miga-base 0.7.26.0 → 0.7.26.1

data/utils/enveomics/Scripts/FastQ.toFastA.awk

@@ -0,0 +1,24 @@
+#!/usr/bin/env awk -f
+#
+# @author  Luis M. Rodriguez-R
+# @update  Dec-26-2015
+# @license artistic license 2.0
+#
+
+BEGIN {
+  for (i = 0; i < ARGC; i++) {
+     if(ARGV[i] == "--help"){
+       print "Description:\n"
+       print "  Translates FastQ files into FastA.\n"
+       print "Usage:\n"
+       print "  FastQ.toFastA.awk < in.fq > out.fa\n"
+       exit
+     }
+  }
+}
+
+NR%4 == 1, NR%4 == 2 {
+   if(NR%4 == 1){ gsub(/^@/,">") }
+   print $0
+}
+

data/utils/enveomics/Scripts/GFF.catsbj.pl

@@ -0,0 +1,127 @@
+#!/usr/bin/env perl
+
+# @author  Luis M. Rodriguez-R
+# @license Artistic-2.0
+
+use warnings;
+use strict;
+use List::Util qw/min max/;
+use Getopt::Std;
+
+sub HELP_MESSAGE { die "
+
+Description:
+  Generates a list of coordinates from a GFF table concatenating the subject
+  sequences.
+  
+  See also: BlastTab.recplot2.R and BlastTab.catsbj.pl
+
+Usage:
+  $0 [options] seq.fa map.gff > abs-coords.tsv
+
+  seq.fa	Subject sequences (contigs) in FastA format.
+  map.gff	Features to map in GFF.
+   
+  Options:
+  -L path       Generate a file with the absolute coordinates of the
+                concatenated contigs. This is identical to the .lim file
+                generated by BlastTab.catsbj.pl.
+  -i            Preserve exact coordinates and include inter-feature windows as
+                separate bins. By default, the coordinates are set in the
+                midpoint between features when non-contiguous.
+  -s		The FastA provided is to be treated as a subset of the subject.
+   		By default, it expects all the contigs to be present in the
+		BLAST.
+  -q		Run quietly.
+  -h		Display this message and exit.
+   
+"; }
+
+my %o;
+getopts('L:isqh', \%o);
+my($fa, $map) = @ARGV;
+($fa and $map) or &HELP_MESSAGE;
+$o{h} and &HELP_MESSAGE;
+
+my %seq = ();
+my @seq = ();
+my $tot = 0;
+
+SEQ:{
+  print STDERR "== Reading reference sequences\n" unless $o{q};
+  open FA, "<", $fa or die "Cannot read the file: $fa: $!\n";
+  my $cur_seq = '';
+  while(<FA>){
+    chomp;
+    if(m/^>(\S+)/){
+      my $c = $1;
+      $seq{$c} = exists $seq{$cur_seq} ? $seq{$cur_seq}+1 : 1;
+      push @seq, $c;
+      $cur_seq = $c;
+    }else{
+      s/[^A-Za-z]//g;
+      $seq{$cur_seq} += length $_;
+    }
+  }
+  close FA;
+  print STDERR " Found ".(scalar @seq)." sequences.\n" unless $o{q};
+}
+
+$o{L} ||= '/dev/null';
+open LIM, ">", $o{L} or die "Cannot create the file: $o{L}: $!\n";
+my $l = 0;
+for my $s (@seq){
+  print LIM "$s\t".(++$l)."\t$seq{$s}\n";
+  ($l, $seq{$s}) = ($seq{$s}, $l);
+}
+close LIM;
+
+MAP: {
+  print STDERR "== Reading mapping\n" unless $o{q};
+  open GFF, "<", $map or die "Cannot read the file: $map: $!\n";
+  my $last_end = 1;
+  my $last_name = "NA";
+  print "1\tNA\tNA\n";
+  my $i = 0;
+  FEATURE: while(<GFF>){
+    next if /^\s*(#.*)?$/; # Blank or comment lines
+    chomp;
+    my @ln = split /\t/;
+    $ln[4] or die "Cannot parse line $map:$.: $_\n";
+    unless(exists $seq{$ln[0]}){
+      die "Cannot find the subject sequence: $ln[0]\n" unless $o{s};
+      next FEATURE;
