miga-base 0.7.26.3 → 1.0.0.sr1

data/utils/enveomics/Scripts/FastA.fragment.rb

@@ -1,92 +1,100 @@
 #!/usr/bin/env ruby
 
-# @author  Luis M. Rodriguez-R
-# @license artistic license 2.0
+# frozen_string_literal: true
 
-$:.push File.expand_path("../lib", __FILE__)
-require "enveomics_rb/enveomics"
-require "enveomics_rb/stat"
+$:.push File.expand_path('../lib', __FILE__)
+require 'enveomics_rb/enveomics'
+require 'enveomics_rb/stats'
+$VERSION = 1.0
 
-o = {q:false, completeness:nil, minlen:500, shuffle:true}
+o = { q: false, completeness: nil, minlen: 500, shuffle: true }
 OptionParser.new do |opts|
-  opts.banner = "
-Simulates incomplete (fragmented) drafts from complete genomes.
+  opts.version = $VERSION
+  Enveomics.opt_banner(
+    opts, 'Simulates incomplete (fragmented) drafts from complete genomes',
+    "#{File.basename($0)} -i in.fasta -o out.fasta -c 0.5 [options]"
+  )
 
-Usage: #{$0} [options]"
-  opts.separator ""
-  opts.separator "Mandatory"
-  opts.on("-i", "--in FILE",
-    "Path to the FastA file containing the complete sequences."
-    ){ |v| o[:in] = v }
-  opts.on("-o", "--out FILE", "Path to the FastA to create."){ |v| o[:out] = v }
-  opts.on("-c", "--completeness FLOAT",
-    "Fraction of genome completeness to simulate from 0 to 1."
-    ){ |v| o[:completeness] = v.to_f }
-  opts.separator ""
-  opts.separator "Options"
-  opts.on("-m", "--minlen INT",
-    "Minimum fragment length to report. By default: #{o[:minlen]}."
-    ){ |v| o[:minlen] = v.to_i }
-  opts.on("-s", "--sorted", "Keep fragments sorted as in the input file. ",
-    "By default, fragments are shuffled."){ |v| o[:shuffle] = !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 'Mandatory'
+  opts.on(
+    '-i', '--in FILE',
+    'Path to the FastA file containing the complete sequences',
+    'Supports compression with .gz extension, use - for STDIN'
+  ) { |v| o[:in] = v }
+  opts.on(
+    '-o', '--out FILE', 'Path to the FastA to create',
+    'Supports compression with .gz extension, use - for STDOUT'
+  ) { |v| o[:out] = v }
+  opts.on(
+    '-c', '--completeness FLOAT',
+    'Fraction of genome completeness to simulate from 0 to 1'
+  ) { |v| o[:completeness] = v.to_f }
+
+  opts.separator ''
+  opts.separator 'Options'
+  opts.on(
+    '-m', '--minlen INT',
+    "Minimum fragment length to report. By default: #{o[:minlen]}"
+  ) { |v| o[:minlen] = v.to_i }
+  opts.on(
+    '-s', '--sorted', 'Keep fragments sorted as in the input file',
+    'By default, fragments are shuffled'
+  ) { |v| o[:shuffle] = !v }
+  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 "-i is mandatory" if o[:in].nil?
-abort "-o is mandatory" if o[:out].nil?
-abort "-c is mandatory" if o[:completeness].nil?
+
+raise Enveomics::OptionError.new('-i is mandatory') if o[:in].nil?
+raise Enveomics::OptionError.new('-o is mandatory') if o[:out].nil?
+raise Enveomics::OptionError.new('-c is mandatory') if o[:completeness].nil?
 
