bio-vcf 0.8.1 → 0.8.2

data/lib/bio-vcf/vcfsample.rb

@@ -51,7 +51,16 @@ module BioVcf
       def cache_method(name, &block)
         self.class.send(:define_method, name, &block)
       end
-    
+
+      def [] name
+        if @format[name]
+          v = fetch_values(name) 
+          return nil if VcfValue::empty?(v)
+          return ConvertStringToValue::convert(v)
+        end
+        nil
+      end
+      
       def method_missing(m, *args, &block)
         name = m.to_s.upcase
         # p [:here,name,m ,@values]

data/ragel/gen_vcfheaderline_parser.rb

@@ -0,0 +1,483 @@
+
+# line 1 "gen_vcfheaderline_parser.rl"
+# Ragel lexer for VCF-header
+#
+# This is a partial lexer for the VCF header format. Bio-vcf uses this
+# to generate meta information in (for example) JSON format. The
+# advantage of using a full state engine is that it allows for easy
+# parsing of key-value pairs with syntax checking and, for example,
+# escaped quotes in quoted string values. This edition validates ID and
+# Number fields only.
+#
+# Note the .rb version is generated from ./ragel/gen_vcfheaderline_parser.rl
+
+module BioVcf
+
+  module VcfHeaderParser
+
+    module RagelKeyValues
+  
+=begin
+
+# line 57 "gen_vcfheaderline_parser.rl"
+
+=end
+
+
+# line 28 "gen_vcfheaderline_parser.rb"
+class << self
+	attr_accessor :_simple_lexer_actions
+	private :_simple_lexer_actions, :_simple_lexer_actions=
+end
+self._simple_lexer_actions = [
+	0, 1, 0, 1, 1, 1, 2, 1, 
+	3, 1, 4, 1, 5, 1, 6, 1, 
+	9, 2, 0, 1, 2, 7, 9, 2, 
+	8, 9, 3, 7, 8, 9
+]
+
+class << self
+	attr_accessor :_simple_lexer_key_offsets
+	private :_simple_lexer_key_offsets, :_simple_lexer_key_offsets=
+end
+self._simple_lexer_key_offsets = [
+	0, 0, 1, 2, 5, 6, 7, 8, 
+	14, 20, 27, 32, 34, 36, 38, 40, 
+	40, 40, 42, 44, 50, 57, 64, 68, 
+	74, 81, 89, 97, 105, 113, 120, 128, 
+	130, 132, 133, 134, 135, 136, 137, 138, 
+	139, 140, 141, 142, 144, 160, 167, 172, 
+	176, 184, 192, 196
+]
+
+class << self
+	attr_accessor :_simple_lexer_trans_keys
+	private :_simple_lexer_trans_keys, :_simple_lexer_trans_keys=
+end
+self._simple_lexer_trans_keys = [
+	35, 35, 65, 70, 73, 76, 84, 61, 
+	73, 78, 65, 90, 97, 122, 48, 57, 
+	65, 90, 97, 122, 61, 48, 57, 65, 
+	90, 97, 122, 32, 34, 39, 9, 13, 
+	34, 92, 34, 92, 39, 92, 39, 92, 
+	48, 57, 48, 57, 48, 57, 65, 90, 
+	97, 122, 68, 48, 57, 65, 90, 97, 
+	122, 61, 48, 57, 65, 90, 97, 122, 
+	65, 90, 97, 122, 48, 57, 65, 90, 
+	97, 122, 117, 48, 57, 65, 90, 97, 
+	122, 61, 109, 48, 57, 65, 90, 97, 
+	122, 61, 98, 48, 57, 65, 90, 97, 
+	122, 61, 101, 48, 57, 65, 90, 97, 
+	122, 61, 114, 48, 57, 65, 90, 97, 
+	122, 61, 48, 57, 65, 90, 97, 122, 
+	43, 45, 46, 65, 71, 82, 48, 57, 
+	48, 57, 73, 79, 76, 84, 69, 82, 
+	82, 77, 65, 78, 70, 79, 44, 60, 
+	32, 34, 39, 44, 46, 60, 9, 13, 
+	43, 45, 48, 57, 65, 90, 97, 122, 
+	32, 34, 39, 44, 60, 9, 13, 44, 
+	46, 60, 48, 57, 44, 60, 48, 57, 
+	44, 60, 48, 57, 65, 90, 97, 122, 
+	44, 60, 48, 57, 65, 90, 97, 122, 
+	44, 60, 48, 57, 44, 60, 0
+]
+
+class << self
+	attr_accessor :_simple_lexer_single_lengths
+	private :_simple_lexer_single_lengths, :_simple_lexer_single_lengths=
+end
+self._simple_lexer_single_lengths = [
+	0, 1, 1, 3, 1, 1, 1, 2, 
+	0, 1, 3, 2, 2, 2, 2, 0, 
+	0, 0, 0, 0, 1, 1, 0, 0, 
+	1, 2, 2, 2, 2, 1, 6, 0, 
+	2, 1, 1, 1, 1, 1, 1, 1, 
+	1, 1, 1, 2, 6, 5, 3, 2, 
+	2, 2, 2, 2
+]
+
+class << self
+	attr_accessor :_simple_lexer_range_lengths
