miga-base 1.2.15.2 → 1.2.15.4

data/utils/enveomics/Scripts/BlastTab.addlen.rb

@@ -1,63 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R
-# @license: artistic license 2.0
-#
-
-require 'optparse'
-
-o = { sbj: false, q: false }
-ARGV << '-h' if ARGV.size == 0
-OptionParser.new do |opts|
-  opts.banner = "
-Appends an extra column to a BLAST with the length of the query or the subject
-sequence. You can pipe two instances to add both:
-  cat input.blast | #{$0} -f queries.fa | #{$0} -f subjects.fa -s > output.blast
-
-Usage: #{$0} [options] < input.blast > output.blast"
-  opts.separator ''
-  opts.separator 'Mandatory'
-  opts.on('-f', '--fasta FILE', 'Path to the FastA file'){ |v| o[:fasta] = v }
-  opts.separator ''
-  opts.separator 'Options'
-  opts.on('-s', '--subject',
-    'Use the subject column of the BLAST, by default the query column is used'
-    ){ o[:sbj] = true }
-  opts.on('-q', '--quiet', 'Run quietly (no STDERR output)'){ o[:q] = true }
-  opts.on('-h', '--help', 'Display this screen') do
-    puts opts
-    exit
-  end
-  opts.separator ''
-end.parse!
-abort '-f is mandatory' if o[:fasta].nil?
-
-len = {}
-id  = ''
-$stderr.puts "Reading FastA file: #{o[:fasta]}" unless o[:q]
-fh = File.open(o[:fasta], 'r')
-fh.each_line do |ln|
-   defline = /^>(\S+)/.match(ln)
-   if defline.nil?
-      ln.gsub! /[^A-Za-z]/, ''
-      abort 'Error: Unsupported format, expecting FastA' if len[id].nil?
-      len[id] = len[id] + ln.size
-   else
-      id = defline[1]
-      len[id] = 0
-   end
-end
-fh.close
-
-unless o[:q]
-  $stderr.puts 'Appending %s length column' % (o[:sbj] ? 'subject' : 'query')
-end
-ARGF.each_line do |ln|
-  ln.chomp!
-  row = ln.split /\t/
-  id = o[:sbj] ? row[1] : row[0]
-  abort "Impossible to find sequence of #{id}" if len[id].nil?
-  puts "#{ln}\t#{len[id]}"
-end
-

data/utils/enveomics/Scripts/BlastTab.advance.bash

@@ -1,48 +0,0 @@
-#!/bin/bash
-
-#
-# @author  Luis M. Rodriguez-R
-# @update  Mar-23-2016
-# @license artistic license 2.0
-#
-
-if [[ ! $2 ]] ; then
-   echo "
-.DESCRIPTION
-   Calculates the percentage of a partial BLAST result. The
-   value produced slightly subestimates the actual advance,
-   due to un-flushed output and trailing queries that could
-   be processed but generate no results.
-
-.USAGE
-   $0 blast.txt qry.fasta
-
-   blast.txt	Incomplete Tabular BLAST output.
-   qry.fasta	FastA file with query sequences.
-";
-   exit 1;
-fi
-
-if [[ ! -r $1 ]]; then
-   echo "Cannot open file: $1";
-   exit 1;
-fi
-
-if [[ ! -r $2 ]]; then
-   echo "Cannot open file: $2";
-   exit 1;
-fi
-
-LAST_Q=`tail -n 2 $1 | head -n 1 | awk '{print $1}'`
-LAST_Q_NO=`grep -n "^>$LAST_Q\\( \\|$\\)" $2 | sed -e 's/:.*//'`
-if [[ ! $LAST_Q_NO ]]; then
-   echo "Cannot find sequence: $LAST_Q";
-   echo "Make sure you are providing the right query file.";
-   exit 1;
-fi
-TOTAL_Q_NO=`cat $2 | wc -l | sed -e 's/ *//'`
-let PERC=100*$LAST_Q_NO/$TOTAL_Q_NO
-
-echo "$PERC%: $LAST_Q_NO / $TOTAL_Q_NO"
-exit 0;
-

