miga-base 0.3.0.0 → 0.3.0.1

data/utils/enveomics/Scripts/ani.rb

@@ -0,0 +1,362 @@
+#!/usr/bin/env ruby
+
+# @author  Luis M. Rodriguez-R
+# @license Artistic-2.0
+
+require "optparse"
+require "tmpdir"
+has_rest_client = true
+has_sqlite3 = true
+begin
+  require "rubygems"
+  require "restclient"
+rescue LoadError
+  has_rest_client = false
+end
+begin
+  require "sqlite3"
+rescue LoadError
+  has_sqlite3 = false
+end
+
+o = {win:1000, step:200, id:70, len:700, correct:true, hits:50, q:false, bin:"",
+  program:"blast+", thr:1, dec:2, auto:false, lookupfirst:false,
+  dbregions:true, dbrbm: true, min_actg:0.95}
+ARGV << "-h" if ARGV.size==0
+OptionParser.new do |opts|
+  opts.banner = "
+Calculates the Average Nucleotide Identity between two genomes.
+
+Usage: #{$0} [options]"
+  opts.separator ""
+  opts.separator "Mandatory"
+  opts.on("-1", "--seq1 FILE",
+    "Path to the FastA file containing the genome 1."){ |v| o[:seq1] = v }
+  opts.on("-2", "--seq2 FILE",
+    "Path to the FastA file containing the genome 2."){ |v| o[:seq2] = v }
+  if has_rest_client
+    opts.separator "    Alternatively, you can supply a NCBI-acc with the " +
+      "format ncbi:CP014272 instead of files."
+  else
+    opts.separator "    Install rest-client to enable NCBI-acc support."
+  end
+  opts.separator ""
+  opts.separator "Search Options"
+  opts.on("-w", "--win INT",
+    "Window size in the ANI calculation (in bp).  By default: " +
+    "#{o[:win].to_s}."){ |v| o[:win] = v.to_i }
+  opts.on("-s", "--step INT",
+    "Step size in the ANI calculation (in bp).  By default: " +
+    "#{o[:step].to_s}."){ |v| o[:step] = v.to_i }
+  opts.on("-l", "--len INT",
+    "Minimum alignment length (in bp).  By default: #{o[:len]}."
+    ){ |v| o[:len] = v.to_i }
+  opts.on("-i", "--id NUM",
+    "Minimum alignment identity (in %).  By default: #{o[:id]}."
+    ){ |v| o[:id] = v.to_f }
+  opts.on("-n", "--hits INT",
+    "Minimum number of hits.  By default: #{o[:hits]}."
+    ){ |v| o[:hits] = v.to_i }
+  opts.on("-N", "--nocorrection",
+    "Report values without post-hoc correction."){ |v| o[:correct] = false }
+  opts.on("--min-actg FLOAT",
+    "Minimum fraction of ACTGN in the sequences before assuming proteins.",
+    "By default: #{o[:min_actg]}."
+    ){ |v| o[:min_actg] = v.to_f }
+  opts.separator ""
+  opts.separator "Software Options"
+  opts.on("-b", "--bin DIR",
+    "Path to the directory containing the binaries of the search program."
+    ){ |v| o[:bin] = v }
+  opts.on("-p", "--program STR",
+    "Search program to be used.  One of: blast+ (default), blast, blat."
+    ){ |v| o[:program] = v }
+  opts.on("-t", "--threads INT",
+    "Number of parallel threads to be used.  By default: #{o[:thr]}."
+    ){ |v| o[:thr] = v.to_i }
+  opts.separator ""
+  opts.separator "SQLite3 Options"
+  opts.on("-S", "--sqlite3 FILE",
+    "Path to the SQLite3 database to create (or update) with the results."
+    ){ |v| o[:sqlite3] = v }
+  opts.separator "    Install sqlite3 gem to enable database support." unless
+    has_sqlite3
+  opts.on("--name1 STR",
+    "Name of --seq1 to use in --sqlite3.  By default determined by filename."
+    ){ |v| o[:seq1name] = v }
+  opts.on("--name2 STR",
+    "Name of --seq2 to use in --sqlite3.  By default determined by filename."
