miga-base 0.7.23.0 → 0.7.25.3

data/utils/enveomics/Scripts/gi2tax.rb

@@ -1,103 +0,0 @@
-#!/usr/bin/env ruby
-
-#
-# @author  Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
-# @license artistic license 2.0
-#
-
-$:.push File.expand_path(File.dirname(__FILE__) + "/lib")
-require "enveomics_rb/remote_data"
-use "nokogiri"
-
-#================================[ Options parsing ]
-o = {
-  :q=>false, :gis=>[], :dbfrom=>"nuccore", :header=>true,
-  :exact_gi=>false, :no_nil=>false, :ret=>"ScientificName",
-  :ranks=>%w(superkingdom phylum class order family genus species)}
-OptionParser.new do |opt|
-  opt.banner = "
-  Maps a list of NCBI GIs to their corresponding taxonomy using the NCBI
-  EUtilities. Avoid using this script on millions of entries at a time, since
-  each entry elicits two requests to NCBI's servers.
-
-  *IMPORTANT NOTE*: NCBI is phasing out support for GIs. Please use acc.ver
-  instead with NCBIacc2tax.rb.
-
-  Usage: #{$0} [options]".gsub(/^ +/,"")
-  opt.separator ""
-  opt.on("-g", "--gis GI1,GI2,...", Array,
-    "Comma-separated list of GIs. Required unless -i is passed."
-    ){ |v| o[:gis]=v }
-  opt.on("-i", "--infile FILE",
-    "Raw text file containing the list of GIs, one per line.",
-    "Required unless -g is passed."){ |v| o[:infile]=v }
-  opt.on("-p", "--protein",
-    "Use if the GIs are proteins. Otherwise, GIs are assumed to be from " +
-    "the Nuccore Database."){ o[:dbfrom]="protein" }
-  opt.on("-r", "--ranks RANK1,RANK2,...", Array,
-    "Taxonomic ranks to report. By default: #{o[:ranks].join(",")}."
-    ){ |v| o[:ranks]=v }
-  opt.on("-n", "--noheader",
-    "Do not include a header in the output."){ o[:header]=false }
-  opt.on("-t", "--taxids",
-    "Return Taxonomy IDs instead of scientific names."){ o[:ret]="TaxId" }
-  opt.on("--exact-gi",
-    "Returns only taxonomy associated with the exact GI passed.",
-    "By default, it attempts to update accession versions if possible."
-    ){ |v| o[:exact_gi]=v }
-  opt.on("--ignore-missing",
-    "Does not report missing GIs in the output file.",
-    "By default, it reports GI and empty values for all other columns."
-    ){ |v| o[:no_nil]=v }
-  opt.on("-q", "--quiet", "Run quietly."){ |v| o[:q]=true }
-  opt.on("-h", "--help","Display this screen") do
-    puts opt
-    exit
-  end
-  opt.separator ""
-end.parse!
-
-#================================[ Functions ]
-def gi2taxid(db, gi)
-  doc = Nokogiri::XML( RemoteData.elink({:dbfrom=>db,
-    :db=>"taxonomy", :id=>gi}) )
-  doc.at_xpath("/eLinkResult/LinkSet/LinkSetDb/Link/Id")
-end
-#================================[ Main ]
-begin
-  o[:gis] += File.readlines(o[:infile]).map{ |l| l.chomp } unless
-    o[:infile].nil?
-  o[:ranks].map!{ |r| r.downcase }
-  puts (["GI", "TaxId"] + o[:ranks].map{ |r| r.capitalize }).join("\t") if
-    o[:header]
-  o[:gis].each do |gi|
-    taxid = gi2taxid(o[:dbfrom], gi)
-    status = ""
-    if taxid.nil? and not o[:exact_gi]
-      new_gi, status = RemoteData.update_gi(o[:dbfrom], gi)
-      taxid = gi2taxid(o[:dbfrom], new_gi) unless new_gi.nil?
-    end
-    if taxid.nil?
-      warn "Cannot find link to taxonomy: #{gi} #{status}"
-      puts ([gi, ""] + o[:ranks].map{ |i| "" }).join("\t") unless o[:no_nil]
-      next
-    end
-    taxonomy = {}
-    unless taxid.nil?
-      doc = Nokogiri::XML( RemoteData.efetch({:db=>"taxonomy",
-        :id=>taxid.content}) )
-      taxonomy[ doc.at_xpath("/TaxaSet/Taxon/Rank").content ] =
-        doc.at_xpath("/TaxaSet/Taxon/#{o[:ret]}").content
-      doc.xpath("/TaxaSet/Taxon/LineageEx/Taxon").each do |taxon|
-        taxonomy[ taxon.at_xpath("./Rank").content ] =
-          taxon.at_xpath("./#{o[:ret]}").content
-      end
-    end
-    puts ([gi, taxid.content] +
-      o[:ranks].map{ |rank| taxonomy[ rank ] ||= "" }).join("\t")
-  end
-rescue => err
-  $stderr.puts "Exception: #{err}\n\n"
-  err.backtrace.each { |l| $stderr.puts l + "\n" }
-  err
-end

