ngoto-bio 1.2.9.9001

data/lib/bio/db/embl/format_embl.rb

@@ -0,0 +1,190 @@
+#
+# = bio/db/embl/format_embl.rb - EMBL format generater
+#
+# Copyright::  Copyright (C) 2008
+#              Jan Aerts <jandot@bioruby.org>,
+#              Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: format_embl.rb,v 1.1.2.7 2008/06/19 12:45:15 ngoto Exp $
+#
+
+require 'bio/sequence/format'
+
+module Bio::Sequence::Format::NucFormatter
+
+  # INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.
+  # Embl format output class for Bio::Sequence.
+  class Embl < Bio::Sequence::Format::FormatterBase
+
+    # helper methods
+    include Bio::Sequence::Format::INSDFeatureHelper
+    
+    private
+
+    # wrapping with EMBL style
+    def embl_wrap(prefix, str)
+      wrap(str.to_s, 80, prefix)
+    end
+
+    # Given words (an Array of String) are wrapping with EMBL style.
+    # Each word is never splitted inside the word.
+    def embl_wrap_words(prefix, array)
+      width = 80
+      result = []
+      str = nil
+      array.each do |x|
+        if str then
+          if str.length + 1 + x.length > width then
+            str = nil
+          else
+            str.concat ' '
+            str.concat x
+          end
+        end
+        unless str then
+          str = prefix + x
+          result.push str
+        end
+      end
+      result.join("\n")
+    end
+
+    # format reference
+    # ref:: Bio::Reference object
+    # hash:: (optional) a hash for RN (reference number) administration
+    def reference_format_embl(ref, hash = nil)
+      lines = Array.new
+      if ref.embl_gb_record_number or hash then
+        refno = ref.embl_gb_record_number.to_i
+        hash ||= {}
+        if refno <= 0 or hash[refno] then
+          refno = hash.keys.sort[-1].to_i + 1
+          hash[refno] = true
+        end
+        lines << embl_wrap("RN   ", "[#{refno}]")
+      end
+      if ref.comments then
+        ref.comments.each do |cmnt|
+          lines << embl_wrap("RC   ", cmnt)
+        end
+      end
+      unless ref.sequence_position.to_s.empty? then
+        lines << embl_wrap("RP   ",   "#{ref.sequence_position}")
+      end
+      unless ref.doi.to_s.empty? then
+        lines << embl_wrap("RX   ",   "DOI; #{ref.doi}.")
+      end
+      unless ref.pubmed.to_s.empty? then
+        lines << embl_wrap("RX   ",   "PUBMED; #{ref.pubmed}.")
+      end
+      unless ref.authors.empty? then
+        auth = ref.authors.collect do |x|
+          y = x.to_s.strip.split(/\, *([^\,]+)\z/)
+          y[1].gsub!(/\. +/, '.') if y[1]
+          y.join(' ')
+        end
+        lastauth = auth.pop
+        auth.each { |x| x.concat ',' }
+        auth.push(lastauth.to_s + ';')
+        lines << embl_wrap_words('RA   ', auth)
+      end
+      lines << embl_wrap('RT   ',
+                         (ref.title.to_s.empty? ? '' :
+                          "\"#{ref.title}\"") + ';')
+      unless ref.journal.to_s.empty? then
+        volissue = "#{ref.volume.to_s}"
+        volissue = "#{volissue}(#{ref.issue})" unless ref.issue.to_s.empty? 
+        rl = "#{ref.journal}"
+        rl += " #{volissue}" unless volissue.empty? 
+        rl += ":#{ref.pages}" unless ref.pages.to_s.empty?
+        rl += "(#{ref.year})" unless ref.year.to_s.empty?
+        rl += '.'
+        lines << embl_wrap('RL   ', rl)
+      end
+      lines << "XX"
+      return lines.join("\n")
+    end
+
+    def seq_format_embl(seq)
+      counter = 0
+      result = seq.gsub(/.{1,60}/) do |x|
+        counter += x.length
+        x = x.gsub(/.{10}/, '\0 ')
+        sprintf("     %-66s%9d\n", x, counter)
+      end
+      result.chomp!
+      result
+    end
+
+    def seq_composition(seq)
+      { :a => seq.count('aA'),
+        :c => seq.count('cC'),
+        :g => seq.count('gG'),
+        :t => seq.count('tTuU'),
+        :other => seq.count('^aAcCgGtTuU')
+      }
+    end
+
+    # moleculue type
+    def mol_type_embl
+      if mt = molecule_type then
+        mt
+      elsif f = (features or []).find { |f| f.feature == 'source' } and
+          q = f.qualifiers.find { |q| q.qualifier == 'mol_type' } then
+        q.value
+      else
+        'NA'
+      end
+    end
+
+    # CC line. Comments.
+    def comments_format_embl(cmnts)
+      return '' if !cmnts or cmnts.empty?
+      cmnts = [ cmnts ] unless cmnts.kind_of?(Array)
+      a = []
+      cmnts.each do |str|
+        a.push embl_wrap('CC   ', str)
+      end
+      unless a.empty? then
+        a.push "XX   "
+        a.push '' # dummy to put "\n" at the end of the string
+      end
+      a.join("\n")
+    end
+
+
+    # Erb template of EMBL format for Bio::Sequence
+    erb_template <<'__END_OF_TEMPLATE__'
+ID   <%= primary_accession || entry_id %>; SV <%= sequence_version %>; <%= topology %>; <%= mol_type_embl %>; <%= data_class %>; <%= division %>; <%= seq.length %> BP.
+XX   
+<%= embl_wrap('AC   ', accessions.reject{|a| a.nil?}.join('; ') + ';') %>
+XX   
+DT   <%= format_date(date_created || null_date) %> (Rel. <%= release_created || 0 %>, Created)
+DT   <%= format_date(date_modified || null_date) %> (Rel. <%= release_modified || 0 %>, Last updated, Version <%= entry_version || 0 %>)
+XX   
+<%= embl_wrap('DE   ', definition) %>
+XX   
+<%= embl_wrap('KW   ', (keywords || []).join('; ') + '.') %>
+XX   
+OS   <%= species %>
+<%= embl_wrap('OC   ', (classification || []).join('; ') + '.') %>
+XX   
+<% hash = {}; (references || []).each do |ref| %><%= reference_format_embl(ref, hash) %>
+<% end %><% (dblinks || []).each do |r|
+%>DR   <%= r.database %>; <%= r.id %><% unless r.secondary_ids.empty? %>; <%= r.secondary_ids[0] %><% end %>.
+<% end %><% if dblinks and !dblinks.empty? then
+ %>XX   
+<% end %><%= comments_format_embl(comments)
+%>FH   Key             Location/Qualifiers
+FH   
+<%= format_features_embl(features || []) %>XX   
+SQ   Sequence <%= seq.length %> BP; <% c = seq_composition(seq) %><%= c[:a] %> A; <%= c[:c] %> C; <%= c[:g] %> G; <%= c[:t] %> T; <%= c[:other] %> other;
+<%= seq_format_embl(seq) %>
+//
+__END_OF_TEMPLATE__
+
+  end #class Embl
+
+end #module Bio::Sequence::Format::NucFormatter
+