+    ){ |v| o[:seq2name] = v }
+  opts.on("--[no-]save-regions",
+    "Save (or don't save) the fragments in the --sqlite3 database.",
+    "By default: #{o[:dbregions]}."){ |v| o[:dbregions] = !!v }
+  opts.on("--[no-]save-rbm",
+    "Save (or don't save) the reciprocal best matches in the --sqlite3 db.",
+    "By default: #{o[:dbrbm]}."){ |v| o[:dbrbm] = !!v }
+  opts.on("--lookup-first",
+    "Indicates if the ANI should be looked up first in the database.",
+    "Requires --sqlite3, --auto, --name1, and --name2.",
+    "Incompatible with --res, --tab, and --out."){ |v| o[:lookupfirst] = v }
+  opts.separator ""
+  opts.separator "Other Output Options"
+  opts.on("-d", "--dec INT",
+    "Decimal positions to report. By default: #{o[:dec]}"
+    ){ |v| o[:dec] = v.to_i }
+  opts.on("-o", "--out FILE",
+    "Saves a file describing the alignments used for two-way ANI."
+    ){ |v| o[:out] = v }
+  opts.on("-r", "--res FILE",
+    "Saves a file with the final results."){ |v| o[:res] = v }
+  opts.on("-T", "--tab FILE",
+    "Saves a file with the final two-way results in a tab-delimited form.",
+    "The columns are (in that order):",
+    "ANI, standard deviation, fragments used, fragments in the smallest genome."
+    ){ |v| o[:tab]=v }
+  opts.on("-a", "--auto",
+    "ONLY outputs the ANI value in STDOUT (or nothing, if calculation fails)."
+    ){ o[:auto] = 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 "-1 is mandatory" if o[:seq1].nil?
+abort "-2 is mandatory" if o[:seq2].nil?
+abort "SQLite3 requested (-S) but sqlite3 not supported.  First install gem " +
+  "sqlite3." unless o[:sqlite3].nil? or has_sqlite3
+abort "Step size must be smaller than window size." if o[:step] > o[:win]
+o[:bin] = o[:bin]+"/" if o[:bin].size > 0
+if o[:lookupfirst]
+  abort "--lookup-first needs --sqlite3" if o[:sqlite3].nil?
+  abort "--lookup-first requires --auto" unless o[:auto]
+  abort "--lookup-first requires --name1" if o[:seq1name].nil?
+  abort "--lookup-first requires --name2" if o[:seq2name].nil?
+  abort "--lookup-first conflicts with --res" unless o[:res].nil?
+  abort "--lookup-first conflicts with --tab" unless o[:tab].nil?
+  abort "--lookup-first conflicts with --out" unless o[:out].nil?
+end
+
+# Create SQLite3 file
+unless o[:sqlite3].nil?
+  $stderr.puts "Accessing SQLite3 file: #{o[:sqlite3]}." unless o[:q]
+  sqlite_db = SQLite3::Database.new o[:sqlite3]
+  sqlite_db.execute "create table if not exists regions( " +
+    "seq varchar(256), id int, source varchar(256), `start` int," +
+    " `end` int )"
+  sqlite_db.execute "create table if not exists rbm( seq1 varchar(256), " +
+    "seq2 varchar(256), id1 int, id2 int, id float, evalue float, " +
+    "bitscore float )"
+  sqlite_db.execute "create table if not exists ani( seq1 varchar(256), " +
+    "seq2 varchar(256), ani float, sd float, n int, omega int )"
+end
+
+# Look-up first
+if o[:lookupfirst]
+  val = sqlite_db.execute "select ani from ani where seq1=? and seq2=?",
+    [o[:seq1name], o[:seq2name]]
+  val = sqlite_db.execute "select ani from ani where seq1=? and seq2=?",
+    [o[:seq2name], o[:seq1name]] if val.empty?
+  unless val.empty?
+    puts val.first.first
+    exit
+  end
+end
+
+Dir.mktmpdir do |dir|
+  $stderr.puts "Temporal directory: #{dir}." unless o[:q]
+
+  # Create databases.
+  $stderr.puts "Creating databases." unless o[:q]
+  minfrg = nil
+  seq_names = []
+  seq_len = {}
+  actg_cnt = {}
+  [:seq1, :seq2].each do |seq|
+    abort "GIs are no longer supported by NCBI. Please use NCBI-acc instead" if
+      /^gi:/.match(o[seq])
+    acc = /^ncbi:(\S+)/.match(o[seq])
+    if not acc.nil?