+    }
+    $i++;
+    my $start = $seq{$ln[0]}+$ln[3];
+    my $end   = $seq{$ln[0]}+$ln[4];
+    my $name  = "feat_$i";
+    if($ln[8] =~ /^gene_id=(\d+)/){ # <- GeneMark style
+      $name = "gene_id_$1";
+    }elsif($ln[8] =~ /^ID=\d+_(\d+)/){ # <- Prodigal style
+      $name = $ln[0]."_".$1;
+    }elsif($ln[8] =~ /^ID=([^;]+)/){
+      $name = $1;
+    }
+    if($o{i}){
+      $start = $last_end if $start < $last_end;
+      print "$start\t$last_name~$name\tGAP\n" unless $start==$last_end;
+      print "$end\t$name\tFEAT\n";
+    }else{
+      my $midpoint = int(($last_end + $start)/2);
+      print "$last_end\t$last_name\tFEAT\n" unless $last_end==1;
+    }
+    $last_name = $name;
+    $last_end = $end;
+  }
+  if($last_end > 1){
+    if($o{i}){
+      print "$l\t$last_name~NA\tGAP\n" unless $last_end==$l;
+    }else{
+      print "$l\t$last_name\tFEAT\n";
+    }
+  }
+  close GFF;
+  print STDERR " done.\n" unless $o{q};
+}
+

data/utils/enveomics/Scripts/GenBank.add_fields.rb

@@ -0,0 +1,84 @@
+#!/usr/bin/env ruby
+
+#
+# @author: Luis M. Rodriguez-R
+# @update: Feb-06-2015
+# @license: artistic license 2.0
+#
+
+require 'optparse'
+
+o = {:q=>FALSE, :k=>1, :split=>"#"}
+ARGV << '-h' if ARGV.size==0
+OptionParser.new do |opts|
+   opts.banner = "
+Adds annotations to GenBank files.
+
+Usage: #{$0} [options]"
+   opts.separator ""
+   opts.separator "Mandatory"
+   opts.on("-g", "--genbank FILE", "Input GenBank file."){ |v| o[:gb]=v }
+   opts.on("-t", "--table FILE", "Input file containing the annotations. It must be a ",
+   				"tab-delimited raw table including a header row with ",
+				"the names of the fields."){ |v| o[:table]=v }
+   opts.on("-o", "--out FILE", "Output file containing the annotated GenBank."){ |v| o[:out]=v }
+   opts.separator ""
+   opts.separator "Other Options"
+   opts.on("-k", "--key NUMBER", "Key of the column to use as identifier. By default: #{o[:k]}"){ |v| o[:k] = v.to_i }
+   opts.on("-s", "--split STRING", "String that separates multiple entries in the annotation features. By default: \"#{o[:split]}\""){ |v| o[:k] = 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 "-g is mandatory" if o[:gb].nil?
+abort "-t is mandatory" if o[:table].nil?
+abort "-o is mandatory" if o[:out].nil?
+
+##### MAIN:
+begin
+   puts "Reading annotation table: #{o[:table]}." unless o[:q]
+   ifh = File.open(o[:table], "r")
+   header = ifh.gets.chomp.split(/\t/)
+   puts "  * using #{header[ o[:k]-1 ]} column as feature identifier."
+   annot = {}
+   while ln=ifh.gets
+      row = ln.chomp.split(/\t/)
+      warn "WARNING: #{header[ o[:k]-1 ]} #{row[ o[:k]-1 ]} found more than once." unless annot[ row[ o[:k]-1 ] ].nil?
+      annot[ row[ o[:k]-1 ] ] = row
+   end
+   ifh.close
+   puts "  * found #{annot.size} annotation entries with #{header.size} fields." unless o[:q]
+   puts "Annotating GenBank." unless o[:q]
+   ifh = File.open(o[:gb], "r")
+   ofh = File.open(o[:out], "w")
+   found = 0
+   notfound = 0
+   while ln=ifh.gets
+      ofh.print ln
+      m = /^(?<sp>\s+)\/#{header[ o[:k]-1 ]}="(?<id>.+)"/.match(ln)
+      next if m.nil?
+      if annot[ m[:id] ].nil?
