miga-base 0.7.24.0 → 0.7.26.0

data/utils/enveomics/Scripts/AAsubs.log2ratio.rb

@@ -1,171 +0,0 @@
-#!/usr/bin/env ruby
-#
-# @author  Luis M. Rodriguez-R
-# @update  Dec-21-2015
-# @license artistic license 2.0
-#
-
-$:.push File.expand_path(File.dirname(__FILE__) + "/lib")
-require "enveomics_rb/enveomics"
-
-o = {permutations: 1000, bootstraps: 1000, overwrite: false}
-OptionParser.new do |opt|
-   opt.banner = "
-   Estimates the log2-ratio of different amino acids in homologous sites using
-   an AAsubs file (see BlastPairwise.AAsubs.pl). It provides the point
-   estimation (.obs file), the bootstrap of the estimation (.boot file) and the
-   null model based on label-permutation (.null file).
-
-   Usage: #{$0} [options]".gsub(/^ +/,"")
-   opt.separator ""
-   opt.separator "Mandatory"
-   opt.on("-i", "--input FILE",
-      "Input file in AAsubs format (see BlastPairwise.AAsubs.pl)."
-      ){ |v| o[:file] = v}
-   opt.separator ""
-   opt.separator "Output files"
-   opt.on("-O", "--obs-file FILE",
-      "Output file with the log2-ratios per amino acid.",
-      "By default, '--input value'.obs."
-      ){ |v| o[:obs] = v }
-   opt.on("-B", "--bootstrap-file FILE",
-      "Output file with the bootstrap results of log2-ratios per amino acid.",
-      "By default, '--input value'.boot."
-      ){ |v| o[:boot] = v }
-   opt.on("-N", "--null-file FILE",
-      "Output file with the permutation results of log2-ratios per amino acid.",
-      "By default, '--input value'.null."
-      ){ |v| o[:null] = v }
-   opt.on("--overwrite",
-      "Overwrite existing files. By default, skip steps if the files already" +
-      " exist."){ |v| o[:overwrite] = v }
-   opt.separator ""
-   opt.separator "Parameters"
-   opt.on("-b", "--bootstraps INT",
-      "Number of bootstraps to run. By default: #{o[:bootstraps]}."
-      ){ |v| o[:bootstraps] = v.to_i }
-   opt.on("-p", "--permutations INT",
-      "Number of permutations to run. By default: #{o[:permutations]}."
-      ){ |v| o[:permutations] = v.to_i }
-   opt.on("-q", "--quiet", "Run quietly (no STDERR output)."){ o[:q] = TRUE }
-   opt.on("-h", "--help", "Display this screen.") do
-      puts opt
-      exit
-   end
-   opt.separator ""
-end.parse!
-
-# Initialize
-abort "--input is mandatory" if o[:file].nil?
-ALPHABET = %w(A C D E F G H I K L M N P Q R S T V W Y X)
-o[:obs] ||= "#{o[:file]}.obs"
-o[:boot] ||= "#{o[:file]}.boot"
-o[:null] ||= "#{o[:file]}.null"
-
-# Functions
-def dist_summary(a,b)
-   ALPHABET.map do |i|
-      Math.log(a[i].reduce(0,:+).to_f/b[i].reduce(0,:+), 10)
-   end
-end
-def empty_sample
-   Hash[ALPHABET.map{|k| [k, []]}]
-end
-
-# Initialize
-$stderr.puts "Initializing." unless o[:q]
-sample_A = empty_sample
-sample_B = empty_sample
-last_label = nil
-prot_index = -1
-
-# Read file
-$stderr.puts "Reading input file." unless o[:q]
-ifh = File.open(o[:file], "r")
-ifh.each do |l|
-   r = l.chomp.split /\t/
-   if r.first != last_label
-      prot_index +=1
-      last_label = r.first
-      ALPHABET.each do |a|
-         sample_A[a][prot_index] = 0
-         sample_B[a][prot_index] = 0
-      end
-   end
-   [1,2].each do |ds|
-      unless %w(- *).include? r[ds]