data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl

@@ -1,55 +0,0 @@
-#!/usr/bin/env perl
-
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license: artistic license 2.0
-# @last_update: Mar-23-2015
-#
-
-use strict;
-use warnings;
-
-die "
-Usage:
-   sort blast.txt ... | $0 > blast.bh.txt
-   $0 blast_sorted.txt ... > blast.bh.txt
-   $0 -h|--help|-?
-
-   blast.txt ...	One or more files in Tabular BLAST format.
-   blast_sorted.txt ...	One or more files in Tabular BLAST format pre-sorted.
-   blast.bh.txt		Output file in BLAST format containing best-hits only.
-   -h|--help|-?		Any of these flags trigger this help message and exits.
-
-   NOTE: This script assumes that the BLAST is sorted.  Because it can read
-   from the STDIN, calling this script without arguments cause it to still until
-   killed or until an EOF (^D) is presented.
-
-" if exists $ARGV[0] and $ARGV[0] =~ /^\-?\-(h(elp)?|\?)/i;
-
-my $last_qry = '';
-my @best_res;
-
-sub best_result($$){
-   my($r1, $r2)=@_;
-   return $r1 unless $r2;
-   return $r1->[11] > $r2->[11] ? @$r1 : @$r2;
-}
-
-my $i=0;
-while(<>){
-   chomp;
-   #print STDERR " Reading entry $i...                             \r" unless $i%1000;
-   my @res = split /\t/;
-   die "\nCannot parse BLAST line $.: $_\n" unless exists $res[1];
-   if($last_qry eq $res[0]){
-      @best_res = &best_result(\@res, \@best_res);
-   }else{
-      print join("\t", @best_res), "\n" if $#best_res>0;
-      @best_res = @res;
-      $last_qry = $res[0];
-   }
-}
-print join("\t", @best_res), "\n" if @best_res;
-
-
-

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

@@ -1,104 +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 hits from a BLAST result concatenating the subject
-  sequences.  This can be used, e.g., to analyze BLAST results against
-  draft genomes.
-
-Usage:
-  $0 [options] seq.fa map.bls
-
-  seq.fa	Subject sequences (ref) in FastA format.
-  map.bls	Mapping of the reads to the reference in BLAST Tabular
-   		format.
-   
-  Options:
-  -i <float>	Minimum identity to report a result.  By default: 70.
-  -l <int>	Minimum alignment length to report a result.  By default: 60.
-  -s		The FastA provided is to be treated as a subset of the subject.
-   		By default, it expects all the BLAST subjects to be present in
-		the FastA.
-  -q		Run quietly.
-  -h		Display this message and exit.
-   
-  This script creates two files using <map.bls> as prefix with extensions
-  .rec (for the recruitment plot) and .lim (for the limits of the different
-  sequences in <seq.fa>).
-
-";}
-
-my %o;
-getopts('i:l:sqh', \%o);
-my($fa, $map) = @ARGV;
-($fa and $map) or &HELP_MESSAGE;
-$o{h} and &HELP_MESSAGE;
-$o{i} ||= 70;
-$o{l} ||= 60;
-
-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 $o{q};
-}
-
-open LIM, ">", "$map.lim" or die "Cannot create the file: $map.lim: $!\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 BLS, "<", $map or die "Cannot read the file: $map: $!\n";
-  open REC, ">", "$map.rec" or die "Cannot create the file: $map.rec: $!\n";
-  RESULT: while(<BLS>){
-    chomp;
-    my @ln = split /\t/;
-    $ln[11] or die "Cannot parse line $map:$.: $_\n";
-    next unless $ln[3]>=$o{l};
-    next unless $ln[2]>=$o{i};
-    unless(exists $seq{$ln[1]}){
-      die "Cannot find the subject sequence: $ln[1]\n" unless $o{s};
-      next RESULT;
-    }
-    my $start = $seq{$ln[1]}+min($ln[8], $ln[9]);
-    my $end   = $seq{$ln[1]}+max($ln[8], $ln[9]);
-    print REC "$start\t$end\t$ln[2]\t$ln[11]\t$ln[0]",
-          (exists($ln[13])?"\t".($ln[2]*$ln[3]/min($ln[12],$ln[13]))."\t":
-          exists($ln[12])?"\t".($ln[2]*$ln[3]/$ln[12])."\t":""),"\n";
-  }
-  close BLS;
-  close REC;
-  print STDERR " done.\n" unless $o{q};
-}
-