+	 notfound += 1
+	 next
+      end
+      found += 1
+      annot[ m[:id] ].each_index do |i|
+         next if i == o[:k]-1 or annot[ m[:id] ][i]==""
+	 annot[ m[:id] ][i].split(/#{o[:split]}/).each{ |v| ofh.puts "#{m[:sp]}/#{header[i]}=\"#{v}\"" }
+      end
+   end
+   ofh.close
+   ifh.close
+   puts "  * annotated #{found} features." unless o[:q]
+   puts "  * couldn't find #{notfound} features in the annotation table." unless o[:q] or notfound==0
+   $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/HMM.essential.rb

@@ -0,0 +1,351 @@
+#!/usr/bin/env ruby
+
+# @author  Luis M. Rodriguez-R
+# @license artistic license 2.0
+
+$:.push File.expand_path('../lib', __FILE__)
+require 'enveomics_rb/enveomics'
+use 'tmpdir'
+use 'zlib'
+
+o = {
+  bin: '', thr: 2, q: false, stats: true, genes: true, bacteria: false,
+  archaea: false, genomeeq: false, metagenome: false, list: false,
+  collection: 'dupont_2012'
+}
+OptionParser.new do |opts|
+  opts.banner = "
+Finds and extracts a collection of essential proteins suitable for genome
+completeness evaluation and phylogenetic analyses. Important note: most complete
+bacterial genomes contain only 106/111 genes in this collection, therefore
+producing a completeness of 95.5%, and most archaeal genomes only contain 26/111
+genes, producing a completeness of 23.4%. Use the options --bacteria and/or 
+--archaea to ignore models often missing in one or both domains. Note that even
+with these options, some complete archaeal genomes result in very low values of
+completeness (e.g., Nanoarchaeum equitans returns 88.5%).
+
+Requires HMMer 3.0+ (http://hmmer.janelia.org/software).
+
+Usage: #{$0} [options]"
+  opts.separator ''
+  opts.separator 'Mandatory'
+  opts.on(
+    '-i', '--in FILE',
+    'Path to the FastA file (.gz allowed) with all the proteins in a genome'
+  ) { |v| o[:in] = v }
+  opts.separator ''
+  opts.separator 'Options'
+  opts.on(
+    '-c', '--collection STR',
+    'Reference collection of essential proteins to use. One of:',
+    '> dupont_2012 (default): https://doi.org/10.1038/ismej.2011.189',
+    '  modified by https://doi.org/10.1038/ismej.2015.5',
+    '> lee_2019: https://doi.org/10.1093/bioinformatics/btz188',
+    '  modified by https://doi.org/10.7717/peerj.1319'
+  ) { |v| o[:collection] = v }
+  opts.on(
+    '-o', '--out FILE',
+    'Path to the output FastA file with the translated essential genes',
+    'By default the file is not produced'
+  ) { |v| o[:out] = v }
+  opts.on(
+    '-m', '--per-model STR',
+    'Prefix of translated genes in independent files with the name of the',
+    'model appended. By default files are not produced'
+  ) { |v| o[:permodel] = v }
+  opts.on(
+    '-R', '--report FILE',
+    'Path to the report file. By default, the report is sent to the STDOUT'
+  ) { |v| o[:report] = v }
+  opts.on(
+    '--hmm-out FILE',
+    'Save HMMsearch output in this file. By default, not saved'
+  ) { |v| o[:hmmout] = v }
+  opts.on(
+    '--alignments FILE',
+    'Save the aligned proteins in this file. By default, not saved'
+  ) { |v| o[:alignments] = v }
+  opts.on(
+    '-B', '--bacteria',
+    'If set, ignores models typically missing in Bacteria'
+  ) { |v| o[:bacteria] = v }
+  opts.on(
+    '-A', '--archaea',
+    'If set, ignores models typically missing in Archaea'
+  ) { |v| o[:archaea] = v }
+  opts.on(
+    '-G', '--genome-eq',
+    'If set, ignores models not suitable for genome-equivalents estimations',
+    'See Rodriguez-R et al, 2015, ISME J 9(9):1928-1940'
+  ) { |v| o[:genomeeq] = v }
+  opts.on(
+    '-r', '--rename STR',
+    'If set, renames the sequences with the string provided and appends it',
+    'with pipe and the gene name (except in --per-model files)'
+  ) { |v| o[:rename] = v }
+  opts.on(
+    '-n', '--no-stats',
+    'If set, no statistics are reported on genome evaluation'
+  ) { |v| o[:stats] = v }