-	 abort "Unknown amino acid in line #{$.}: '#{r[ds]}'." unless
-	    ALPHABET.include? r[ds]
-	 sample_A[ r[ds] ][ prot_index ] += 1 if ds==1
-	 sample_B[ r[ds] ][ prot_index ] += 1 if ds==2
-      end
-   end
-end
-ifh.close
-$stderr.puts "  > Found #{prot_index+1} proteins." unless o[:q]
-$stderr.puts "  > Saving #{o[:obs]}" unless o[:q]
-sum = dist_summary(sample_A, sample_B)
-File.open(o[:obs], "w") do |fh|
-   fh.puts ["AA", "log10_AB"].join("\t")
-   ALPHABET.each do |i|
-      fh.puts [i, sum.shift].join("\t")
-   end
-end
-
-# Permutations
-if File.size? o[:null] and not o[:overwrite]
-   $stderr.puts "Skipping permutations." unless o[:q]
-else
-   $stderr.puts "Permutating." unless o[:q]
-   permut_sum = []
-   o[:permutations].times do |i|
-      permut_A = empty_sample
-      permut_B = empty_sample
-      (0 .. prot_index).each do |j|
-	 # Copy counts of the protein
-	 ALPHABET.each do |k|
-	    permut_A[k][j] = sample_A[k][j]
-	    permut_B[k][j] = sample_B[k][j]
-	 end
-	 # Swap labels at random
-	 permut_A,permut_B = permut_B,permut_A if rand(2)==1
-      end
-      permut_sum << dist_summary(permut_A, permut_B)
-   end
-   $stderr.puts "  > Performed #{o[:permutations]} permutations." unless o[:q]
-   $stderr.puts "  > Saving #{o[:null]}" unless o[:q]
-   File.open(o[:null], "w") do |fh|
-      fh.puts ALPHABET.join("\t")
-      permut_sum.each{ |s| fh.puts s.join("\t") }
-   end
-end
-
-# Bootstraps
-if File.size? o[:boot] and not o[:overwrite]
-   $stderr.puts "Skipping bootstraps." unless o[:q]
-else
-   $stderr.puts "Bootstrapping." unless o[:q]
-   boot_sum = []
-   o[:bootstraps].times do |i|
-      boot_A = empty_sample
-      boot_B = empty_sample
-      (0 .. prot_index).each do |j|
-	 # Sample randomly with replacement
-	 jr = rand(prot_index+1)
-	 # Copy counts of the protein
-	 ALPHABET.each do |k|
-	    boot_A[k][j] = sample_A[k][jr]
-	    boot_B[k][j] = sample_B[k][jr]
-	 end
-      end
-      boot_sum << dist_summary(boot_A, boot_B)
-   end
-   $stderr.puts "  > Performed #{o[:bootstraps]} bootstraps." unless o[:q]
-   $stderr.puts "  > Saving #{o[:boot]}" unless o[:q]
-   File.open(o[:boot], "w") do |fh|
-      fh.puts ALPHABET.join("\t")
-      boot_sum.each{ |s| fh.puts s.join("\t") }
-   end
-end
-
-$stderr.puts "Done. Yayyy!" unless o[:q]

data/utils/enveomics/Scripts/Aln.cat.rb

@@ -1,163 +0,0 @@
-#!/usr/bin/env ruby
-#
-# @author  Luis M. Rodriguez-R
-# @update  Nov-30-2015
-# @license artistic license 2.0
-#
-
-$:.push File.expand_path(File.dirname(__FILE__) + "/lib")
-require "enveomics_rb/enveomics"
-
-o = {:q=>false, :missing=>"-", :model=>"AUTO", :removeinvar=>false,
-   :undefined=>"-.Xx?"}
-OptionParser.new do |opt|
-   opt.banner = "
-   Concatenates several multiple alignments in FastA format into a single
-   multiple alignment.  The IDs of the sequences (or the ID prefixes, if using
-   --ignore-after) must coincide across files.
-
-   Usage: #{$0} [options] aln1.fa aln2.fa ... > aln.fa".gsub(/^ +/,"")
-   opt.separator ""
-   opt.on("-c", "--coords FILE",
-      "Output file of coordinates in RAxML-compliant format."
-      ){ |v| o[:coords]=v }
-   opt.on("-i", "--ignore-after STRING",
-      "Remove everything in the IDs after the specified string."