data/utils/enveomics/Scripts/BlastTab.cogCat.rb

@@ -1,76 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Mar-23-2016
-# @license artistic license 2.0
-#
-
-require "optparse"
-
-o = {:cog=>false, :desc=>false, :q=>false, :w=>true}
-ARGV << "-h" if ARGV.size==0
-OptionParser.new do |opts|
-   opts.banner = "Replaces the COG gene IDs in a BLAST for the COG category."
-   opts.separator ""
-   opts.separator "Mandatory"
-   opts.on("-w", "--whog FILE", "Path to the whog file."){ |v| o[:whog]=v }
-   opts.on("-i", "--blast FILE",
-      "Path to the Tabular BLAST file with COG IDs as subject."
-      ){ |v| o[:blast]=v }
-   opts.separator ""
-   opts.separator "Optional"
-   opts.on("-g", "--cog",
-      "If set, returns the COG ID, not the COG category."){ o[:cog]=true }
-   opts.on("-d", "--desc",
-      "Includes COG description (requires -g/--cog)."){ o[:desc]=true }
-   opts.on("-n", "--noverbose", "Run quietly, but show warnings."){ o[:q]=true }
-   opts.on("-q", "--quiet", "Run quietly."){ o[:q]=true; o[:w]=false }
-   opts.on("-h", "--help", "Display this screen") do
-      puts opts
-      exit
-   end
-   opts.separator ""
-end.parse!
-
-abort "-w/--whog is mandatory." if o[:whog].nil?
-abort "-i/--blast is mandatory." if o[:blast].nil?
-
-$stderr.puts "Parsing whog file." unless o[:q]
-cat = {}
-curCats = []
-fh = File.open o[:whog], "r"
-while ln=fh.gets
-   ln.chomp!
-   next if /^\s*$/.match ln
-   if m=/^\[([A-Z]+)\] (COG\d+) (.*)/.match(ln)
-      curCats = o[:cog] ? [ m[2]+(o[:desc]?" #{m[3]}":"") ] : m[1].split(//)
-   elsif /^_+$/.match ln
-      curCats = []
-   elsif m=/^\s+(?:.+?:\s+)?(.*)/.match(ln)
-      m[1].split(/\s+/).each do |g|
-         cat[g] ||= []
-	 curCats.each { |i| cat[g] << i }
-      end
-   else
-      abort "Impossible to parse line #{$.}: #{ln}"
-   end
-end
-fh.close
-
-$stderr.puts "Parsing BLAST." unless o[:q]
-fh = File.open(o[:blast], "r")
-while ln=fh.gets
-   row = ln.split(/\t/)
-   if cat[ row[1] ].nil?
-      $stderr.puts "Warning: line #{$.}: #{row[1]}: " +
-	 "Impossible to find category.\n" if o[:w]
-   else
-      cat[ row[1] ].each do |c|
-         row[1] = c
-	 puts row.join("\t")
-      end
-   end
-end
-fh.close
-

