OptionParser.new do |opts|
-  cmd = File.basename($0)
-  opts.banner = <<~BANNER
-
-    [Enveomics Collection: #{cmd} v#{$VERSION}]
-
-    [DEPRECATED: Please use rbm.rb instead]
-
-    Finds the reciprocal best matches between two sets of sequences
-
-    Usage: #{cmd} [options]
-
-  BANNER
-
-  opts.separator 'Mandatory'
-  opts.on(
-    '-1', '--seq1 FILE',
-    'Path to the FastA file containing the set 1'
-  ) { |v| o[:seq1] = v }
-  opts.on(
-    '-2', '--seq2 FILE',
-    'Path to the FastA file containing the set 2'
-  ) { |v| o[:seq2] = v }
-  opts.separator ''
-  opts.separator 'Search Options'
-  opts.on(
-    '-n', '--nucl',
-    'Sequences are assumed to be nucleotides (proteins by default)',
-    'Incompatible with -p diamond'
-  ) { |v| o[:nucl] = true }
-  opts.on(
-    '-l', '--len INT', Integer,
-    'Minimum alignment length (in residues)',
-    "By default: #{o[:len]}"
-  ) { |v| o[:len] = v }
-  opts.on(
-    '-f', '--fract FLOAT', Float,
-    'Minimum alignment length (as a fraction of the query)',
-    'If set, requires BLAST+ or Diamond (see -p)',
-    "By default: #{o[:fract]}"
-  ) { |v| o[:fract] = v }
-  opts.on(
-    '-i', '--id NUM', Float,
-    'Minimum alignment identity (in %)',
-    "By default: #{o[:id]}"
-  ){ |v| o[:id] = v }
-  opts.on(
-    '-s', '--score NUM', Float,
-    'Minimum alignment score (in bits)',
-    "By default: #{o[:score]}"
-  ) { |v| o[:score] = v }
-  opts.separator ''
-  opts.separator 'Software Options'
-  opts.on(
-    '-b', '--bin DIR',
-    'Path to the directory containing the binaries of the search program'
-  ) { |v| o[:bin] = v }
-  opts.on(
-    '-p', '--program STR',
-    'Search program to be used.  One of: blast+ (default), blast, diamond'
-  ) { |v| o[:program] = v.downcase.to_sym }
-  opts.on(
-    '-t', '--threads INT', Integer,
-    'Number of parallel threads to be used',
-    "By default: #{o[:thr]}"
-  ) { |v| o[:thr] = v }
-  opts.separator ''
-  opts.separator 'Other Options'
-  opts.on('-q', '--quiet', 'Run quietly (no STDERR output)') { o[:q] = true }
-  opts.on('-h', '--help', 'Display this screen') { puts opts ; exit }
-  opts.separator ''
-end.parse!
-
-abort '-1 is mandatory' if o[:seq1].nil?
-abort '-2 is mandatory' if o[:seq2].nil?
-if o[:program] == :diamond && o[:nucl]
-  abort '-p diamond is incompatible with -n'
-end
-if o[:fract] > 0.0 && o[:program] == :blast
-  abort 'Argument -f/--fract requires -p blast+ or -p diamond'
-end
-o[:bin] = o[:bin] + '/' if o[:bin].size > 0
-$quiet = o[:q]
-
-Dir.mktmpdir do |dir|
-  say('Temporal directory: ', dir)
-
-  # Create databases
-  say 'Creating databases'
-  [:seq1, :seq2].each do |seq|
-    case o[:program]
-    when :blast
-      `"#{o[:bin]}formatdb" -i "#{o[seq]}" -n "#{dir}/#{seq}" \
-        -p #{o[:nucl] ? 'F' : 'T'}`
-    when :'blast+'
-      `"#{o[:bin]}makeblastdb" -in "#{o[seq]}" -out "#{dir}/#{seq}" \
-        -dbtype #{o[:nucl] ? 'nucl' : 'prot'}`
-    when :diamond
-      `"#{o[:bin]}diamond" makedb --in "#{o[seq]}" \
-        --db "#{dir}/#{seq}.dmnd" --threads "#{o[:thr]}"`
-    else
-      abort "Unsupported program: #{o[:program]}"
-    end
-  end
-
-  # Best-hits
-  rbh = {}
-  n2 = 0
-  say ' Running comparisons'
-  [2, 1].each do |i|
-    qry_seen = {}
-    q = o[:"seq#{i}"]
-    s = "#{dir}/seq#{i == 1 ? 2 : 1}"
-    say('  Query: ', q)
-    case o[:program]
-    when :blast
-      `"#{o[:bin]}blastall" -p #{o[:nucl] ? 'blastn' : 'blastp'} -d "#{s}" \