-      ){ |v| o[:ignoreafter]=v }
-   opt.on("-I", "--remove-invariable", "Remove invariable sites.",
-      "Note: Invariable sites are defined as columns with only one state and",
-      "undefined characters.  Additional ambiguous characters may exist and",
-      "should be declared using --undefined."){ |v| o[:removeinvar]=v }
-   opt.on("-u", "--missing-char CHAR",
-      "Character denoting missing data. By default: '#{o[:missing]}'.") do |v|
-	 abort "Missing positions can only be denoted by single characters, " +
-	    "offending value: '#{v}'." if v.length != 1
-	 o[:missing]=v
-      end
-   opt.on("-m", "--model STRING",
-      "Name of the model to use if --coords is used. See RAxML's docs; ",
-      "supported values in v8+ include:",
-      "o For DNA alignments:",
-      "  'DNA[F|X]', or 'DNA[F|X]/3' (to estimate rates per codon position,",
-      "  particular notation for this script).",
-      "o General protein alignments:",
-      "  'AUTO' (default in this script), 'DAYHOFF' (1978), 'DCMUT' (MBE 2005;",
-      "  22(2):193-199), 'JTT' (Nat 1992;358:86-89), 'VT' (JCompBiol 2000;",
-      "  7(6):761-776), 'BLOSUM62' (PNAS 1992;89:10915), and 'LG' (MBE 2008;",
-      "  25(7):1307-1320).",
-      "o Specialized protein alignments:",
-      "  'MTREV' (mitochondrial, JME 1996;42(4):459-468), 'WAG' (globular, MBE",
-      "  2001;18(5):691-699), 'RTREV' (retrovirus, JME 2002;55(1):65-73), ",
-      "  'CPREV' (chloroplast, JME 2000;50(4):348-358), and 'MTMAM' (nuclear",
-      "  mammal proteins, JME 1998;46(4):409-418)."){|v| o[:model]=v}
-   opt.on("--undefined STRING",
-      "All characters to be regarded as 'undefined'. It should include all",
-      "ambiguous and missing data chars.  Ignored unless --remove-invariable.",
-      "By default: '#{o[:undefined]}'."){|v| o[:undefined]=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!
-alns = ARGV
-abort "Alignment files are mandatory" if alns.nil? or alns.empty?
-
-##### MAIN:
-begin
-   $stderr.puts "Reading." unless o[:q]
-   a = {}
-   n = alns.size-1
-   lengths = []
-   (0 .. n).each do |i|
-      key = nil
-      File.open(alns[i],"r").each do |ln|
-	 ln.chomp!
-	 if ln =~ /^>(\S+)/
-	    key = $1
-	    key.sub!(/#{o[:ignoreafter]}.*/,"") unless o[:ignoreafter].nil?
-	    a[key] ||= []
-	    a[key][i] = ""
-	 else
-	    abort "#{alns[i]}: Leading line is not a def-line, is this a "+
-	       "valid FastA file?" if key.nil?
-	    ln.gsub!(/\s/,"")
-	    a[key][i] += ln
-	 end
-      end
-      abort "#{alns[i]}: Empty alignment?" if key.nil?
-      lengths[i] = a[key][i].length
-   end
-   if o[:removeinvar]
-      $stderr.puts "Removing invariable sites." unless o[:q]
-      invs = 0
-      (0 .. n).each do |i|
-	 olen = lengths[i]
-	 (0 .. (lengths[i]-1)).each do |pos|
-	    chr = nil
-	    inv = true
-	    a.keys.each do |key|
-	       next if a[key][i].nil?
-	       chr = a[key][i][pos] if
-		  chr.nil? or o[:undefined].chars.include? chr
-	       if chr != a[key][i][pos] and
-		     not o[:undefined].chars.include? a[key][i][pos]
-		  inv = false
-		  break
-	       end
-	    end
-	    if inv
-	       a.keys.each{|key| a[key][i][pos]="!" unless a[key][i].nil?}
-	       lengths[i] -= 1
-	       invs += 1
-	    end
-	 end
-	 a.keys.each{|key| a[key][i].gsub!("!", "") unless a[key][i].nil?}
-      end
-      $stderr.puts "  Removed #{invs} sites." unless o[:q]
-   end
-   $stderr.puts "Concatenating." unless o[:q]
-   a.keys.each do |key|
-      (0 .. n).each do |i|
-	 a[key][i] = (o[:missing] * lengths[i]) if a[key][i].nil?
-      end
-      abort "Inconsistent lengths in '#{key}'
-      exp:#{lengths.join(" ")}
-      obs:#{a[key].map{|i| i.length}.join(" ")}." unless
-	 lengths == a[key].map{|i| i.length}
-      puts ">#{key}", a[key].join("").gsub(/(.{1,60})/, "\\1\n")
-      a.delete(key)
-   end
-   $stderr.puts "  #{lengths.inject(:+)} columns." unless o[:q]
-   unless o[:coords].nil?