data/utils/enveomics/Scripts/in_silico_GA_GI.pl

@@ -1,96 +0,0 @@
-# usage perl in_silico_GA.pl [options]
-
-use Getopt::Long;
-use Math::Random qw(:all);
-
-$argu=GetOptions('in=s'=>\$infile, # input fasta chr file
-                 'out=s'=>\$outfile, # output file name
-                 'coverage=s'=>\$cov, # desired output
-                 'seq_error=s'=>\$seq_error, # sequencing error
-                 'read_len=s'=>\$read_len, # simulated read length
-                 'ins_len=s'=>\$ins_len,  # insertion length
-                 'ins_var=s'=>\$ins_var);
-
-$chr='';
-open(IN,$infile);
-open(OUT,">$outfile");
-%code=();
-$code{'0'}='C';
-$code{'1'}='A';
-$code{'2'}='T';
-$code{'3'}='G';
-
-while(<IN>){
-  chomp;
-  if(!/^\>/){
-	$chr.=$_;
-  }
-  else{
-    $gi=$_;
-    if($gi= ~/^\>gi\|(\S+)\|\S+\|\S+/){
-      $gi=$1;}
-
-}
-}
-close(IN);
-  
-$chr_size=length $chr;
-print "chromosome size: $chr_size\n";
-$seg_size=2*$read_len+$ins_len;
-$reads_number=int($cov*$chr_size/($read_len*2));
-print "generated reads $reads_number x 2\n";
-
-for(1..$reads_number){
-  $index=$_;
-  $l=length $index;
-  $k=8-$l;
-  $kk='0' x $k;
-  $id= 'read'.$kk.$index.'_'.$gi;
-
-#make start site;
-  $start_site=int(rand($chr_size));
-#make short seg length;
-  $seg_length=int(random_normal(1,$seg_size,$ins_var));
-
-#extract the segment
-  $seg=substr($chr,$start_site,$seg_length);
-  $s_len=length $seg;
-  $gap=$seg_length-$s_len;
-  if($gap!=0){
-	$makeup=substr($chr,0,$gap);
-	$seg.=$makeup;
-  }
-
-  $id.='.start'.$start_site.'.seg_len'.$seg_length;
-
-#get the reads
-  $seq1=substr($seg,0,$read_len);
-  #$seg=~tr/ATCG/TAGC/ this line can change the orientation of the second read;
-  $seq2=substr($seg,-$read_len);
-# sequencing error introducing
-  @seq1=split(//,$seq1);
-  @seq2=split(//,$seq2);
-  @mut1=random_binomial($read_len,1,$seq_error);
-  @mut2=random_binomial($read_len,1,$seq_error);
-
-  for(0..$#mut1){
-	$i=$_;
-	if($mut1[$i]==1){
-	  $r=int(rand(4));
-	  $seq1[$i]=$code{$r};
-	}
-	if($mut2[$i]==1){
-	  $r=int(rand(4));
-	  $seq2[$i]=$code{$r};
-	}
-  }
-  $seq1=join('',@seq1);
-  $seq2=join('',@seq2);
-
-  $id1=$id.'#0/1';
-  $id2=$id.'#0/2';
-  
-  print OUT ">$id1\n$seq1\n>$id2\n$seq2\n";
-}
-	
-

data/utils/enveomics/Scripts/lib/enveomics.R

@@ -1 +0,0 @@
-../../enveomics.R

data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb

@@ -1,24 +0,0 @@
-
-#
-# @author: Luis M. Rodriguez-R
-# @license: artistic license 2.0
-#
-
-require "optparse"
-ARGV << "-h" if ARGV.size==0
-
-def use(gems, mandatory=true)
-  gems = [gems] unless gems.is_a? Array
-  begin
-    require "rubygems"
-    while ! gems.empty?
-      require gems.shift
-    end
-    return true
-  rescue LoadError
-    abort "\nUnmet requirements, please install required gems:" +
-      gems.map{ |gem| "\n   gem install #{gem}" }.join + "\n\n" if mandatory
-    return false
-  end
-end
-