-        -i "#{q}" -v 1 -b 1 -a #{o[:thr]} -m 8 -o "#{dir}/#{i}.tab"`
-    when :'blast+'
-      `"#{o[:bin]}#{o[:nucl] ? 'blastn' : 'blastp'}" -db "#{s}" -query "#{q}" \
-        -max_target_seqs 1 -num_threads #{o[:thr]} -out "#{dir}/#{i}.tab" \
-        -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend \
-        sstart send evalue bitscore qlen slen"`
-    when :diamond
-      `"#{o[:bin]}diamond" blastp --threads "#{o[:thr]}" --db "#{s}.dmnd" \
-        --query "#{q}" --sensitive --daa "#{dir}/#{i}.daa" --quiet \
-        && "#{o[:bin]}diamond" view --daa "#{dir}/#{i}.daa" --outfmt \
-        6 qseqid sseqid pident length mismatch gapopen qstart qend sstart \
-        send evalue bitscore qlen slen --out "#{dir}/#{i}.tab" --quiet`
-    else
-      abort "Unsupported program: #{o[:program]}"
-    end
-
-    n = 0
-    File.open("#{dir}/#{i}.tab", 'r') do |fh|
-      fh.each do |ln|
-        ln.chomp!
-        row = ln.split(/\t/)
-        row[12] = '1' unless [:'blast+', :diamond].include? o[:program]
-        next unless qry_seen[row[0]].nil? &&
-          row[3].to_i >= o[:len] && row[2].to_f >= o[:id] &&
-          row[11].to_f >= o[:score] && row[3].to_f / row[12].to_i >= o[:fract]
-
-        qry_seen[row[0]] = 1
-        n += 1
-        if i == 2
-          rbh[row[0]] = row[1]
-        elsif !rbh[row[1]].nil? && rbh[row[1]] == row[0]
-          puts ln
-          n2 += 1
-        end
-      end
-    end
-    say "    #{n} sequences with hit"
-  end
-  say "  #{n2} RBMs"
-end

data/utils/enveomics/Scripts/rbm.rb

@@ -1,108 +0,0 @@
-#!/usr/bin/env ruby
-
-# frozen_string_literal: true
-
-$VERSION = 1.01
-$:.push File.expand_path('../lib', __FILE__)
-require 'enveomics_rb/rbm'
-require 'tmpdir'
-
-bms_dummy = Enveomics::RBM.new('1', '2').bms1
-o = { q: false, out: '-' }
-%i[thr len id fract score bin program nucl].each do |k|
-  o[k] = bms_dummy.opt(k)
-end
-
-OptionParser.new do |opts|
-  opts.version = $VERSION
-  cmd = File.basename($0)
-  opts.banner = <<~BANNER
-
-    [Enveomics Collection: #{cmd} v#{$VERSION}]
-
-    Finds the reciprocal best matches between two sets of sequences
-
-    Usage: #{cmd} [options]
-
-  BANNER
-
-  opts.separator 'Mandatory'
-  opts.on(
-    '-1', '--seq1 FILE',
-    'Path to the FastA file containing the set 1'
-  ) { |v| o[:seq1] = v }
-  opts.on(
-    '-2', '--seq2 FILE',
-    'Path to the FastA file containing the set 2'
-  ) { |v| o[:seq2] = v }
-  opts.on(
-    '-o', '--out FILE',
-    'Reciprocal Best Matches in BLAST tabular format.',
-    'Supports compression with .gz extension, use - for STDOUT (default)'
-  ) { |v| o[:out] = v }
-  opts.separator ''
-  opts.separator 'Search Options'
-  opts.on(
-    '-n', '--nucl',
-    'Sequences are assumed to be nucleotides (proteins by default)',
-    'Incompatible with -p diamond'
-  ) { |v| o[:nucl] = true }
-  opts.on(
-    '-l', '--len INT', Integer,
-    'Minimum alignment length (in residues)',
-    "By default: #{o[:len]}"
-  ) { |v| o[:len] = v }
-  opts.on(
-    '-f', '--fract FLOAT', Float,
-    'Minimum alignment length (as a fraction of the query)',
-    'If set, requires BLAST+ or Diamond (see -p)',
-    "By default: #{o[:fract]}"
-  ) { |v| o[:fract] = v }
-  opts.on(
-    '-i', '--id NUM', Float,
-    'Minimum alignment identity (in %)',
-    "By default: #{o[:id]}"
-  ){ |v| o[:id] = v }
-  opts.on(
-    '-s', '--score NUM', Float,
-    'Minimum alignment score (in bits)',
-    "By default: #{o[:score]}"
