miga-base 0.7.23.0 → 0.7.25.3

data/utils/enveomics/Scripts/Table.barplot.R

@@ -1,31 +0,0 @@
-#!/usr/bin/env Rscript
-#
-# @author  Luis M. Rodriguez-R
-# @update  Dec-29-2015
-# @license artistic license 2.0
-#
-
-#= Load stuff
-args <- commandArgs(trailingOnly = F)  
-enveomics_R <- file.path(dirname(
-   sub("^--file=", "", args[grep("^--file=", args)])),
-   "lib", "enveomics.R")
-source(file.path(enveomics_R, "R", "cliopts.R"))
-source(file.path(enveomics_R, "R", "utils.R"))
-source(file.path(enveomics_R, "R", "barplot.R"))
-
-#= Generate interface
-opt <- enve.cliopts(enve.barplot,
-   file.path(enveomics_R, "man", "enve.barplot.Rd"),
-   positional_arguments=c(1,3),
-   usage="usage: %prog [options] output.pdf [width height]",
-   mandatory=c("x"), vectorize=c("sizes","order","col"),
-   number=c("sizes","order"),
-   o_desc=list(x="A tab-delimited file containing header (first row) and row names (first column)."))
-
-#= Run it!
-args = as.list(opt$args)
-for(i in 2:3) if(length(args)>=i) args[[i]] <- as.numeric(args[[i]])
-do.call("pdf", args)
-do.call("enve.barplot", opt$options)
-dev.off()

data/utils/enveomics/Scripts/Table.df2dist.R

@@ -1,30 +0,0 @@
-#!/usr/bin/env Rscript
-#
-# @author  Luis M. Rodriguez-R
-# @update  Jan-04-2016
-# @license artistic license 2.0
-#
-
-#= Load stuff
-args <- commandArgs(trailingOnly = F)  
-enveomics_R <- file.path(dirname(
-   sub("^--file=", "", args[grep("^--file=", args)])),
-   "lib", "enveomics.R")
-source(file.path(enveomics_R, "R", "cliopts.R"))
-source(file.path(enveomics_R, "R", "df2dist.R"))
-
-#= Generate interface
-opt <- enve.cliopts(enve.df2dist,
-   file.path(enveomics_R, "man", "enve.df2dist.Rd"),
-   positional_arguments=1,
-   usage="usage: %prog [options] output.mat",
-   mandatory=c("x"),
-   number=c("default.d", "max.sim"),
-   o_desc=list(x="A tab-delimited table with the distances."),
-   p_desc="Transform a tab-delimited list of distances into a squared matrix.")
-
-#= Run it!
-opt$options[['x']] <- read.table(opt$options[['x']],
-   header=TRUE, sep="\t", as.is=TRUE)
-dist <- do.call("enve.df2dist", opt$options)
-write.table(as.matrix(dist), opt$args[1], quote=FALSE, sep="\t", col.names=NA)

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

@@ -1,61 +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('k:s:ihn', \%o);
-my($list, $table) = @ARGV;
-
-($list and $table) or die "
-.Description:
-   Extracts (and re-orders) a subset of rows from a raw table.
-
-.Usage: $0 [options] list.txt table.txt > subset.txt
-   
-   Options:
-      -k <int>	Column of the table to use as key to filter.  By default, 1.
-      -s <str>	String to use as separation between rows.  By default, tabulation.
-      -i	If set, reports the inverse of the list (i.e., reports only rows
-      		absent in the list).  Implies -n.
-      -h	Keep first row of the table (header) untouched.
-      -n	No re-order.  The output has the same order of the table.  By
-      		default, it prints in the order of the list.
-
-   list.txt	List of IDs to extract.
-   table.txt	Table file containing the superset.
-   subset.txt	Table file to be created.
-
-";
-
-$o{k} ||= 1;
-$o{s} ||= "\t";
-$o{n}=1 if $o{i};
-my $HEADER = "";
-
-my $tbl2 = $o{n} ? $list : $table;
-open TBL, "<", $tbl2 or die "Cannot read file: $tbl2: $!\n";
-$HEADER = <TBL> if $o{h} and not $o{n};
-my %tbl2 = map { my $l=$_; chomp $l; my @r=split $o{s}, $l; $r[ $o{n} ? 0 : $o{k}-1] => $l } <TBL>;
-close TBL;
-
-my $tbl1 = $o{n} ? $table : $list;
-open TBL, "<", $tbl1 or die "Cannot read file: $tbl1: $!\n";
-$HEADER = <TBL> if $o{h} and $o{n};
-print $HEADER;
-while(my $ln = <TBL>){
-   chomp $ln;
-   next unless $ln;
-   my @ln = split $o{s}, $ln;
-   my $good = exists $tbl2{ $ln[$o{n} ? $o{k}-1 : 0] };
-   $good = not $good if $o{i};
-   print "".($o{n} ? $ln : $tbl2{$ln[0]})."\n" if $good;
-}
-close TBL;
-