data/utils/enveomics/Scripts/BlastTab.filter.pl

@@ -1,47 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Mar-23-2015
-# @license: artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-my %o;
-getopts('si', \%o);
-my($list, $blast) = @ARGV;
-
-($list and $blast) or die "
-.Description:
-   Extracts a subset of hits (queries or subjects) from a tabular BLAST.
-
-.Usage: $0 [options] list.txt blast.txt > subset.txt
-   
-   Options:
-      -s	If set, assumes that list.txt contains subject IDs.
-   		By default: assumes query IDs.
-      -i	If set, reports the inverse of the list (i.e., reports
-      		only hits absent in the list).
-
-   list.txt	List of IDs to extract.
-   blast.txt	Tabular BLAST file containing the superset of hits.
-   subset.txt	Tabulat BLAST file to be created.
-
-";
-
-open LI, "<", $list or die "Cannot read file: $list: $!\n";
-my %li = map { chomp; $_ => 1 } <LI>;
-close LI;
-
-open BLAST, "<", $blast or die "Cannot read file: $blast: $!\n";
-while(my $ln = <BLAST>){
-   chomp $ln;
-   my @ln = split("\t", $ln);
-   my $good = exists $li{$ln[ ($o{s} ? 1 : 0) ]};
-   $good = not $good if $o{i};
-   print "$ln\n" if $good;
-}
-close BLAST;
-