-  ) { |v| o[:score] = v }
-  opts.separator ''
-  opts.separator 'Software Options'
-  opts.on(
-    '-b', '--bin DIR',
-    'Path to the directory containing the binaries of the search program'
-  ) { |v| o[:bin] = v }
-  opts.on(
-    '-p', '--program STR',
-    'Search program to be used',
-    'One of: blast+ (default), blast, diamond, blat'
-  ) { |v| o[:program] = v.downcase.to_sym }
-  opts.on(
-    '-t', '--threads INT', Integer,
-    'Number of parallel threads to be used',
-    "By default: #{o[:thr]}"
-  ) { |v| o[:thr] = v }
-  opts.separator ''
-  opts.separator 'Other Options'
-  opts.on('-q', '--quiet', 'Run quietly (no STDERR output)') { $QUIET = true }
-  opts.on('-h', '--help', 'Display this screen') { puts opts ; exit }
-  opts.separator ''
-end.parse!
-
-raise Enveomics::OptionError.new('-1 is mandatory') if o[:seq1].nil?
-raise Enveomics::OptionError.new('-2 is mandatory') if o[:seq2].nil?
-raise Enveomics::OptionError.new(
-  'Argument -f/--fract requires -p blast+ or -p diamond'
-) if o[:fract] > 0.0 && !%i[blast+ diamond].include?(o[:program])
-
-rbm = Enveomics::RBM.new(o[:seq1], o[:seq2], o)
-ofh = writer(o[:out])
-rbm.each { |bm| ofh.puts bm.to_s }
-ofh.close
-
-say('Forward Best Matches: ', rbm.bms1.count)
-say('Reverse Best Matches: ', rbm.bms2.count)
-say('Reciprocal Best Matches: ', rbm.count)
-

data/utils/enveomics/Scripts/sam.filter.rb

@@ -1,148 +0,0 @@
-#!/usr/bin/env ruby
-
-# frozen_string_literal: true
-
-$VERSION = 1.0
-$:.push File.expand_path('../lib', __FILE__)
-require 'enveomics_rb/enveomics'
-use 'shellwords'
-
-o = {
-  q: false, threads: 2, m_format: :sam, g_format: :fasta, identity: 95.0,
-  o: '-', header: true
-}
-
-OptionParser.new do |opt|
-  Enveomics.opt_banner(
-    opt, 'Filters a SAM or BAM file by target sequences and/or identity',
-    "#{File.basename($0)} -m map.sam -o filtered_map.sam [options]"
-  )
-
-  opt.separator 'Input/Output'
-  opt.on(
-    '-g', '--genome PATH',
-    'Genome assembly',
-    'Supports compression with .gz extension, use - for STDIN'
-  ) { |v| o[:g] = v }
-  opt.on(
-    '-m', '--mapping PATH',
-    'Mapping file',
-    'Supports compression with .gz extension, use - for STDIN'
-  ) { |v| o[:m] = v }
-  opt.on(
-    '-o', '--out-sam PATH',
-    'Output filtered file in SAM format',
-    'Supports compression with .gz extension, use - for STDOUT (default)'
-  ) { |v| o[:o] = v }
-  opt.separator ''
-
-  opt.separator 'Formats'
-  opt.on(
-    '--g-format STRING',
-    'Genome assembly format: fasta (default) or list'
-  ) { |v| o[:g_format] = v.downcase.to_sym }
-  opt.on(
-    '--m-format STRING',
-    'Mapping file format: sam (default) or bam',
-    'sam supports compression with .gz file extension'
-  ) { |v| o[:m_format] = v.downcase.to_sym }
-  opt.separator ''
-
-  opt.separator 'General'
-  opt.on(
-    '-i', '--identity FLOAT', Float,
-    "Set a fixed threshold of percent identity (default: #{o[:identity]})"
-  ) { |v| o[:identity] = v }
-  opt.on('--no-header', 'Do not include the headers') { |v| o[:header] = v }
-  opt.separator ''
-  opt.on(
-    '-t', '--threads INT', Integer, "Threads to use (default: #{o[:threads]})"
-  ) { |v| o[:threads] = v }
-  opt.on('-l', '--log PATH', 'Log file to save output') { |v| o[:log] = v }
-  opt.on('-q', '--quiet', 'Run quietly') { |v| o[:q] = v }
-  opt.on('-h', '--help', 'Display this screen') do
-    puts opt
-    exit
-  end
-  opt.separator ''
-end.parse!