data/utils/enveomics/Scripts/Table.merge.pl

@@ -1,77 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Sep-20-2015
-# @license: artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-
-my %o;
-getopts('si:o:ne:h:H:r:', \%o);
-my @files = @ARGV;
-
-$#files>0 or die "
-.Description:
-   Merges multiple (two-column) lists into one table.
-
-.Usage:
-   $0 [options] files... > output.txt
-   
-   Options:
-      -s	Values are read as Strings.  By default, values are read as numbers.
-      -i <str>	Input field-delimiter.  By default: tabulation (\"\\t\").
-      -o <str>	Output field-delimiter.  By default: tabulation (\"\\t\").
-      -n	No-header.  By default, the header is determined by the file names.
-      -e <str>	Default string when no value is found.  By default, the \"empty\" value
-      		is 0 if values are numeric (i.e., unless -s is set) or an empty string
-		otherwise.
-      -h <str>	Header of the first column, containing the IDs.  By default: \"Tag\".
-      -H <str>	Format of filenames capturing the column header in the first capturing
-		parenthesis.  Non-capturing paretheses can be defined as (?:...).  By
-		default: \"(?:.*/)?([^\\.]+)\", which captures the part of the basename
-		of the file before the first dot (if any).
-      -r <int>	Number of leading rows to ignore in the input files. Zero by default.
-
-";
-$o{i} ||= "\t";
-$o{o} ||= "\t";
-$o{e} ||= ($o{s} ? "" : 0);
-$o{h} ||= "Tag";
-$o{H} ||= "(?:.*/)?([^\\.]+)";
-$o{r} += 0;
-
-my $notes = {};
-
-print $o{h} unless $o{n};
-my $i = 0;
-for my $file (@files){
-   unless($o{n}){
-      $file =~ m/$o{H}/ or die "Filename '$file' doesn't match format '$o{H}'.";
-      my $tag=$1;
-      print $o{o}.$tag;
-   }
-   open IN, "<", $file or die "Cannot read file: $file: $!\n";
-   while(<IN>){
-      next if $. <= $o{r};
-      chomp;
-      my @l = split $o{i};
-      $l[1]+=0 unless $o{s};
-      $notes->{$l[0]} ||= [];
-      $notes->{$l[0]}->[$i] = $l[1];
-   }
-   close IN;
-   $i++;
-}
-print "\n" unless $o{n};
-
-for my $id (keys %$notes){
-   print $id;
-   for my $i (0 .. $#files){
-      print $o{o}.(( defined $notes->{$id}->[$i] ? $notes->{$id}->[$i] : $o{e} ));
-   }
-   print "\n";
-}
-

data/utils/enveomics/Scripts/Table.replace.rb

@@ -1,69 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update  Feb 01 2016
-# @license artistic license 2.0
-#
-
-require "optparse"
-
-o = {delimiter: "\t", key: 1, default: ""}
-ARGV << "-h" if ARGV.size==0
-OptionParser.new do |opts|
-   opts.banner = "\nReplaces a field in a table using a mapping file."
-   opts.on("-m", "--map FILE",
-      "Mapping file with two columns (key and replacement)."){ |v| o[:map] = v }
-   opts.on("-i", "--in FILE", "Input table."){ |v| o[:in] = v }
-   opts.on("-o", "--out FILE", "Output table."){ |v| o[:out] = v }
-   opts.on("-k", "--key INT",
-      "Column to replace in --in. By deafult: 1."){ |v| o[:key] = v.to_i }
-   opts.on("-u", "--unknown STR",
-      "String to use whenever the key is not found in --map."
-      ){ |v| o[:default] = v }
-   opts.on("-d", "--delimiter STR",
-      "String delimiting columns. By default, tabulation."
-      ){ |v| o[:delimiter] = v }
-   opts.on("-h", "--help", "Display this screen") do
-      puts opts
-      exit
-   end
-   opts.separator ""
-end.parse!
-abort "-m is mandatory" if o[:map].nil?
-abort "-i is mandatory" if o[:in].nil?
-abort "-o is mandatory" if o[:out].nil?
-
-class String
-   def is_number?
-      true if Float(self) rescue false
-   end
-end
-
-begin
-   # Read mapping file
-   ifh = File.open(o[:map], "r")
-   map = {}
-   while(ln = ifh.gets)
-      row = ln.chomp.split(o[:delimiter])
-      map[ row[0] ] = row[1]
-   end
-   ifh.close
-   # Process table
-   ifh = File.open(o[:in], "r")
-   ofh = File.open(o[:out], "w")
-   while(ln = ifh.gets)
-      row = ln.chomp.split(o[:delimiter])
-      k = row[ o[:key]-1 ]
-      v = map[ k ]
-      v = o[:default] if v.nil?
-      row[ o[:key]-1 ] = v
-      ofh.puts(row.join(o[:delimiter]))
-   end
-   ifh.close
-   ofh.close
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts " - " + l + "\n" }
-   err
-end

