protk 1.3.1.pre3 → 1.4.0

data/bin/pepxml_to_table.rb

@@ -19,6 +19,8 @@ include LibXML
 tool=Tool.new([:explicit_output])
 tool.option_parser.banner = "Convert a pepXML file to a tab delimited table.\n\nUsage: pepxml_to_table.rb [options] file1.pep.xml"
 
+tool.add_boolean_option(:invert_probabilities,false,["--invert-probabilities","Output 1-p instead of p for all probability values"])
+
 exit unless tool.check_options(true)
 
 input_file=ARGV[0]
@@ -29,7 +31,7 @@ else
   output_fh=$stdout
 end
 
-output_fh.write "protein\tpeptide\tassumed_charge\tcalc_neutral_pep_mass\tneutral_mass\tretention_time\tstart_scan\tend_scan\tsearch_engine\traw_score\tpeptideprophet_prob\tinterprophet_prob\n"
+output_fh.write "protein\tpeptide\tassumed_charge\tcalc_neutral_pep_mass\tneutral_mass\tretention_time\tstart_scan\tend_scan\tsearch_engine\traw_score\tpeptideprophet_prob\tinterprophet_prob\texperiment_label\n"
 
 XML::Error.set_handler(&XML::Error::QUIET_HANDLER)
 
@@ -52,6 +54,9 @@ spectrum_queries.each do |query|
   neutral_mass=query.attributes['precursor_neutral_mass']
   assumed_charge=query.attributes['assumed_charge']
 
+  experiment_label=""
+  experiment_label=query.attributes['experiment_label'] unless query.attributes['experiment_label'].nil?
+
   top_search_hit=query.find("./#{pepxml_ns_prefix}search_result/#{pepxml_ns_prefix}search_hit",pepxml_ns)[0]
   peptide=top_search_hit.attributes['peptide']
   protein=top_search_hit.attributes['protein']
@@ -76,6 +81,9 @@ spectrum_queries.each do |query|
   when /MS\-GF/
     search_score_nodes=top_search_hit.find("./#{pepxml_ns_prefix}search_score[@name=\"EValue\"]",[pepxml_ns])
     raw_score=search_score_nodes[0].attributes['value']    
+  when /MASCOT/
+    search_score_nodes=top_search_hit.find("./#{pepxml_ns_prefix}search_score[@name=\"ionscore\"]",[pepxml_ns])
+    raw_score=search_score_nodes[0].attributes['value']
   end
 
   
@@ -87,7 +95,12 @@ spectrum_queries.each do |query|
   peptide_prophet_prob=pp_result[0].value if ( pp_result.length>0 )
   interprophet_prob=ip_result[0].value if ( ip_result.length>0)
   
-  output_fh.write "#{protein}\t#{peptide}\t#{assumed_charge}\t#{calc_neutral_pep_mass}\t#{neutral_mass}\t#{retention_time}\t#{start_scan}\t#{end_scan}\t#{search_engine}\t#{raw_score}\t#{peptide_prophet_prob}\t#{interprophet_prob}\n"
+  if tool.invert_probabilities
+    peptide_prophet_prob = (1.0-peptide_prophet_prob.to_f).round(3) if peptide_prophet_prob!=""
+    interprophet_prob = (1.0 - interprophet_prob.to_f).round(3) if interprophet_prob!=""
+  end
+
+  output_fh.write "#{protein}\t#{peptide}\t#{assumed_charge}\t#{calc_neutral_pep_mass}\t#{neutral_mass}\t#{retention_time}\t#{start_scan}\t#{end_scan}\t#{search_engine}\t#{raw_score}\t#{peptide_prophet_prob}\t#{interprophet_prob}\t#{experiment_label}\n"
 
 end
 

data/bin/protein_prophet.rb

@@ -38,7 +38,7 @@ prophet_tool.add_value_option(:minindep,0,['--minindep mp',"Minimum percentage o
 exit unless prophet_tool.check_options(true)
 
 # Obtain a global environment object
-genv=Constants.new
+genv=Constants.instance
 
 input_stagers=[]
 inputs=ARGV.collect { |file_name| file_name.chomp}
@@ -60,10 +60,50 @@ if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
   cmd << " #{inputs.join(" ")} #{output_file}"
 
+  if ( prophet_tool.iproph )
+    cmd << " IPROPHET "
+  end
+
+  if ( prophet_tool.nooccam )
+    cmd << " NOOCCAM "
+  end
+
+  if ( prophet_tool.groupwts )
+    cmd << " GROUPWTS "
+  end
+
+  if ( prophet_tool.normprotlen )
+    cmd << " NORMPROTLEN "
+  end
+
+  if ( prophet_tool.logprobs )
+    cmd << " LOGPROBS "
+  end
+
+  if ( prophet_tool.allpeps )
+    cmd << " ALLPEPS "
+  end
+
+  if ( prophet_tool.unmapped )
+    cmd << " UNMAPPED "
+  end
+
   if ( prophet_tool.glyco )
     cmd << " GLYC "
   end
 