data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl

@@ -1,194 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-use LWP::Simple;
-use JSON;
-use File::Copy;
-
-my($blast, $cache_file, $max_cache) = @ARGV;
-($blast) or die "
-Description:
-   Takes a BLAST against KEGG_PEP (or KO) and retrieves the pathways in which the subject
-   peptides are involved.
-
-Usage:
-   $0 blast.txt[ cache_file] > output.txt
-
-   blast.txt	Input (filtered) BLAST file.
-   cache_file	(optional) File containing the saved cache.  If unset, the
-   		cache won't be recoverable across instances of this script.
-		It is strongly recommended to set a file.  Multiple
-		parallel instances of this script may use the same cache
-		file.
-   output.txt	Tab-delimited output file, with the columns:
-   		 o Query ID
-		 o Subject ID
-		 o Pathway ID
-		 o Pathway (reference) description
-		 o Organism
-
-";
-
-$max_cache ||= 0;
-$cache_file ||= "";
-
-sub read_cache($){
-   my ($cache_file) = @_;
-   my $cache = {};
-   my $n = 0;
-   if($cache_file and -s $cache_file){
-      local $/;
-      my $json = "";
-      while(-e "$cache_file.tmp"){
-         print STDERR "Locked cache (read), waiting 1 sec.\n";
-	 sleep 1;
-      }
-      open CACHE, "<", $cache_file or die "Cannot read file: $cache_file: $!\n";
-      while(<CACHE>){ $json.=$_ }
-      close CACHE;
-      $cache = decode_json($json);
-      $n = scalar keys %$cache;
-   }
-   return ($cache, $n);
-}
-
-sub write_cache($$){
-   my($cache, $cache_file) = @_;
-   if($cache_file){
-      # Get previously saved entries.
-      my($cache2, $cache_n2) = &read_cache($cache_file);
-      for my $k (keys %$cache2){
-	 $cache->{$k} ||= $cache2->{$k} unless $k eq "###:paths";
-      }
-      $cache->{'###:paths'} ||= {};
-      for my $p (keys %{$cache2->{'###:paths'}}){
-         $cache->{'###:paths'}->{$p} ||= $cache2->{'###:paths'}->{$p};
-      }
-      # Save merged cache.
-      if(-s $cache_file){ copy $cache_file, "$cache_file.pre" or die "Cannot create file: $cache_file.tmp: $!\n" }
-      my $json = encode_json($cache);
-      while(-e "$cache_file.tmp"){
-         print STDERR "Locked cache (write), waiting 1 sec.\n";
-	 sleep 1;
-      }
-      open CACHE, ">", "$cache_file.tmp" or die "Cannot create file: $cache_file.tmp: $!\n";
-      print CACHE $json;
-      close CACHE;
-      copy "$cache_file.tmp", $cache_file or die "Cannot create file: $cache_file: $!\n";
-      unlink "$cache_file.tmp" or die "Cannot unlink file: $cache_file.tmp: $!\n";
-   }
-}
-
-sub download_pathways($$){
-   my($cache, $ids) = @_;
-   my @todownload = ();
-   for my $id (@$ids){
-      push @todownload, $id unless exists $cache->{'###:paths'}->{$id};
-   }
-   while($#todownload>=0){
-      my @downloading = splice(@todownload, 0, 100);
-      my $path = get "http://rest.kegg.jp/list/".join("+", @downloading);
-      if($path){
-	 chomp $path;
-	 for my $p (split /\n/, $path){
-	    my @wl = split /\t/, $p;
-	    $wl[1] =~ s/ - /\t/;
-	    $cache->{'###:paths'}->{$wl[0]} = $wl[1];
-	 }
-      }
-   }
-   return $cache;
-}
-
-sub download($$){
-   my($cache, $todownload) = @_;
-   $cache->{'###:paths'} ||= {};
-   return $cache unless $#$todownload>=0;
-   $cache->{$_} = [] for @$todownload;
-   my $list = get "http://rest.kegg.jp/link/pathway/".join("+", @$todownload);
-   $list ||= "";
-   chomp $list;
-   my @pathids = ();
-   for my $res (split /\n/, $list){
-      my @rel = split /\t/, $res;
-      $#rel==1 or die "Unexpected number of columns:\n$res\n";
-      my $id = $rel[1];
-      push @pathids, $id;
-      unless(exists $cache->{$rel[0]}){
-	 #print STDERR "Request/response difference in ID: ".$rel[0].", searching match.\n";
-         for my $id (@$todownload){
-	    $rel[0] = $id if lc $id eq lc $rel[0];
-	 }
-	 die "Cannot find corresponding request.\n" unless exists $cache->{$rel[0]};
-      }
-      push @{ $cache->{$rel[0]} }, $id;
-   }
-   return &download_pathways($cache, \@pathids);
-}
-
-sub print_out($$){
-   my($cache, $hits) = @_;
-   for my $hit (@$hits){
-      die "Impossible to find gene in cache: ".$hit->[1]."\n" unless exists $cache->{$hit->[1]};
-      for my $path (@{$cache->{$hit->[1]}}){
-	 next if $path =~ /^path:ko\d/;
-	 unless(exists $cache->{'###:paths'}->{$path}){
-	    print STDERR "Cannot find pathway in cache: $path (from ".$hit->[1]."), emergency download\n";
-	    $cache = &download_pathways($cache, [$path]);
-	    die "Impossible to find pathway: $path.\n" unless exists $cache->{'###:paths'}->{$path};
-	 }
-	 print "", join("\t", $hit->[0], $hit->[1], $path, $cache->{'###:paths'}->{$path}), "\n";
-      }
-   }
-}
-
-print STDERR "Loading cache.\n";
-my ($cache, $n) = &read_cache($cache_file);
-print STDERR "   $n entries loaded.\n";
-my @nopath = ();
-for my $k (keys %$cache){
-   next if $k eq "###:paths";
-   for my $p (@{ $cache->{$k} }){
-      push @nopath, $p unless exists $cache->{'###:paths'}->{$p};
-   }
-}
-if($#nopath>=0){
-   print STDERR "   Sanitizing ".@nopath." pathways in cache.\n";
-   while($#nopath>=0){
-      my @paths = ();
-      for(1 .. 15){ push @paths, shift @nopath unless $#nopath==-1 }
-      $cache = &download_pathways($cache, \@paths);
-   }
-   &write_cache($cache, $cache_file);
-}
-
-my $lines=0;
-my $downs=0;
-my @buff = ();
-my @todownload = ();
-print STDERR "Mapping genes.\n";
-open BLAST, "<", $blast or die "Cannot read file: $blast: $!\n";
-while(<BLAST>){
-   chomp;
-   my @l = split /\t/;
-   print STDERR "   Mapping line ".(++$lines).". \r";
-   unless(($#todownload+2)%100){
-      print STDERR "+\r";
-      print STDERR " *\r" unless ++$downs%10;
-      $cache = &download($cache, \@todownload);
-      @todownload = ();
-      &print_out($cache, \@buff);
-      @buff = ();
-      &write_cache($cache, $cache_file) unless $downs%10;
-   }
-   push @buff, \@l;
-   push @todownload, $l[1] unless exists $cache->{$l[1]};
-}
-print STDERR "\nDone.\n";
-close BLAST;
-
-$cache = &download($cache, \@todownload);
-&print_out($cache, \@buff);
-&write_cache($cache, $cache_file);
-