 begin
   # Read input sequences
   g_id  = []
   g_seq = []
-  File.open(o[:in], "r") do |ifh|
-    id = ""
-    ifh.each_line do |ln|
-      if ln =~ /^>(\S*)/
-        g_id  << $1
-        g_seq << ""
-      else
-        g_seq[g_seq.size-1] += ln.gsub(/[^A-Za-z]/,"")
-      end
+  ifh = reader(o[:in])
+  id = ''
+  ifh.each_line do |ln|
+    if ln =~ /^>(\S*)/
+      g_id  << $1
+      g_seq << ''
+    else
+      g_seq[g_seq.size - 1] += ln.gsub(/[^A-Za-z]/, '')
     end
   end
-  
+  ifh.close
+
   # Fragment genomes
   f = {}
   binlen = [1, (o[:minlen].to_f/(1.5**2)).ceil].max
   p = [0.001, [1.0, 1.0 - (o[:completeness]/1.25 + 0.1)].min].max
-  while not g_seq.empty?
+  while !g_seq.empty?
     id  = g_id.shift
     seq = g_seq.shift
     gL  = seq.length
-    while not seq.empty?
-      fL = [0, ((Enve::Stat.r_geom(p).to_f +
-                  Enve::Stat.r_unif(-0.5,0.5))*binlen).round].max
-      f["#{f.size+1}_#{id}"] = seq[0,fL] if fL >= o[:minlen]
-      seq = seq[(fL+1) .. -1]
-      seq = "" if seq.nil?
+    while !seq.empty?
+      rand_x =
+        Enveomics::Stats.r_geom(p).to_f + Enveomics::Stats.r_unif(-0.5, 0.5)
+      fL = [0, (rand_x * binlen).round].max
+      f["#{f.size+1}_#{id}"] = seq[0, fL] if fL >= o[:minlen]
+      seq = seq[(fL + 1) .. -1]
+      seq = '' if seq.nil?
     end
   end
 
   # Save output
   k = f.keys
   k.shuffle! if o[:shuffle]
-  File.open(o[:out], "w") do |ofh|
-    k.each do |id|
-      ofh.puts ">#{id}"
-      ofh.puts f[id].gsub(/(\S{50})/, "\\1\n")
-    end
+  ofh = writer(o[:out])
+  k.each do |id|
+    ofh.puts ">#{id}"
+    ofh.puts f[id].gsub(/(\S{50})/, "\\1\n")
   end
-  
+  ofh.close
 rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts l + "\n" }
-   err
+  $stderr.puts "Exception: #{err}\n\n"
+  err.backtrace.each { |l| $stderr.puts l + "\n" }
+  err
 end
 
-

data/utils/enveomics/Scripts/FastA.sample.rb

@@ -1,43 +1,57 @@
 #!/usr/bin/env ruby
 
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license Artistic-2.0
-#
+# frozen_string_literal: false
 
-require 'optparse'
+$VERSION = 1.0
+$:.push File.expand_path('../lib', __FILE__)
+require 'enveomics_rb/enveomics'
 
-o = {q: false, rep: false}
-ARGV << '-h' if ARGV.size==0
+o = { q: false, rep: false }
 
 OptionParser.new do |opt|
-  opt.banner = "
-Samples a random set of sequences from a multi-FastA file.
-
-Usage: #{$0} [options]"
-  opt.separator ''
+  Enveomics.opt_banner(
+    opt, 'Samples a random set of sequences from a multi-FastA file',
+    "#{File.basename($0)} -i seq.fa -o 10pc.fa -f 0.1 [options]"
+  )
   opt.separator 'Mandatory'
-  opt.on('-i', '--in PATH', 'Input FastA file.'){ |v| o[:i] = v }
-  opt.on('-o', '--out PATH', 'Output FastA file.'){ |v| o[:o] = v }
-  opt.on('-f', '--fraction FLOAT',
+  opt.on(
+    '-i', '--in PATH',
+    'Input FastA file',
+    'Supports compression with .gz extension, use - for STDIN'
+  ) { |v| o[:i] = v }
+  opt.on(
+    '-o', '--out PATH',
+    'Output FastA file',
+    'Supports compression with .gz extension, use - for STDOUT'
+  ) { |v| o[:o] = v }
+  opt.on(
+    '-f', '--fraction FLOAT', Float,
     'Fraction of sequences to sample [0-1].',
-    'Mandatory unless -n is provided.'){ |v| o[:f] = v.to_f }
+    'Mandatory unless -c is provided.'
+  ) { |v| o[:f] = v }
   opt.separator ''
+
   opt.separator 'Options'
-  opt.on('-c', '--number INT',
-    'Number of sequences to sample.',
-    'Mandatory unless -f is provided.'){ |v| o[:n] = v.to_i }
-  opt.on('-r', '--replacement','Sample with replacement'){ |v| o[:rep] = v }
-  opt.on('-q', '--quiet', 'Run quietly (no STDERR output).'){ o[:q] = true }
+  opt.on(
+    '-c', '--number INT', Integer,
+    'Number of sequences to sample',
+    'Mandatory unless -f is provided'
+  ) { |v| o[:n] = v }
+  opt.on('-r', '--replacement','Sample with replacement') { |v| o[:rep] = v }
+  opt.on('-q', '--quiet', 'Run quietly (no STDERR output)') { o[:q] = true }
   opt.on('-h', '--help', 'Display this screen.') do
     puts opt
     exit
   end
   opt.separator ''
 end.parse!
-abort '-i is mandatory.' if o[:i].nil?
-abort '-o is mandatory.' if o[:o].nil?
-abort '-f or -n is mandatory.' if o[:f].nil? and o[:n].nil?
+
+raise Enveomics::OptionError.new('-i is mandatory') if o[:i].nil?
+raise Enveomics::OptionError.new('-o is mandatory') if o[:o].nil?
+if o[:f].nil? && o[:n].nil?
+  raise Enveomics::OptionError.new('-f or -n is mandatory')
+end
+$QUIET = o[:q]
 