+      abort "NCBI-acc requested but rest-client not supported.  First " +
+        "install gem rest-client." unless has_rest_client
+      response = RestClient.get(
+        "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
+        {params:{db:"nuccore",rettype:"fasta",id:acc[1],idtype:"acc"}})
+      abort "Unable to reach NCBI EUtils, error code " +
+        response.code.to_s + "." unless response.code == 200
+      o[seq] = "#{dir}/ncbi-#{seq.to_s}.fa"
+      fo = File.open(o[seq], "w")
+      fo.puts response.to_str
+      fo.close
+      seq_names << ( o[ "#{seq}name".to_sym ].nil? ?
+        "ncbi:#{acc[1]}" : o[ "#{seq}name".to_sym ] )
+    else
+      seq_names << ( o[ "#{seq}name".to_sym ].nil? ?
+        File.basename(o[seq], ".fna") : o[ "#{seq}name".to_sym ] )
+    end
+    $stderr.puts "  Reading FastA file: #{o[seq]}" unless o[:q]
+    sqlite_db.execute("delete from regions where seq=?",
+      [seq_names.last]) unless o[:sqlite3].nil?
+    buffer = ""
+    frgs = 0
+    seq_len[seq] = 0
+    actg_cnt[seq] = 0
+    seqs = 0
+    disc = 0
+    seqn = ""
+    from = 1
+    fi = File.open(o[seq], "r")
+    fo = File.open("#{dir}/#{seq.to_s}.fa", "w")
+    fi.each_line do |ln|
+      if ln =~ /^>(\S+)/
+        seqs += 1
+        disc += buffer.size
+        buffer = ""
+        seqn = $1
+        from = 1
+      else
+        ln.gsub!(/[^A-Za-z]/, '')
+        seq_len[seq]  += ln.length
+        actg_cnt[seq] += ln.gsub(/[^ACTGN]/,"").length
+        buffer = buffer + ln
+        while buffer.size > o[:win]
+          seq_i = buffer[0, o[:win]]
+          if seq_i =~ /^N+$/
+            disc += seq_i.size
+          else
+            frgs += 1
+            fo.puts ">#{frgs}"
+            fo.puts seq_i
+            sqlite_db.execute("insert into regions values(?,?,?,?,?)",
+              [seq_names.last, frgs, seqn, from, from+o[:win]]) if
+                not o[:sqlite3].nil? and o[:dbregions]
+          end
+          buffer = buffer[o[:step] .. -1]
+          from += o[:win]
+        end
+      end
+    end
+    fi.close
+    fo.close
+    actg_frx = actg_cnt[seq].to_f/seq_len[seq].to_f
+    abort "Input sequences appear to be proteins " +
+      "(ACTGN fraction: %.2f%%)." % (actg_frx*100) if actg_frx < o[:min_actg]
+    $stderr.puts "    Created #{frgs} fragments from #{seqs} sequences, " +
+      "discarded #{disc} bp." unless o[:q]
+    minfrg ||= frgs
+    minfrg = frgs if minfrg > frgs
+    case o[:program].downcase
+    when "blast"
+      `"#{o[:bin]}formatdb" -i "#{dir}/#{seq.to_s}.fa" -p F`
+    when "blast+"
+      `"#{o[:bin]}makeblastdb" -in "#{dir}/#{seq.to_s}.fa" -dbtype nucl`
+    when "blat"
+      # Nothing to do
+    else
+      abort "Unsupported program: #{o[:program]}."
+    end
+  end # [:seq1, :seq2].each
+
+  # Best-hits.
+  $stderr.puts "Running one-way comparisons." unless o[:q]
+  rbh = []
+  id2 = 0
+  sq2 = 0
+  n2  = 0
+  unless o[:sqlite3].nil?
+    sqlite_db.execute "delete from rbm where seq1=? and seq2=?", seq_names
+    sqlite_db.execute "delete from ani where seq1=? and seq2=?", seq_names
+  end
+  unless o[:out].nil?
+    fo = File.open(o[:out], "w")
+    fo.puts %w(identity aln.len mismatch gap.open evalue bitscore).join("\t")
+  end
+  res = File.open(o[:res], "w") unless o[:res].nil?