-
-$QUIET = o[:q]
-
-# Functions
-
-##
-# Parses one line +ln+ in SAM format and outputs filtered lines to +ofh+
-# Filters by minimum +identity+ and +target+ sequences, and prints
-# the headers if +header+
-def parse_sam_line(ln, identity, target, header, ofh)
-  if ln =~ /^@/ || ln =~ /^\s*$/
-    ofh.puts ln if header
-    return
-  end
-
-  # No match
-  row = ln.chomp.split("\t")
-  return if row[2] == '*'
-
-  # Filter by target
-  return if !target.nil? && !target.include?(row[2])
-
-  # Exclude unless concordant or unaligned
-  length = row[9].size
-  row.shift(11) # Discard non-flag columns
-  flags = Hash[row.map { |i| i.sub(/:.:/, ':').split(':', 2) }]
-  return if flags['YT'] && !%w[CP UU].include?(flags['YT'])
-
-  # Filter by identity
-  unless flags['MD']
-    raise Enveomics::ParseError.new(
-      "SAM line missing MD flag:\n#{ln}\nFlags: #{flags}"
-    )
-  end
-  mismatches = flags['MD'].scan(/[^\d]/).count
-  id = 100.0 * (length - mismatches) / length
-  ofh.puts ln if id >= identity
-end
-
-# Reading targets
-if o[:g]
-  say 'Loading target sequences to filter'
-  reader = reader(o[:g])
-  target =
-    case o[:g_format]
-    when :fasta
-      reader.each.map { |ln| $1 if ln =~ /^>(\S+)/ }.compact
-    when :list
-      reader.each.map(&:chomp)
-    else
-      raise Enveomics::OptionError.new(
-        "Unsupported target sequences format: #{o[:g_format]}"
-      )
-    end
-  reader.close
-else
-  target = nil
-end
-
-# Reading and filtering mapping
-say 'Reading mapping file'
-ofh = writer(o[:o])
-case o[:m_format]
-when :sam
-  reader = reader(o[:m])
-  reader.each { |ln| parse_sam_line(ln, o[:identity], target, o[:header], ofh) }
-  reader.close
-when :bam
-  cmd = ['samtools', 'view', o[:m], '-@', o[:threads]]
-  cmd << '-h' if o[:header]
-  IO.popen(cmd.shelljoin) do |fh|
-    fh.each { |ln| parse_sam_line(ln, o[:identity], target, o[:header], ofh) }
-  end
-else
-  raise Enveomics::OptionError.new(
-    "Unsupported mapping format: #{o[:m_format]}"
-  )
-end
-ofh.close
-

data/utils/enveomics/Tests/Makefile

@@ -1,10 +0,0 @@
-
-# Makefile for the Enve-omics collection
-# @update Oct 13 2013
-# @author Luis M. Rodriguez-R <lmrodriguez at gmail dot com>
-
-include ../globals.mk
-
-all:
-	@echo NOTHING TO DO YET
-