data/utils/enveomics/Scripts/Table.round.rb

@@ -1,63 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author: Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Feb 04 2015
-# @license: artistic license 2.0
-#
-
-require 'optparse'
-
-o = {:ndigits=>0, :action=>:round, :delimiter=>"\t"}
-ARGV << '-h' if ARGV.size==0
-OptionParser.new do |opts|
-   opts.banner = "\nRounds numbers in a table."
-   opts.on("-i", "--in FILE", "Input table."){ |v| o[:in] = v}
-   opts.on("-o", "--out FILE", "Output table."){ |v| o[:out] = v }
-   opts.on("-n", "--ndigits INT", "Number of decimal digits. By default: #{o[:ndigits]}"){ |v| o[:ndigits] = v.to_i }
-   opts.on("-f", "--floor", "Floors the values instead of rounding them. Ignores -n."){ o[:action] = :floor }
-   opts.on("-c", "--ceil", "Ceils the values instead of rounding them. Ignores -n."){ o[:action] = :ceil }
-   opts.on("-d", "--delimiter STR", "String delimiting columns. By default, tabulation."){ |v| o[:delimiter] = 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?
-
-class String
-   def is_number?
-      true if Float(self) rescue false
-   end
-end
-
-begin
-   ifh = File.open(o[:in], "r")
-   ofh = File.open(o[:out], "w")
-   while(ln = ifh.gets)
-      ln.chomp!
-      row = []
-      ln.split(o[:delimiter]).each do |value|
-	 if value.is_number?
-	    case o[:action]
-	    when :round
-	       value = value.to_f.round(o[:ndigits])
-	    when :floor
-	       value = value.to_f.floor
-	    when :ceil
-	       value = value.to_f.ceil
-	    end
-	 end
-	 row.push value.to_s
-      end
-      ofh.puts(row.join(o[:delimiter]))
-   end
-   ifh.close
-   ofh.close
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts " - " + l + "\n" }
-   err
-end

data/utils/enveomics/Scripts/Table.split.pl

@@ -1,57 +0,0 @@
-#!/usr/bin/env perl
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update Feb-01-2016
-# @license artistic license 2.0
-#
-
-use warnings;
-use strict;
-use Getopt::Std;
-use Symbol;
-
-my %o;
-getopts('i:o:d:e:h', \%o);
-my $file = shift @ARGV;
-
-($file and not $o{h}) or die "
-.Description:
-   Split a file with multiple columns into multiple two-columns lists.
-
-.Usage:
-   $0 [options] file
-   
-   Options:
-      -i <str>	Input field-delimiter.  By default: tabulation (\"\\t\").
-      -o <str>	Prefix of the output files.  By default: no prefix (\"\").
-      -d <str>	Output directory. By default: current directory (\"\").
-
-";
-$o{i} ||= "\t";
-$o{o} ||= "";
-$o{o} = $o{d}."/".$o{o} if $o{d};
-
-my $open=0;
-my @fhs=();
-open IN, "<", $file or die "Cannot read file: $file: $!\n";
-while(<IN>){
-   chomp;
-   my @row = split $o{i};
-   my $h = shift @row;
-   if($open){
-      for my $i (0 .. $#row){
-         print { qualify_to_ref $fhs[$i] } $h.$o{i}.$row[$i]."\n" if $row[$i];
-      }
-   }else{
-      $open++;
-      for my $l (@row){
-         $l =~ s/[\.\/:]/_/g;
-	 my $gs = gensym;
-	 open($gs, '>', $o{o}.$l.".txt") or die "Cannot create file: $o{o}$l.txt: $!\n";
-	 push @fhs, $gs;
-      }
-   }
-}
-close IN;
-close $_ for @fhs;
-