-      $stderr.puts "Generating coordinates." unless o[:q]
-      coords = File.open(o[:coords],"w")
-      s = 0
-      names = (alns.map do |a|
-	 File.basename(a).gsub(/\..*/,"").gsub(/[^A-Za-z0-9_]/,"_")
-      end)
-      (0 .. n).each do |i|
-	 l = lengths[i]
-	 next unless l > 0
-	 names[i] += "_#{i}" while names.count(names[i])>1
-	 if o[:model] =~ /(DNA.?)\/3/
-	    coords.puts "#{$1}, #{names[i]}codon1 = #{s+1}-#{s+l}\\3"
-	    coords.puts "#{$1}, #{names[i]}codon2 = #{s+2}-#{s+l}\\3"
-	    coords.puts "#{$1}, #{names[i]}codon3 = #{s+3}-#{s+l}\\3"
-	 else
-	    coords.puts "#{o[:model]}, #{names[i]} = #{s+1}-#{s+l}"
-	 end
-	 s += l
-      end
-      coords.close
-   end
-   # Save the output matrix
-   $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/Aln.convert.pl

@@ -1,35 +0,0 @@
-#!/usr/bin/env perl
-
-#
-# @author: Luis M. Rodriguez-R
-# @update: Mar-23-2015
-# @license: artistic license 2.0
-#
-
-use Bio::AlignIO;
-
-my($iformat,$oformat) = @ARGV;
-($iformat and $oformat) or die "
-Usage:
-   $0 in-format out-format < in_file > output_file
-
-   in-format	Input file's format.
-   out-format	Output file's format.
-   in_file	Input file.
-   out_file	Output file.
-
-Example:
-   # Re-format example.fa into Stockholm
-   $0 fasta stockholm < example.fa > example.stk
-
-Supported formats are:
-   bl2seq, clustalw, emboss, fasta, maf, mase, mega,
-   meme, metafasta, msf, nexus, pfam, phylip, po,
-   prodom, psi, selex, stockholm, XMFA, arp
-
-";
-
-$in  = Bio::AlignIO->new(-fh => \*STDIN, -format => $iformat);
-$out = Bio::AlignIO->new(-fh => \*STDOUT, -format => $oformat);
-while ( my $aln = $in->next_aln ) { $out->write_aln($aln) }
-

data/utils/enveomics/Scripts/AlphaDiversity.pl

@@ -1,152 +0,0 @@
-#!/usr/bin/env perl
-
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Nov-29-2015
-# @license: artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-use List::Util qw/min max sum/;
-
-sub VERSION_MESSAGE(){print "Alpha-diversity indices (enveomics)\n"}
-sub HELP_MESSAGE(){die "
-Description:
-   Takes a table of OTU abundance in one or more samples and calculates the Rao
-   (Q_alpha), Rao-Jost (Q_alpha_eqv), Shannon (Hprime), and inverse Simpson
-   (1_lambda) indices of alpha diversity for each sample.
-   
-   To use it with Qiime OTU Tables, run it as:
-   $0 -i OTU_Table.txt -h
-
-Usage:
-   $0 [opts]
-
-   -i <str>	* Input table (columns:samples, rows:OTUs, first column:OTU
-		names).
-   -r <int>	Number of rows to ignore.  By default: 0.
-   -c <int>	Number of columns to ignore after the first column (i.e.,
-		between the first column, containing the name of the categories,
-		and the first column of abundance values).  By default: 0.
-   -C <int>	Number of columns to ignore at the end of each line.
-		By default: 0.
-   -d <str>	Delimiter.  Supported escaped characters are: \"\\t\"
-		(tabulation), and \"\\0\" (null bit).  By default: \"\\t\".
-   -h		If set, the first row is assumed to have the names of the
-		samples.
-   -D <str>	Distances file.  A squared matrix (or bottom-left half matrix)
-		with the distances between categories (OTUs or functions).  The
-		first column must contain the names of the categories, and it
-		shouldn't have headers.  If not set, all distances are assumed
-		to be one.  Only used for Rao.
-   -R		Do not calculate Rao indices.  This significantly decreases the
-		total running time. Note that Rao indices are highly susceptible
-		to precision errors, and shouldn't be trusted for very big
-		numbers.