data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb

@@ -1,253 +0,0 @@
-
-#
-# @author: Luis M. Rodriguez-R
-# @update: Jul-14-2015
-# @license: artistic license 2.0
-#
-
-module JPlace
-   ##### CLASSES:
-   # Placement.new(placement[, fields]): Initializes a new read placement.
-   # placement: A hash containing the placement.
-   # fields: If passed, sets the field order for all subsequent placements.
-   class Placement
-      attr_writer :flag # This attribute is used by JPlace.distances.rb as a placeholder
-      attr_reader :p, :n, :m, :flag
-      @@fields = nil
-      def self.fields=(fields)
-	 @@fields=fields
-      end
-      def self.fields
-	 @@fields
-      end
-      def initialize(placement, fields=nil)
-	 @@fields = fields if @@fields.nil? and not fields.nil?
-	 # Save only the best (first) placement:
-	 abort "Placements must contain a 'p' field.\n" if placement["p"].nil?
-	 abort "Placements must contain a 'p' field with at least one entry.\n" if placement["p"][0].nil?
-	 @p = [placement["p"][0]]
-	 # Find name-only placements (EPA-style):
-	 unless placement["n"].nil?
-	    @n = placement["n"]
-	    @m = @n.map{ |n| 1 }
-	 end
-	 # Find multiplicity placements (pplacer-style):
-	 unless placement["nm"].nil?
-	    @n = placement["nm"].map{ |nm| nm[0] }
-	    @m = placement["nm"].map{ |nm| nm[1].to_i }
-	 end
-	 abort "Placements must contain one of 'n' or 'nm' fields.\n" if @n.nil? or @m.nil?
-      end
-      def nm
-	 (0 .. (self.n.length-1)).map{ |i| {:n=>self.n[i], :m=>self.m[i]} }
-      end
-      def get_field_value(field)
-	 abort "Impossible to read placement with undefined fields." if @@fields.nil?
-	 f = @@fields.find_index(field)
-	 abort "Undefined field #{field}." if f.nil?
-	 self.p[0][f]
-      end
-      def set_field_value(field, value)
-	 f = @@fields.find_index(field)
-	 abort "Undefined field #{field}." if f.nil?
-	 self.p[0][f] = value
-      end
-      def edge_num
-	 self.get_field_value('edge_num').to_i
-      end
-      def likelihood
-	 self.get_field_value('likelihood').to_f
-      end
-      def like_weight_ratio
-	 self.get_field_value('like_weight_ratio').to_f
-      end
-      def distal_length
-	 (self.get_field_value('distal_length') || 0).to_f
-      end
-      def pendant_length
-	 (self.get_field_value('pendant_length') || 0).to_f
-      end
-      def to_s
-	 "#<Placement of #{self.n}: #{self.p}>"
-      end
-   end
-
-   # Ancilliary class Tree
-   class Tree
-      @@HAS_ICONV = nil
-      def self.has_iconv?
-	 if @@HAS_ICONV.nil?
-	    @@HAS_ICONV = true
-	    begin
-	       require 'rubygems'
-	       require 'iconv'
-	    rescue LoadError
-	       @@HAS_ICONV = false
-	    end
-	 end
-	 @@HAS_ICONV
-      end
-      def self.from_nwk(nwk)
-	 if Tree.has_iconv?
-	    ic = Iconv.new('UTF-8//IGNORE','UTF-8')
-	    nwk = ic.iconv(nwk + ' ')[0..-2]
-	 end
-	 Node.new(nwk)
-      end
-   end
-   
-   # Node.new(nwk[, parent]): Initializes a new Node.
-   # nwk: Node's description in Newick format.
-   # parent: Node's parent, or nil if root node.
-   class Node
-      # Class
-      @@edges = []
-      def self.edges
-	 @@edges
-      end
-      def self.register(node)
-	 @@edges[node.index] = node unless node.index.nil?
-      end
-      # Class-level functions related to JPlace
-      def self.link_placement(placement)
-	 abort "Trying to link placement in undefined edge #{placement.edge_num}: #{placement.to_s}" if @@edges[placement.edge_num].nil?
-	 @@edges[placement.edge_num].add_placement!(placement)
-      end
-      def self.unlink_placement(placement)
-	 @@edges[placement.edge_num].delete_placement!(placement)
-      end
-      # Instance
-      attr_reader :children, :length, :name, :label, :index, :nwk, :parent, :placements, :collapsed
-      def initialize(nwk, parent=nil)
-	 abort "Empty newick.\n" if nwk.nil? or nwk==''