data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb

@@ -1,227 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @update: Feb-06-2015
-# @license artistic license 2.0
-#
-
-require 'optparse'
-
-$opts = {:warns=>false}
-ARGV << '-h' if ARGV.size==0
-OptionParser.new do |opt|
-   opt.separator "Re-formats Silva taxonomy into NCBI-like taxonomy dump files."
-   opt.separator ""
-   opt.separator "Mandatory arguments"
-   opt.on("-k", "--silvaranks FILE", "Input Silva ranks file (e.g., tax_ranks_ssu_115.txt)."){ |v| $opts[:silvaranks]=v }
-   opt.on("-f", "--silvaref FILE", "Input Silva ref alignment file (e.g., SSURef_NR99_115_tax_silva_full_align_trunc.fasta)."){ |v| $opts[:silvaref]=v }
-   opt.separator ""
-   opt.separator "Additional options"
-   opt.on("-p", "--patch FILE", "If passed, it replaces the paths specified in the patch."){ |v| $opts[:patch]=v }
-   opt.on("-s", "--seqinfo FILE", "If passed, it creates a CSV seq-info file compatible with taxtastic."){ |v| $opts[:seqinfo]=v }
-   opt.on("-t", "--taxfile FILE", "If passed, it creates a simple TSV taxonomy file."){ |v| $opts[:taxfile]=v }
-   opt.on("-n", "--ncbi FILE", "If passed, output folder for the NCBI dump files (e.g., taxdmp)."){ |v| $opts[:ncbi]=v }
-   opt.on("-w", "--warns", "Verbously display warnings."){ $opts[:warns]=true }
-   opt.on("-h", "--help","Display this screen") do
-      puts opt
-      exit
-   end
-   opt.separator ""
-end.parse!
-abort "-k/--silvaranks is mandatory." if $opts[:silvaranks].nil?
-abort "-k/--silvaranks must exist." unless File.exists? $opts[:silvaranks]
-abort "-f/--silvaref is mandatory." if $opts[:silvaref].nil?
-abort "-f/--silvaref must exist." unless File.exists? $opts[:silvaref]
-
-class Node
-   attr_accessor :id, :tax, :leaf, :name_type
-   attr_reader :name, :rank, :parent, :children
-   def initialize(name, rank=nil)
-      @name = name
-      @rank = rank.nil? ? "no rank" : rank
-      @children = []
-      @leaf = false
-      @name_type = "scientific name";
-   end
-   def parent=(node)
-      @parent=node
-      node.add_child(self)
-   end
-   def add_child(node)
-      @children << node
-   end
-   def ncbirank
-      ncbirank =
-	 self.rank == "superkingdom" ? "no rank" :
-	 self.rank == "domain" ? "superkingdom" :
-	 self.rank == "major_clade" ? "no rank" : self.rank
-      return ncbirank
-   end
-   def path
-      if self.parent.nil?
-         self.name
-      else
-         "#{self.parent.path};#{self.name}"
-      end
-   end
-   def each_desc internals, leaves, &blk
-      blk[self] if (leaves and self.leaf) or (internals and not self.leaf)
-      self.children.each {|child| child.each_desc internals, leaves, &blk}
-   end
-   def to_s
-      "#{self.name} (#{self.rank})"
-   end
-end
-
-class Taxonomy
-   attr_reader :root, :next_id
-   def initialize
-      @root = Node.new('root')
-      @root.id = 1
-      @next_id = 2
-   end
-   def register(node)
-      node.id = self.next_id
-      node.parent = self.root if node.parent.nil?
-      @next_id += 1
-   end
-   def node(path)
-      node = self.root
-      path.each do |level|
-         node.children.each do |child|
-	    if child.name == level
-	       node = child
-	       break
-	    end
-	 end
-	 unless node.name == level
-	    $stderr.puts "Warning: Impossible to find #{level} at #{node.to_s}, making it up." if $opts[:warns]
-	    child = Node.new(level)
-	    child.parent = node
-	    self.register(child)
-	    node = child
-	 end
-      end
-      node
-   end
-   def each_node &blk
-      self.root.each_desc true, true, &blk