+	private :_simple_lexer_range_lengths, :_simple_lexer_range_lengths=
+end
+self._simple_lexer_range_lengths = [
+	0, 0, 0, 0, 0, 0, 0, 2, 
+	3, 3, 1, 0, 0, 0, 0, 0, 
+	0, 1, 1, 3, 3, 3, 2, 3, 
+	3, 3, 3, 3, 3, 3, 1, 1, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 5, 1, 1, 1, 
+	3, 3, 1, 0
+]
+
+class << self
+	attr_accessor :_simple_lexer_index_offsets
+	private :_simple_lexer_index_offsets, :_simple_lexer_index_offsets=
+end
+self._simple_lexer_index_offsets = [
+	0, 0, 2, 4, 8, 10, 12, 14, 
+	19, 23, 28, 33, 36, 39, 42, 45, 
+	46, 47, 49, 51, 55, 60, 65, 68, 
+	72, 77, 83, 89, 95, 101, 106, 114, 
+	116, 119, 121, 123, 125, 127, 129, 131, 
+	133, 135, 137, 139, 142, 154, 161, 166, 
+	170, 176, 182, 186
+]
+
+class << self
+	attr_accessor :_simple_lexer_indicies
+	private :_simple_lexer_indicies, :_simple_lexer_indicies=
+end
+self._simple_lexer_indicies = [
+	0, 1, 2, 1, 3, 4, 5, 1, 
+	6, 1, 7, 1, 8, 1, 11, 12, 
+	10, 10, 9, 14, 14, 14, 13, 15, 
+	14, 14, 14, 13, 16, 17, 18, 16, 
+	13, 20, 21, 19, 23, 24, 22, 20, 
+	26, 25, 23, 28, 27, 27, 22, 29, 
+	13, 30, 13, 31, 31, 31, 13, 33, 
+	14, 14, 14, 32, 34, 14, 14, 14, 
+	32, 35, 35, 32, 36, 36, 36, 32, 
+	38, 14, 14, 14, 37, 15, 39, 14, 
+	14, 14, 37, 15, 40, 14, 14, 14, 
+	37, 15, 41, 14, 14, 14, 37, 15, 
+	42, 14, 14, 14, 37, 43, 14, 14, 
+	14, 37, 44, 44, 45, 45, 45, 45, 
+	46, 37, 47, 37, 48, 49, 1, 50, 
+	1, 51, 1, 52, 1, 7, 1, 53, 
+	1, 54, 1, 6, 1, 55, 1, 56, 
+	1, 7, 1, 57, 57, 1, 16, 17, 
+	18, 57, 8, 57, 16, 58, 29, 59, 
+	59, 1, 16, 17, 18, 57, 57, 16, 
+	1, 57, 60, 57, 29, 1, 57, 57, 
+	30, 1, 61, 61, 31, 31, 31, 1, 
+	62, 62, 36, 36, 36, 1, 63, 63, 
+	47, 1, 63, 63, 1, 0
+]
+
+class << self
+	attr_accessor :_simple_lexer_trans_targs
+	private :_simple_lexer_trans_targs, :_simple_lexer_trans_targs=
+end
+self._simple_lexer_trans_targs = [
+	2, 0, 3, 4, 32, 40, 5, 6, 
+	43, 0, 8, 20, 24, 0, 9, 44, 
+	10, 11, 13, 12, 45, 16, 12, 45, 
+	16, 14, 15, 14, 15, 46, 47, 48, 
+	0, 21, 22, 23, 49, 0, 25, 26, 
+	27, 28, 29, 30, 31, 51, 50, 50, 
+	33, 37, 34, 35, 36, 38, 39, 41, 
+	42, 7, 17, 19, 18, 7, 7, 7
+]
+
+class << self
+	attr_accessor :_simple_lexer_trans_actions
+	private :_simple_lexer_trans_actions, :_simple_lexer_trans_actions=
+end
+self._simple_lexer_trans_actions = [
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 26, 1, 1, 1, 15, 0, 7, 
+	0, 0, 0, 1, 17, 1, 0, 3, 
+	0, 1, 1, 0, 0, 0, 0, 0, 
+	20, 0, 5, 1, 0, 23, 0, 0, 
+	0, 0, 0, 5, 1, 1, 1, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 1, 0, 9, 11, 13
+]
+
+class << self
+	attr_accessor :_simple_lexer_eof_actions
+	private :_simple_lexer_eof_actions, :_simple_lexer_eof_actions=
+end
+self._simple_lexer_eof_actions = [
+	0, 0, 0, 0, 0, 0, 0, 26, 
+	15, 15, 15, 15, 15, 15, 15, 15, 
+	15, 15, 15, 15, 20, 20, 20, 20, 
+	23, 23, 23, 23, 23, 23, 23, 23, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	0, 0, 0, 0, 0, 0, 0, 0, 
+	9, 11, 13, 13
+]
+
+class << self
+	attr_accessor :simple_lexer_start
+end
+self.simple_lexer_start = 1;
+class << self
+	attr_accessor :simple_lexer_first_final
+end
+self.simple_lexer_first_final = 43;
+class << self
+	attr_accessor :simple_lexer_error
+end
+self.simple_lexer_error = 0;
+
+class << self
+	attr_accessor :simple_lexer_en_main
+end
+self.simple_lexer_en_main = 1;
+
+
+# line 61 "gen_vcfheaderline_parser.rl"
+# %% this just fixes our syntax highlighting...