+  [1,2].each do |i|
+    qry_seen = []
+    q = "#{dir}/seq#{i}.fa"
+    s = "#{dir}/seq#{i==1?2:1}.fa"
+    case o[:program].downcase
+    when "blast"
+      `"#{o[:bin]}blastall" -p blastn -d "#{s}" -i "#{q}" \
+      -F F -v 1 -b 1 -a #{o[:thr]} -m 8 -o "#{dir}/#{i}.tab"`
+    when "blast+"
+      `"#{o[:bin]}blastn" -db "#{s}" -query "#{q}" \
+      -dust no -max_target_seqs 1 \
+      -num_threads #{o[:thr]} -outfmt 6 -out "#{dir}/#{i}.tab"`
+    when "blat"
+      `#{o[:bin]}blat "#{s}" "#{q}" -out=blast8 "#{dir}/#{i}.tab"`
+    else
+      abort "Unsupported program: #{o[:program]}."
+    end
+    fh = File.open("#{dir}/#{i}.tab", "r")
+    id = 0
+    sq = 0
+    n  = 0
+    fh.each_line do |ln|
+      ln.chomp!
+      row = ln.split(/\t/)
+      if qry_seen[ row[0].to_i ].nil? and row[3].to_i >= o[:len] and
+          row[2].to_f >= o[:id]
+        qry_seen[ row[0].to_i ] = 1
+        identity_corr = 100 - (100-row[2].to_f)/(o[:correct] ? 0.8621 : 1.0)
+        id += identity_corr
+        sq += identity_corr ** 2
+        n  += 1
+        if i==1
+          rbh[ row[0].to_i ] = row[1].to_i
+        else
+          if !rbh[ row[1].to_i ].nil? and rbh[ row[1].to_i ]==row[0].to_i
+            id2 += identity_corr
+            sq2 += identity_corr ** 2
+            n2  += 1
+            fo.puts [identity_corr,row[3..5],
+              row[10..11]].join("\t") unless o[:out].nil?
+            sqlite_db.execute("insert into rbm values(?,?,?,?,?,?,?)",
+              seq_names + [row[1], row[0], row[2], row[10], row[11]]
+              ) if not o[:sqlite3].nil? and o[:dbrbm]
+          end
+        end
+      end
+    end
+    fh.close
+    if n < o[:hits]
+      puts "Insuffient hits to estimate one-way ANI: #{n}." unless o[:auto]
+      res.puts "Insufficient hits to estimate one-way ANI: #{n}" unless
+        o[:res].nil?
+    else
+      printf "! One-way ANI %d: %.#{o[:dec]}f%% (SD: %.#{o[:dec]}f%%), " +
+        "from %i fragments.\n", i, id/n, (sq/n - (id/n)**2)**0.5, n unless
+        o[:auto]
+      res.puts sprintf "<b>One-way ANI %d:</b> %.#{o[:dec]}f%% " +
+        "(SD: %.#{o[:dec]}f%%), from %i fragments.<br/>", i, id/n,
+        (sq/n - (id/n)**2)**0.5, n unless o[:res].nil?
+    end
+  end # [1,2].each
+  if n2 < o[:hits]
+    puts "Insufficient hits to estimate two-way ANI: #{n2}" unless o[:auto]
+    res.puts "Insufficient hits to estimate two-way ANI: #{n2}" unless
+      o[:res].nil?
+  else
+    ani = id2/n2
+    ani_sd = (sq2/n2 - (id2/n2)**2)**0.5
+    printf "! Two-way ANI  : %.#{o[:dec]}f%% (SD: %.#{o[:dec]}f%%), " +
+      "from %i fragments.\n", ani, ani_sd, n2 unless o[:auto]
+    res.puts sprintf "<b>Two-way ANI:</b> %.#{o[:dec]}f%% " +
+      "(SD: %.#{o[:dec]}f%%), from %i fragments.<br/>",
+      ani, ani_sd, n2 unless o[:res].nil?
+    unless o[:tab].nil?
+      tab = File.open(o[:tab], "w")
+      tab.printf "%.#{o[:dec]}f\t%.#{o[:dec]}f\t%i\t%i\n",
+        ani, ani_sd, n2, minfrg
+      tab.close
+    end
+    sqlite_db.execute("insert into ani values(?,?,?,?,?,?)",
+      seq_names + [ani, ani_sd, n2, minfrg]) unless o[:sqlite3].nil?
+    puts ani if o[:auto]
+  end
+  res.close unless o[:res].nil?
+  fo.close unless o[:out].nil?
+end
+

data/utils/enveomics/Scripts/gi2tax.rb

@@ -0,0 +1,103 @@
+#!/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