-   end
-   def each_leaf &blk
-      self.root.each_desc false, true, &blk
-   end
-   def each_internal &blk
-      self.root.each_desc true, false, &blk
-   end
-end
-
-begin
-   taxo = Taxonomy.new()
-   
-   ## Read patch
-   patch = {}
-   unless $opts[:patch].nil?
-      $stderr.puts "Reading patch: #{$opts[:patch]}"
-      f = File.open($opts[:patch], "r")
-      while(ln = f.gets)
-	 m = ln.chomp.split(/\t/)
-	 patch[ m[0] ] = m[1]
-      end
-   end
-   
-   ## Read the Silva ranks
-   $stderr.puts "Reading Silva ranks: #{$opts[:silvaranks]}"
-   f = File.open($opts[:silvaranks], "r")
-   f.gets # header
-   while(ln = f.gets)
-      m = ln.chomp.split(/\t/)
-      m[0] = patch[ m[0] ] unless patch[ m[0] ].nil?
-      p = m[0].split(/;/)
-      raise "Inconsistent path and node name at line #{$.}: #{ln}." unless m[1] == p.pop
-      if m[3] != "w"
-	 node = Node.new(m[1], m[2])
-	 node.name_type = "common name" if m[3] == "a"
-	 node.parent = taxo.node(p)
-	 taxo.register(node)
-      end
-   end
-   f.close
-
-   $stderr.puts "  Top taxa:"
-   taxo.root.children.each do |top|
-      $stderr.puts "    o #{top.to_s} has #{top.children.length} children."
-   end
-
-   ## Read the Silva ref alignment
-   $stderr.puts "Reading Silva ref alignment: #{$opts[:silvaref]}"
-   i = 0
-   f = File.open($opts[:silvaref], "r")
-   while(ln = f.gets)
-      m = />([^\s]+)\s(.*)/.match(ln)
-      next unless m
-      # Patch
-      pm = /(.+);([^;]+)/.match(m[2])
-      path = "#{patch[ pm[1] ].nil? ? pm[1] : patch[ pm[1] ]};#{pm[2]}".split(/;/)
-      # Register
-      node = taxo.node(path)
-      taxo.register(node)
-      refseq = Node.new(m[1], 'refseq')
-      refseq.parent = node
-      refseq.leaf = true
-      taxo.register(refseq)
-      i += 1
-   end
-   f.close
-   $stderr.puts "  Saved #{i} leaves."
-
-   ### NCBI
-   unless $opts[:ncbi].nil?
-      ## Create taxonomy .dmp files
-      $stderr.puts "Creating NCBI-like files: #{$opts[:ncbi]}"
-      Dir.mkdir($opts[:ncbi]) unless Dir.exists?($opts[:ncbi]);
-      # merged.dmp
-      $stderr.puts "  o Creating merged.dmp"
-      File.open(File.join($opts[:ncbi], 'merged.dmp'), 'w'){}
-      # names.dmp
-      $stderr.puts "  o Creating names.dmp"
-      f = File.open(File.join($opts[:ncbi], 'names.dmp'), 'w')
-      taxo.each_internal do |n|
-	 f.puts [n.id, n.name, "", n.name_type].join("\t|\t")+"\t|"
-      end
-      f.close
-      # nodes.dmp
-      $stderr.puts "  o Creating nodes.dmp"
-      f = File.open(File.join($opts[:ncbi], 'nodes.dmp'), 'w')
-      taxo.each_internal do |n|
-	 f.puts ([n.id, n.parent.nil? ? n.id : n.parent.id, n.ncbirank, ""] << Array.new(8,0) << "").join("\t|\t")+"\t|"
-      end
-      f.close
-   end
-
-   ## Taxtastic
-   unless $opts[:seqinfo].nil?
-      $stderr.puts "Creating seq-info file: #{$opts[:seqinfo]}"
-      f = File.open($opts[:seqinfo], 'w')
-      f.puts "\"seqname\",\"tax_id\",\"group_name\""
-      taxo.each_leaf { |n| f.puts "\"#{n.name}\",\"#{n.parent.id}\",\"#{n.parent.name}\"" }
-      f.close
-   end
-   
-   ## Misc
-   unless $opts[:taxfile].nil?
-      $stderr.puts "Creating taxonomy file: #{$opts[:taxfile]}"
-      f = File.open($opts[:taxfile], 'w')
-      f.puts "tax_id\tparent_id\trank\ttax_name"
-      taxo.each_internal do |n|
-	 f.puts [n.id, n.parent.nil? ? n.id : n.parent.id, n.rank, n.name].join("\t")
-      end
-      f.close
-   end
-rescue => err
-   $stderr.puts "Exception: #{err}\n\n"
-   err.backtrace.each { |l| $stderr.puts l + "\n" }
-   err
-end
-
-