+
+def self.run_lexer(buf, options = {})
+  do_debug = (options[:debug] == true)
+  data = buf.unpack("c*") if(buf.is_a?(String))
+  eof = data.length
+  values = []
+  stack = []
+
+  emit = lambda { |type, data, ts, p|
+    # Print the type and text of the last read token
+    # p ts,p
+    puts "#{type}: #{data[ts...p].pack('c*')}" if do_debug
+    values << [type,data[ts...p].pack('c*')]
+  }
+
+  error_code = nil
+  
+  
+# line 242 "gen_vcfheaderline_parser.rb"
+begin
+	p ||= 0
+	pe ||= data.length
+	cs = simple_lexer_start
+end
+
+# line 80 "gen_vcfheaderline_parser.rl"
+  
+# line 251 "gen_vcfheaderline_parser.rb"
+begin
+	_klen, _trans, _keys, _acts, _nacts = nil
+	_goto_level = 0
+	_resume = 10
+	_eof_trans = 15
+	_again = 20
+	_test_eof = 30
+	_out = 40
+	while true
+	_trigger_goto = false
+	if _goto_level <= 0
+	if p == pe
+		_goto_level = _test_eof
+		next
+	end
+	if cs == 0
+		_goto_level = _out
+		next
+	end
+	end
+	if _goto_level <= _resume
+	_keys = _simple_lexer_key_offsets[cs]
+	_trans = _simple_lexer_index_offsets[cs]
+	_klen = _simple_lexer_single_lengths[cs]
+	_break_match = false
+	
+	begin
+	  if _klen > 0
+	     _lower = _keys
+	     _upper = _keys + _klen - 1
+
+	     loop do
+	        break if _upper < _lower
+	        _mid = _lower + ( (_upper - _lower) >> 1 )
+
+	        if data[p].ord < _simple_lexer_trans_keys[_mid]
+	           _upper = _mid - 1
+	        elsif data[p].ord > _simple_lexer_trans_keys[_mid]
+	           _lower = _mid + 1
+	        else
+	           _trans += (_mid - _keys)
+	           _break_match = true
+	           break
+	        end
+	     end # loop
+	     break if _break_match
+	     _keys += _klen
+	     _trans += _klen
+	  end
+	  _klen = _simple_lexer_range_lengths[cs]
+	  if _klen > 0
+	     _lower = _keys
+	     _upper = _keys + (_klen << 1) - 2
+	     loop do
+	        break if _upper < _lower
+	        _mid = _lower + (((_upper-_lower) >> 1) & ~1)
+	        if data[p].ord < _simple_lexer_trans_keys[_mid]
+	          _upper = _mid - 2
+	        elsif data[p].ord > _simple_lexer_trans_keys[_mid+1]
+	          _lower = _mid + 2
+	        else
+	          _trans += ((_mid - _keys) >> 1)
+	          _break_match = true
+	          break
+	        end
+	     end # loop
+	     break if _break_match
+	     _trans += _klen
+	  end
+	end while false
+	_trans = _simple_lexer_indicies[_trans]
+	cs = _simple_lexer_trans_targs[_trans]
+	if _simple_lexer_trans_actions[_trans] != 0
+		_acts = _simple_lexer_trans_actions[_trans]
+		_nacts = _simple_lexer_actions[_acts]
+		_acts += 1
+		while _nacts > 0
+			_nacts -= 1
+			_acts += 1
+			case _simple_lexer_actions[_acts - 1]
+when 0 then
+# line 23 "gen_vcfheaderline_parser.rl"
+		begin
+ ts=p 		end
+when 1 then
+# line 24 "gen_vcfheaderline_parser.rl"
+		begin
+
+    emit.call(:value,data,ts,p)
+  		end
+when 2 then
+# line 28 "gen_vcfheaderline_parser.rl"
+		begin
+
+    emit.call(:kw,data,ts,p)
+  		end
+when 3 then
+# line 46 "gen_vcfheaderline_parser.rl"
+		begin
+ emit.call(:key_word,data,ts,p) 		end
+when 4 then
+# line 47 "gen_vcfheaderline_parser.rl"
+		begin
+ emit.call(:value,data,ts,p) 		end
