miga-base 0.7.25.2 → 0.7.25.3

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

@@ -1,24 +0,0 @@
-#!/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

@@ -1,127 +0,0 @@
-#!/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

@@ -1,84 +0,0 @@
-#!/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

@@ -1,351 +0,0 @@
-#!/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