+  opts.on(
+    '-s', '--no-genes',
+    'If set, statistics won\'t include the lists of missing/multi-copy genes'
+  ) { |v| o[:genes] = v }
+  opts.on(
+    '-M', '--metagenome',
+    'If set, it allows for multiple copies of each gene and turns on',
+    'metagenomic report mode'
+  ) { |v| o[:metagenome] = v }
+  opts.separator ''
+  opts.separator 'Other Options'
+  opts.on(
+    '-L', '--list-models',
+    'If set, it only lists the models and exits. Compatible with -A, -B, -G,',
+    'and -q; ignores all other parameters'
+  ) { |v| o[:list] = v }
+  opts.on(
+    '-b', '--bin DIR',
+    'Path to the directory containing the binaries of HMMer 3.0+'
+  ) { |v| o[:bin] = v }
+  opts.on(
+    '--model-file',
+    'External file containing models to search'
+  ) { |v| o[:model_file] = v }
+  opts.on(
+    '-t', '--threads INT', Integer,
+    "Number of parallel threads to be used.  By default: #{o[:thr]}"
+  ) { |v| o[:thr] = 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? and not o[:list]
+o[:bin] = o[:bin] + '/' if o[:bin].size > 0
+o[:rename] = nil if o[:metagenome]
+
+case o[:collection]
+when 'dupont_2012'
+  not_in_archaea = %w{GrpE Methyltransf_5 TIGR00001 TIGR00002 TIGR00009
+  TIGR00019 TIGR00029 TIGR00043 TIGR00059 TIGR00060 TIGR00061 TIGR00062
+  TIGR00082 TIGR00086 TIGR00092 TIGR00115 TIGR00116 TIGR00152 TIGR00158
+  TIGR00165 TIGR00166 TIGR00168 TIGR00362 TIGR00388 TIGR00396 TIGR00409
+  TIGR00418 TIGR00420 TIGR00422 TIGR00436 TIGR00459 TIGR00460 TIGR00472
+  TIGR00487 TIGR00496 TIGR00575 TIGR00631 TIGR00663 TIGR00775 TIGR00810
+  TIGR00855 TIGR00922 TIGR00952 TIGR00959 TIGR00963 TIGR00964 TIGR00967
+  TIGR00981 TIGR01009 TIGR01011 TIGR01017 TIGR01021 TIGR01024 TIGR01029
+  TIGR01030 TIGR01031 TIGR01032 TIGR01044 TIGR01049 TIGR01050 TIGR01059
+  TIGR01063 TIGR01066 TIGR01067 TIGR01071 TIGR01079 TIGR01164 TIGR01169
+  TIGR01171 TIGR01391 TIGR01393 TIGR01632 TIGR01953 TIGR02012 TIGR02013
+  TIGR02027 TIGR02191 TIGR02350 TIGR02386 TIGR02387 TIGR02397 TIGR02432
+  TIGR02729 TIGR03263 TIGR03594}
+  not_in_bacteria = %w{TIGR00389 TIGR00408 TIGR00471 TIGR00775 TIGR02387}
+  not_as_genomeeq = %w{TIGR02386 TIGR02387 TIGR00471 TIGR00472 TIGR00408
+  TIGR00409 TIGR00389 TIGR00436 tRNA-synth_1d}
+when 'lee_2019'
+  not_in_archaea = %w{ADK AICARFT_IMPCHas ATP-synt ATP-synt_A Chorismate_synt
+  EF_TS eIF-1a Exonuc_VII_L GrpE IPPT OSCP Pept_tRNA_hydro PGK RBFA RecO_C
+  Ribonuclease_P Ribosomal_L17 Ribosomal_L18p Ribosomal_L19 Ribosomal_L20
+  Ribosomal_L21p ribosomal_L24 Ribosomal_S3_C Ribosomal_L5 Ribosomal_L2
+  Ribosomal_L27 Ribosomal_L27A Ribosomal_L28 Ribosomal_L32p Ribosomal_L35p
+  Ribosomal_L9_C Ribosomal_S10 Ribosomal_S16 Ribosomal_S20p Ribosomal_S6
+  RNA_pol_L RRF RsfS RuvX SecE SecG SmpB tRNA_m1G_MT TsaE UPF0054 YajC}
+  not_in_bacteria = %w{AdoHcyase Archease ATP-synt_D ATP-synt_F CarS-like
+  CTP-dep_RFKase Diphthamide_syn DNA_primase_lrg dsDNA_bind DUF357 DUF359
+  DUF655 eIF-6 FbpA HMG-CoA_red NDK PPS_PS Prefoldin PTH2 PyrI Ribosomal_L15e
+  Ribosomal_L21e Ribosomal_L26 Ribosomal_L31e Ribosomal_L32e Ribosomal_L37ae
+  Ribosomal_L39 Ribosomal_L44 Ribosomal_L5e Ribosomal_S17e Ribosomal_S19e
+  Ribosomal_S24e Ribosomal_S27e Ribosomal_S28e Ribosomal_S3Ae Ribosomal_S8e
+  Rib_5-P_isom_A RNase_HII RNA_pol_L_2 RNA_pol_N RNA_pol_Rpb4 RtcB Spt4 TIM
+  Trm56 tRNA-synt_1c tRNA-synt_His TruD vATP-synt_AC39 vATP-synt_E V_ATPase_I}
+  not_as_genomeeq = not_in_archaea + not_in_bacteria
+else
+  raise "Unsupported collection: '#{o[:collection]}'"
+end
+
+begin
+  Dir.mktmpdir do |dir|
+    $stderr.puts "Temporal directory: #{dir}." unless o[:q]
+    if o[:in] =~ /\.gz/
+      tmp_in = File.expand_path('sequences.fa', dir)
+      Zlib::GzipReader.open(o[:in]) do |ifh|
+        File.open(tmp_in, 'w') { |ofh| ofh.print ifh.read }
+      end
+      o[:in] = tmp_in
+    end
+
+    # Create database.