+when 5 then
+# line 48 "gen_vcfheaderline_parser.rl"
+		begin
+ emit.call(:value,data,ts,p) 		end
+when 6 then
+# line 50 "gen_vcfheaderline_parser.rl"
+		begin
+ emit.call(:value,data,ts,p) 		end
+when 7 then
+# line 52 "gen_vcfheaderline_parser.rl"
+		begin
+ error_code="ID"		end
+when 8 then
+# line 53 "gen_vcfheaderline_parser.rl"
+		begin
+ error_code="Number"		end
+when 9 then
+# line 54 "gen_vcfheaderline_parser.rl"
+		begin
+ error_code="key-value" 		end
+# line 376 "gen_vcfheaderline_parser.rb"
+			end # action switch
+		end
+	end
+	if _trigger_goto
+		next
+	end
+	end
+	if _goto_level <= _again
+	if cs == 0
+		_goto_level = _out
+		next
+	end
+	p += 1
+	if p != pe
+		_goto_level = _resume
+		next
+	end
+	end
+	if _goto_level <= _test_eof
+	if p == eof
+	__acts = _simple_lexer_eof_actions[cs]
+	__nacts =  _simple_lexer_actions[__acts]
+	__acts += 1
+	while __nacts > 0
+		__nacts -= 1
+		__acts += 1
+		case _simple_lexer_actions[__acts - 1]
+when 4 then
+# line 47 "gen_vcfheaderline_parser.rl"
+		begin
+ emit.call(:value,data,ts,p) 		end
+when 5 then
+# line 48 "gen_vcfheaderline_parser.rl"
+		begin
+ emit.call(:value,data,ts,p) 		end
+when 6 then
+# line 50 "gen_vcfheaderline_parser.rl"
+		begin
+ emit.call(:value,data,ts,p) 		end
+when 7 then
+# line 52 "gen_vcfheaderline_parser.rl"
+		begin
+ error_code="ID"		end
+when 8 then
+# line 53 "gen_vcfheaderline_parser.rl"
+		begin
+ error_code="Number"		end
+when 9 then
+# line 54 "gen_vcfheaderline_parser.rl"
+		begin
+ error_code="key-value" 		end
+# line 428 "gen_vcfheaderline_parser.rb"
+		end # eof action switch
+	end
+	if _trigger_goto
+		next
+	end
+end
+	end
+	if _goto_level <= _out
+		break
+	end
+	end
+	end
+
+# line 81 "gen_vcfheaderline_parser.rl"
+
+  raise "ERROR: "+error_code+" in "+buf if error_code
+
+  begin
+    res = {}
+    # p values
+    values.each_slice(2) do | a,b |
+      # p '*',a,b
+      res[a[1]] = b[1]
+      # p h[:value] if h[:name]==:identifier or h[:name]==:value or h[:name]==:string
+    end
+  rescue
+    print "ERROR: "
+    p values
+    raise
+  end
+  p res if do_debug
+  res
+end
+    end
+  end 
+end
+
+if __FILE__ == $0
+
+lines = <<LINES
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth",Extra="Yes?">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
+##INFO=<ID=VP,Number=1,Type=String,Description="Variation Property.  Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf",Source="dbsnp",Version="138">
+##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id.  The gene symbol and id are delimited by a colon (:), and each pair is delimited by a vertical bar (|)">
+##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Variant names from HGVS. The order of these variants corresponds to the order of the info in the other clinical  INFO tags.">
+##INFO=<ID=CLNHGVS1,Number=.,Type=String,Description="Variant names from \\"HGVS\\". The order of these 'variants' corresponds to the order of the info in the other clinical  INFO tags.">
+LINES
+
+lines.strip.split("\n").each { |s|
+  print s,"\n"
+  p BioVcf::VcfHeaderParser::RagelKeyValues.run_lexer(s, debug: false)
+}
+
+end # test