 # Functions to parse sequences
 def do_stuff(id, sq)
@@ -53,31 +67,32 @@ def do_stuff(id, sq)
 end
 
 # Parse sequences
-$stderr.puts 'Parsing sequences' unless o[:q]
+say 'Parsing sequences'
 seq = []
-File.open(o[:i], 'r') do |fh|
-  id = nil
-  sq = ''
-  fh.each do |ln|
-    next if ln =~ /^;/
-    if ln =~ /^>(.+)/
-      seq << [id, sq] unless id.nil?
-      id = $1
-      sq = ''
-    else
-      sq << ln
-    end
+fh = reader(o[:i])
+id = nil
+sq = ''
+fh.each do |ln|
+  next if ln =~ /^;/
+  if ln =~ /^>(.+)/
+    seq << [id, sq] unless id.nil?
+    id = $1
+    sq = ''
+  else
+    sq << ln
   end
-  seq << [id, sq] unless id.nil?
 end
-$stderr.puts "  Input sequences: #{seq.size}"
+seq << [id, sq] unless id.nil?
+fh.close
+say "Input sequences: #{seq.size}"
+
 o[:n] ||= (seq.size * o[:f]).round
-seq_o = o[:rep] ? o[:n].times.map{ seq.sample } : seq.sample(o[:n])
-File.open(o[:o], 'w') do |fh|
-  seq_o.each do |i|
-    fh.puts ">#{i[0]}"
-    fh.puts i[1]
-  end
+seq_o = o[:rep] ? o[:n].times.map { seq.sample } : seq.sample(o[:n])
+fh = writer(o[:o])
+seq_o.each do |i|
+  fh.puts ">#{i[0]}"
+  fh.puts i[1]
 end
-$stderr.puts "  Output sequences: #{seq_o.size}"
+fh.close
+say "Output sequences: #{seq_o.size}"
 

data/utils/enveomics/Scripts/FastA.toFastQ.rb

@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'zlib'
+
+o = { qual: 31, encoding: 33 }
+ARGV << '-h' if ARGV.empty?
+OptionParser.new do |opts|
+  opts.banner = "
+Creates a FastQ-compliant file from a FastA file.
+
+Usage: #{$0} [options]"
+  opts.separator ''
+  opts.separator 'Options'
+  opts.on(
+    '-i', '--in FILE', 'Input FastA file (supports .gz compression)'
+  ) { |v| o[:in] = v }
+  opts.on(
+    '-o', '--out FILE', 'Output FastQ file (supports .gz compression)'
+  ) { |v| o[:out] = v }
+  opts.on(
+    '-q', '--quality INT', Integer,
+    'PHRED quality score to use (fixed), in the range [-5, 41]',
+    "By default: #{o[:qual]}"
+  ) { |v| o[:qual] = v }
+  opts.on(
+    '--encoding INT', Integer,
+    "Base encoding (33 or 64). By default: #{o[:encoding]}"
+  ) { |v| o[:encoding] = v }
+  opts.on('-h', '--help', 'Display this screen.') do
+    puts opts
+    exit
+  end
+  opts.separator ''
+end.parse!
+abort '-i is mandatory' if o[:in].nil?
+abort '-o is mandatory' if o[:out].nil?
+abort '-q must be in the range -5 .. 41' if o[:qual] < -5 || o[:qual] > 41
+
+# Determine quality character
+$qchar = (o[:qual] + o[:encoding]).chr
+
+# Create file handlers
+ifh = o[:in] =~ /\.gz$/ ?
+  Zlib::GzipReader.open(o[:in]) : File.open(o[:in], 'r')
+ofh = o[:out] =~ /\.gz$/ ?
+  Zlib::GzipWriter.open(o[:out]) : File.open(o[:out], 'w')
+
+def print_seq(ofh, id, seq)
+  ofh.puts "@#{id}", seq, '+', $qchar * seq.length unless seq.empty?
+end
+
+# Generate FastQ
+id = ''
+seq = ''
+ifh.each_line do |ln|
+  next if ln =~ /^;/
+  if ln =~ /^>(.*)/
+    print_seq(ofh, id, seq)
+    seq = ''
+    id = $1
+  else
+    seq += ln.chomp.upcase.gsub(/[^A-Z]/,'')
+  end
+end
+print_seq(ofh, id, seq)
+ofh.close
+ifh.close
+