+    $stderr.puts 'Searching models.' unless o[:q]
+    models = {}
+    model_id = nil
+    dbh = File.open("#{dir}/essential.hmm", 'w')
+    o[:model_file] ||= File.expand_path(
+      "../lib/data/#{o[:collection]}_essential.hmm.gz", __FILE__)
+    mfh = (File.extname(o[:model_file]) == '.gz') ?
+      Zlib::GzipReader.open(o[:model_file]) :
+      File.open(o[:model_file], 'r')
+    while ln = mfh.gets
+      dbh.print ln
+      ln.chomp!
+      model_id = $1 if ln =~ /^NAME\s+(.+)/
+      models[model_id] = $1 if ln =~ /^DESC\s+(.+)/
+    end
+    dbh.close
+    mfh.close
+    models.delete_if { |m| not_in_archaea.include? m  } if o[:archaea]
+    models.delete_if { |m| not_in_bacteria.include? m } if o[:bacteria]
+    models.delete_if { |m| not_as_genomeeq.include? m } if o[:genomeeq]
+    if o[:list]
+      models.each_pair{ |id,desc| puts [id,desc].join("\t") }
+      exit
+    end
+
+    # Check HMMer version and run HMMsearch.
+    if `"#{o[:bin]}hmmsearch" -h`.lines[1] !~ /HMMER 3/
+      raise 'You have provided an unsupported version of HMMER. ' +
+        'This script requires HMMER 3.0+.'
+    end
+    o[:hmmout] ||= "#{dir}/hmmsearch"
+    `'#{o[:bin]}hmmsearch' --cpu #{o[:thr]} --tblout '#{o[:hmmout]}' \
+      -A '#{dir}/a.sto' --cut_tc --notextw '#{dir}/essential.hmm' '#{o[:in]}' \
+      > '#{dir}/hmmsearch.log'`
+
+    # Parse output
+    $stderr.puts 'Parsing results.' unless o[:q]
+    trash = []
+    genes = {}
+    File.open(o[:hmmout], 'r') do |resh|
+      while ln = resh.gets
+         next if ln =~ /^#/
+         r = ln.split /\s+/
+         next unless models.include? r[2]
+         if o[:metagenome]
+           genes[ r[2] ] = [] if genes[ r[2] ].nil?
+           genes[ r[2] ] << r[0]
+         elsif genes[ r[2] ].nil?
+           genes[ r[2] ] = r[0]
+         else
+           trash << r[2]
+         end
+      end
+    end
+
+    # Report statistics
+    if o[:stats]
+      reph = o[:report].nil? ? $stdout : File.open(o[:report], 'w')
+      modifiers = [:bacteria, :archaea, :genomeeq]
+        .map { |i| o[i] ? i.to_s[0].upcase : '' }.join('')
+      reph.puts "! Collection: #{o[:collection]} #{modifiers}"
+      if o[:metagenome]
+        reph.printf "! Essential genes found: %d/%d.\n", genes.size, models.size
+        gc = [0] * (models.size - genes.size) +
+          genes.values.map{ |g| g.length }.sort
+        reph.printf "! Mean number of copies per model: %.3f.\n",
+          gc.inject(:+).to_f / models.size
+        reph.printf "! Median number of copies per model: %.1f.\n",
+          gc.size.even? ? gc[gc.size/2, 2].inject(:+).to_f / 2 : gc[gc.size/2]
+        if o[:genes] and genes.size != models.size
+          reph.printf "! Missing genes: %s\n",
+            ([''] + models.keys.select{ |m| not genes.keys.include? m }.