-   -q <int>	Estimate the qD index (true diversity order q).  By default: 0.
-   --help	This help message.
-
-   * Mandatory.
-
-"}
-
-# Input arguments
-my %o;
-getopts('i:c:C:d:r:hD:Rq:', \%o);
-
-#$o{B} and (eval("use bignum; 1") or die "Cannot use bignum.\n");
-&HELP_MESSAGE() unless $o{i};
-$o{c} ||= 0;
-$o{C} ||= 0;
-$o{r} ||= 0;
-$o{d} ||= "\\t";
-$o{q} ||= 0;
-
-$o{d}="\t" if $o{d} eq "\\t";
-$o{d}="\0" if $o{d} eq "\\0";
-
-# Distance matrix
-my $D = {};
-if($o{D} and not $o{R}){
-   my @Didx = ();
-   open DIST, "<", $o{D} or die "Cannot read file: $o{D}: $!\n";
-   while(<DIST>){
-      chomp;
-      my @d = split /\t/;
-      my $idx = shift @d;
-      push  @Didx,  $idx;
-      $D->{ $idx } ||= {};
-      $D->{ $idx }->{ $Didx[$_] } = $d[$_] for(0 .. $#d);
-   }
-   close DIST;
-   undef @Didx;
-}
-
-# Abundance matrix
-my @names  = ();
-my @cats   = ();
-my @values = ();
-open TABLE, "<", $o{i} or die "Cannot open file: ".$o{i}.": $!\n";
-<TABLE> for (1 .. $o{r});
-if($o{h}){
-   my $h = <TABLE>;
-   $h or die "Empty table!\n";
-   chomp $h;
-   @names = split $o{d}, $h;
-   shift @names for (0 .. $o{c});
-}
-
-while(<TABLE>){
-   chomp;
-   my @ln = split $o{d};
-   push @cats, shift(@ln);
-   shift @ln for (1 .. $o{c});
-   pop @ln for (1 .. $o{C});
-   push @{$values[$_] ||= []}, $ln[$_] for (0 .. $#ln);
-   push @{$values[$#ln+1]}, sum(@ln);
-}
-close TABLE;
-$names[$#values] = "gamma";
-
-if($o{R}){
-   print "".join($o{d}, qw/Sample Hprime 1_lambda qD/)."\n";
-}else{
-   print "".join($o{d}, qw/Sample Q_alpha Q_alpha_eqv Hprime 1_lambda qD/)."\n";
-}
-for my $i (0 .. $#values){
-   print "".(exists $names[$i] ? $names[$i] : $i).$o{d};
-   my $N = sum @{$values[$i]};
-   my $Q = 0;
-   my $H = 0;
-   my $l = 0;
-   my $qD = 0 unless $o{q}==1;
-   for my $ik (0 .. $#{$values[$i]}){
-      unless($o{R}){
-	 my $Qi = 0;
-	 for my $jk (0 .. $#{$values[$i]}){
-	    my $dij = (!$o{D}) ? 1 : 
-	       exists $D->{ $cats[$ik] }->{ $cats[$jk] } ?
-	       $D->{ $cats[$ik] }->{ $cats[$jk] } :
-	       exists $D->{ $cats[$jk] }->{ $cats[$ik] } ?
-	       $D->{ $cats[$jk] }->{ $cats[$ik] } :
-	       die "Cannot find distance between ".$cats[$ik].
-		  " and ".$cats[$jk].".\n";
-	    $Qi += $dij * ($values[$i]->[$ik]/$N) * ($values[$i]->[$jk]/$N);
-	 }
-	 $Q += $Qi;
-      }
-      my $pi = $N ? $values[$i]->[$ik]/$N : 0;
-      $H  -= $pi * log($pi) if $pi;
-      $l  += $pi**2;
-      $qD += $pi * ($pi**($o{q}-1)) unless $o{q}==1 or not $pi;
-   }
-   $qD = $o{q}==1 ? exp($H) : 1/($qD**(1/($o{q}-1)));
-   if($o{R}){
-      print "".join($o{d}, $H, $l ? 1/$l : "Inf", $qD)."\n";
-   }else{
-      print "".join($o{d}, $Q, ($Q==1 ? "NA" : 1/(1-$Q)), $H, 1/$l, $qD)."\n";
-   }
-}
-