data/utils/enveomics/Scripts/FastQ.maskQual.rb

@@ -0,0 +1,89 @@
+#!/usr/bin/env ruby
+
+$VERSION = 1.2
+$:.push File.expand_path('../lib', __FILE__)
+require 'enveomics_rb/enveomics'
+
+o = { q: false, offset: 33, qual: 15, fasta: false }
+OptionParser.new do |opts|
+  opts.version = $VERSION
+  Enveomics.opt_banner(
+    opts, 'Masks low-quality bases in a FastQ file',
+    "#{File.basename($0)} -i in.fastq -o out.fastq [options]"
+  )
+
+  opts.separator 'Mandatory'
+  opts.on(
+    '-i', '--input FILE',
+    'Path to the FastQ file containing the sequences',
+    'Supports compression with .gz extension, use - for STDIN'
+  ) { |v| o[:in] = v }
+  opts.on(
+    '-o', '--out FILE',
+    'Path to the output FastQ file',
+    'Supports compression with .gz extension, use - for STDOUT'
+  ) { |v| o[:out] = v }
+
+  opts.separator ''
+  opts.separator 'Quality Options'
+  opts.on(
+    '-q', '--qual INT', Integer,
+    "Minimum quality score to allow a base, by default: #{o[:qual]}"
+  ) { |v| o[:qual] = v }
+  opts.on(
+    '--offset INT', Integer,
+    "Q-score offset, by default: #{o[:offset]}"
+  ) { |v| o[:offset] = v }
+
+  opts.separator ''
+  opts.separator 'Other Options'
+  opts.on(
+    '-a', '--fasta', 'Output sequences in FastA format'
+  ) { |v| o[:fasta] = v }
+  opts.on('-q', '--quiet', 'Run quietly (no STDERR output)') { o[:q] = true }
+  opts.on('-h', '--help', 'Display this screen') do
+    puts opts
+    exit
+  end
+  opts.separator ''
+end.parse!
+
+raise Enveomics::OptionError.new('-i is mandatory') if o[:in].nil?
+raise Enveomics::OptionError.new('-o is mandatory') if o[:out].nil?
+$QUIET = o[:q]
+
+# Open in/out files
+say 'Reading FastQ file'
+ifh = reader(o[:in])
+ofh = writer(o[:out])
+
+# Parse and mask
+entry = []
+lno = 0
+ifh.each_line do |ln|
+  lno += 1 # <- Gzip doesn't support $.
+  case lno % 4
+  when 1
+    ln =~ /^@(\S+)/ or
+      raise Enveomics::ParseError.new("Unexpected defline format: #{ln}")
+    entry << ln
+  when 2, 3
+    entry << ln
+  when 0
+    entry << ln
+    q = entry[3].chomp.split('').map { |i| (i.ord - o[:offset]) }
+    q.map { |i| i < o[:qual] }.each_with_index { |i, k| entry[1][k] = 'N' if i }
+    ofh.puts(o[:fasta] ? [entry[0].gsub(/^@/, '>'), entry[1]] : entry)
+    entry = []
+  end
+end
+
+# Finalize
+say "  Lines: #{lno}"
+unless entry.empty?
+  raise Enveomics::ParseError.new('Unexpected trailing lines in FastQ')
+end
+say "  Sequences: #{lno / 4}"
+ifh.close
+ofh.close
+