+                  map{|m| "#{m}: #{models[m]}."}).join("\n!   ")
+        end
+      else
+        reph.printf "! Essential genes found: %d/%d.\n", genes.size, models.size
+        reph.printf "! Completeness: %.1f%%.\n",
+          100.0 * genes.size / models.size
+        reph.printf "! Contamination: %.1f%%.\n",
+          100.0 * trash.size / models.size
+        if o[:genes]
+          reph.printf "! Multiple copies: %s\n",
+            ([''] + trash.uniq.
+                  map{ |m| "#{trash.count(m)+1} #{m}: #{models[m]}." }).
+                  join("\n!   ") unless trash.empty?
+          reph.printf "! Missing genes: %s\n",
+            ([''] + models.keys.select{ |m| not genes.keys.include? m }.
+                  map{ |m| "#{m}: #{models[m]}." }).
+                  join("\n!   ") unless genes.size == models.size
+        end
+      end
+      reph.close unless o[:report].nil?
+    end
+
+    # Extract sequences
+    unless o[:out].nil? and o[:permodel].nil?
+      $stderr.puts 'Extracting sequences.' unless o[:q]
+      faah = File.open(o[:in], 'r')
+      outh = o[:out].nil? ? nil : File.open(o[:out], 'w')
+      geneh = nil
+      in_gene = nil
+      unless o[:permodel].nil?
+        genes.keys.each do |m|
+          File.open("#{o[:permodel]}#{m}.faa", 'w').close
+        end
+      end
+      while ln = faah.gets
+        if ln =~ /^>(\S+)/
+          if o[:metagenome]
+            in_gene = genes.keys.
+              map{ |k| genes[k].include?($1) ? k : nil }.compact.first
+            in_gene = [in_gene, $1] unless in_gene.nil?
+          else
+            in_gene = genes.rassoc($1)
+          end
+          next if in_gene.nil?
+          geneh.close unless geneh.nil?
+          geneh = File.open("#{o[:permodel]}#{in_gene[0]}.faa", 'a+') unless
+            o[:permodel].nil?
+          outh.print(o[:rename].nil? ?
+            ln : ">#{o[:rename]}|#{in_gene[0]}\n") unless outh.nil?
+          geneh.print(o[:rename].nil? ? ln : ">#{o[:rename]}\n") unless
+            geneh.nil?
+        else
+          next if in_gene.nil?
+          outh.print ln unless outh.nil?
+          geneh.print ln unless geneh.nil?
+        end
+      end
+      geneh.close unless geneh.nil?
+      outh.close unless outh.nil?
+      faah.close
+    end
+
+    unless o[:alignments].nil?
+      aln = {}
+      File.open("#{dir}/a.sto", 'r') do |fh|
+        cur_model = nil
+        mask = []
+        fh.each_line do |ln|
+          case ln.chomp
+          when /^# STOCKHOLM/
+            cur_model = nil
+            mask = []
+          when /^#=GS (\S+)\/([\d\-]+)\s+DE/
+            cur_model ||= ( genes.rassoc($1) || [] ).first
+            aln[ cur_model ] ||= [ "# #{cur_model} : #{$1} : #{$2}" ]
+          when /^#=GC RF\s+(\S+)/
+            aln[ cur_model ][ 1 ] ||= $1.upcase.tap do |i|
+              mask.each{ |d| i[d] = '' }
+            end
+          when /^[^#]\S*\s+(\S+)/
+            next if aln[ cur_model ][ 2 ]
+            aln[ cur_model ][ 2 ] = $1.upcase
+            mask = aln[ cur_model ][ 2 ].split('').each_with_index.
+                map{ |v, k| v == '.' ? k : nil }.compact.reverse
+            aln[ cur_model ][ 2 ].delete!('.') unless mask.empty?
+          end
+        end
+      end
+      File.open(o[:alignments], 'w') do |fh|
+        aln.each { |k, v| v.each{ |i| fh.puts i } }
+      end
+    end
+
+    $stderr.puts 'Done.' unless o[:q]
+  end # |dir|
+rescue => err
+  $stderr.puts "Exception: #{err}\n\n"
+  err.backtrace.each { |l| $stderr.puts l + "\n" }
+  err
+end