data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl

@@ -1,104 +0,0 @@
-#!/usr/bin/env perl
-
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update Mar-23-2015
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-
-sub HELP_MESSAGE { die "
-Usage:
-   $0 [options] genes.txt blast.txt ... > blast_metaxa.txt
-
-   genes.gff2		File containing the genes in any supported format
-   			(see option -f).
-   blast.txt ...	One or more tabular BLAST files.
-   blast_metaxa.txt	Input file for MeTaxa.
-
-   Options:
-   -l <float>		Minimum fraction of the gene aligned to consider a
-   			hit.  By default: 0.75.  Ignored if -f 'no'.
-   -f <str>		Format of the genes prediction.  Any of:
-   			 o gff2: GFF v2 as produced by MetaGeneMark.hmm.
-			 o gff3: GFF v3 with id field in the last column.
-			 o tab: Tabular file with columns gene, gene length,
-			   and contig.
-			 o no: Ignores genes file.
-			By default: gff2.
-   -q			Run quietly.
-   -h			Display this message and exit.
-
-";}
-
-my %o;
-getopts('l:f:qh',\%o);
-my($gff, @blasts) = @ARGV;
-($gff and $#blasts>=0) or &HELP_MESSAGE;
-$o{h} and &HELP_MESSAGE;
-$o{f} ||= "gff2";
-$o{f} = lc $o{f};
-$o{l} ||= 0.75;
-
-my %gene;
-if($o{f} ne 'no'){
-   print STDERR "Reading genes collection.\n" unless $o{q};
-   open GFF, "<", $gff or die "Cannot read file: $gff: $!\n";
-   while(<GFF>){
-      next if /^#/;
-      next if /^\s*$/;
-      chomp;
-      my @ln = split /\t/;
-      if($o{f} eq 'gff2'){
-	 exists $ln[8] or die "Cannot parse line $.: $_\n";
-	 my $id = $ln[8];
-	 $id =~ s/gene_id /gene_id_/;
-	 $ln[0] =~ s/ .*//;
-	 $gene{$id} = [$ln[0], (1+$ln[4]-$ln[3])/3];
-      }elsif($o{f} eq 'gff3'){
-	 exists $ln[8] or die "Cannot parse line $.: $_\n";
-	 $ln[8] =~ /id=([^;]+)/ or die "Cannot parse line $.: $_\n";
-	 my $id = $1;
-	 $ln[0] =~ s/ .*//;
-	 $gene{$id} = [$ln[0], (1+$ln[4]-$ln[3])/3];
-      }elsif($o{f} eq 'tab'){
-         exists $ln[2] or die "Cannot parse line $.: $_\n";
-	 $ln[1]+0 or die "$ln[0]: Length zero.\n";
-         $gene{$ln[0]} = [$ln[2], $ln[1]/3];
-      }else{
-         die "Unsupported format: ".$o{f}.".\n";
-      }
-   }
-   close GFF;
-}
-
-my $i=0;
-my $p=0;
-print STDERR "Generating MeTaxa input.\n" unless $o{q};
-for my $blast (@blasts){
-   print STDERR "  o $blast\n" unless $o{q};
-   open BLAST, "<", $blast or die "Cannot read file: $blast: $!\n";
-   while(<BLAST>){
-      chomp;
-      my @l = split /\t/;
-      $i++;
-      my $ctg;
-      if($o{f} eq 'no'){
-         $ctg = $l[0];
-      }else{
-	 exists $gene{$l[0]} or die "Cannot find contig for gene $l[0].\n";
-	 next unless $l[3] >= $o{l}*$gene{$l[0]}->[1];
-	 $ctg = $gene{$l[0]}->[0];
-      }
-      $l[1] =~ m/gi\|(\d+)\|/ or die "Cannot parse GI in $l[1].\n";
-      print "".join("\t", @l, $ctg, $l[0], $1)."\n";
-      $p++;
-   }
-   close BLAST;
-}
-print STDERR " Found $i results, reported $p.\n" unless $o{q};
-