-	 nwk.gsub! /;(.)/, '--\1'
-	 @nwk = nwk
-	 @parent = parent
-	 @placements = []
-	 @collapsed = false
-	 # Find index
-	 index_m = /^(?<pre>.*){(?<idx>[0-9]+)}(?<post>[^\(\),;]*);?$/.match(nwk)
-	 if index_m.nil? and parent.nil? and nwk[nwk.length-1]==';'
-	    @index = nil
-	 else
-	    abort "Unindexed edge found:\n#{@nwk}\n" if index_m.nil?
-	    nwk = index_m[:pre]+index_m[:post]
-	    @index = index_m[:idx].to_i
-	 end
-	 # Find name, label, and length
-	 meta_m = /^(\((?<cont>.+)\))?(?<name>[^:\(\);]*)(:(?<length>[0-9\.Ee+-]*)(?<label>\[[^\[\]\(\);]+\])?)?;?$/.match(nwk) or
-	    abort "Cannot parse node metadata (index #{@index}):\n#{@nwk}\n"
-	 nwk = meta_m[:cont]
-	 @name = meta_m[:name]
-	 @length = meta_m[:length]
-	 @label = meta_m[:label]
-	 # Find children
-	 @children = []
-	 nwk ||= ''
-	 quote = nil
-	 while nwk != ''
-	    i = 0
-	    j = 0
-	    nwk.each_char do |chr|
-	       if quote.nil?
-		  if chr=='"' or chr=="'"
-		     quote = chr
-		  else
-		     i += 1 if chr=='('
-		     i -= 1 if chr==')'
-		     if i==0 and chr==','
-			i=nil
-			break
-		     end
-		  end
-	       else
-		  quote = nil if chr==quote
-	       end
-	       j += 1
-	    end
-	    abort "Unbalanced node at edge {#{@index}}, with leftness #{i}:\n#{@nwk}\n" unless i.nil? or i==0
-	    @children << Node.new(nwk[0 .. j-1],self)
-	    nwk = nwk.length==j ? '' : nwk[j+1 .. -1]
-	 end
-	 Node.register(self)
-      end
-      # Accessors/Setters
-      def name=(new_name)
-	 @name = new_name.gsub(/[\s\(\),;:]/, '_')
-      end
-      # Tree algorithms
-      def post_order &blk
-	 self.children.each { |n| n.post_order &blk }
-	 blk[self]
-      end
-      def in_order &blk
-	 abort "Tree must be dycotomic to traverse in_order, node #{self.cannonical_name} "+
-	    "has #{self.children.lenght} children." unless [0,2].include? self.children.length
-	 self.children[0].in_order &blk unless self.children[0].nil?
-	 blk[self]
-	 self.children[1].in_order &blk unless self.children[1].nil?
-      end
-      def pre_order &blk
-	 blk[self]
-	 self.children.each { |n| n.pre_order &blk }
-      end
-      def path_to_root
-	 if @path_to_root.nil?
-	    @path_to_root = [self]
-	    @path_to_root += self.parent.path_to_root unless self.parent.nil?
-	 end
-	 @path_to_root
-      end
-      def distance_to_root
-	 if @distance_to_root.nil?
-	    @distance_to_root = path_to_root.map{ |n| n.length.nil? ? 0.0 : n.length.to_f }.reduce(0.0, :+)
-	 end
-	 @distance_to_root
-      end
-      def lca(node)
-	 p1 = self.path_to_root
-	 p2 = node.path_to_root
-	 p1.find{ |n| p2.include? n }
-      end
-      def distance(node)
-	 self.distance_to_root + node.distance_to_root - (2.0 * self.lca(node).distance_to_root)
-      end
-      def ==(node) self.index == node.index ; end
-      # Tree representation
-      def cannonical_name
-	 return(self.name) unless self.name.nil? or self.name == ""
-	 return(self.label) unless self.label.nil? or self.label == ""
-	 return("{#{self.index.to_s}}") unless self.index.nil?
-	 ""
-      end
-      def to_s
-	 o = ""
-	 o += "(" + self.children.map{ |c| c.to_s }.join(",") + ")" if self.children.length > 0
-	 o += self.cannonical_name
-	 u = "#{self.length.nil? ? "" : self.length}#{self.label.nil? ? "" : self.label}"
-	 o += ":#{u}" unless u==""
-	 o
-      end
-      # Instance-level functions related to JPlace
-      def collapse!
-	 self.pre_order do |n|
-	    if n!=self
-	       while n.placements.length > 0
-		  p = Node.unlink_placement(n.placements[0])
-		  p.set_field_value('edge_num', self.index)
-		  Node.link_placement(p)
-	       end
-	    end
-	 end
-	 @collapsed = true
-      end
-      def add_placement!(placement)
-	 @placements << placement
-      end
-      def delete_placement!(placement)
-	 @placements.delete(placement)
-      end
-   end
-
-end # module JPlace
-