+  if ( prophet_tool.delude )
+    cmd << " DELUDE "
+  end
+
+  if ( prophet_tool.instances )
+    cmd << " INSTANCES "
+  end
+
+  cmd << " MINPROB=#{prophet_tool.minprob} "
+
+  cmd << " MININDEP=#{prophet_tool.minindep} "
+
   # Run the analysis
   #
   code = prophet_tool.run(cmd,genv)

data/bin/protk_setup.rb

@@ -13,7 +13,7 @@ toolname=ARGV[0]
 if ARGV[1]=='--change-location'
 	location=ARGV[2]
 	p "Changing default location for #{toolname} to #{location}"
-	env=Constants.new
+	env=Constants.instance
 	env.update_user_config({"#{toolname}_root"=>location})
 	exit
 end
@@ -37,7 +37,7 @@ if ( ARGV.length < 1)
 	exit
 end
 
-env=Constants.new
+env=Constants.instance
 
 toolname=ARGV.shift
 

data/bin/protxml_to_gff.rb

@@ -54,7 +54,7 @@ def prepare_fasta(database_path,type)
   when Pathname.new(database_path).exist? # It's an explicitly named db  
     db_filename = Pathname.new(database_path).expand_path.to_s
   else
-    db_filename=Constants.new.current_database_for_name(database_path)
+    db_filename=Constants.instance.current_database_for_name(database_path)
   end
 
 
@@ -84,11 +84,10 @@ tool.add_value_option(:genome_idregex,nil,['--genome-idregex pre','Regex with ca
 
 exit unless tool.check_options(true,[:database,:coords_file])
 
-$protk = Constants.new
+$protk = Constants.instance
 log_level = tool.debug ? "info" : "warn"
 $protk.info_level= log_level
 
-
 input_file=ARGV[0]
 
 if tool.explicit_output
@@ -101,58 +100,67 @@ should_ = tool.debug || (output_fh!=$stdout)
 
 input_protxml=ARGV[0]
 
+$protk.log "Creating GFFDB", :info
 gffdb = GFFDB.create(tool.coords_file) if tool.coords_file
 
 # genome_db = prepare_fasta(tool.genome,'nucl')
+$protk.log "Preparing FASTA index", :info
 prot_db = prepare_fasta(tool.database,'prot')
 
+$protk.log "Parsing protxml", :info
 proteins = parse_proteins(input_protxml)
 
 num_missing_gff_entries = 0
 
 proteins.each do |protein|
 
-	begin
-		# Get the full protein sequence
-		#
-		parsed_name_for_protdb = protein_id_to_protdbid(protein.protein_name)
-		protein_entry = prot_db.get_by_id parsed_name_for_protdb
-		raise ProteinNotInDBError if ( protein_entry == nil)
-
-		protein.sequence = protein_entry.aaseq
-
-		# Get the CDS and parent entries from the gff file
-		#
-		parsed_name_for_gffid = protein_id_to_gffid(protein.protein_name,tool.gff_idregex)
-		gff_parent_entries = gffdb.get_by_id(parsed_name_for_gffid)
-		raise NoGFFEntryFoundError if gff_parent_entries.nil? || gff_parent_entries.length==0
-		raise MultipleGFFEntriesForProteinError if gff_parent_entries.length > 1
-
-		gff_parent_entry = gff_parent_entries.first
-		gff_cds_entries = gffdb.get_cds_by_parent_id(parsed_name_for_gffid)
-
-		# Account for sixframe case. Parent is CDS and there are no children
-		#
-		gff_cds_entries=[gff_parent_entry] if gff_cds_entries.nil? && gff_parent_entry.feature=="CDS"
-
-		peptides = tool.stack_charge_states ? protein.peptides : protein.representative_peptides
-
-		peptides.each do |peptide|
-			peptide_entries = peptide.to_gff3_records(protein_entry.aaseq,gff_parent_entry,gff_cds_entries)
-			peptide_entries.each do |peptide_entry|
-				output_fh.write peptide_entry.to_s
+	if protein.probability >= tool.protein_probability_threshold
+
+		begin
+			$protk.log "Mapping #{protein.protein_name}", :info
+			# Get the full protein sequence
+			#
+			parsed_name_for_protdb = protein_id_to_protdbid(protein.protein_name)
+			protein_entry = prot_db.get_by_id parsed_name_for_protdb
+			raise ProteinNotInDBError if ( protein_entry == nil)
+
+			protein.sequence = protein_entry.aaseq
+
+			# Get the CDS and parent entries from the gff file
+			#
+			parsed_name_for_gffid = protein_id_to_gffid(protein.protein_name,tool.gff_idregex)
+			gff_parent_entries = gffdb.get_by_id(parsed_name_for_gffid)
+			raise NoGFFEntryFoundError if gff_parent_entries.nil? || gff_parent_entries.length==0
+			raise MultipleGFFEntriesForProteinError if gff_parent_entries.length > 1
+
+			gff_parent_entry = gff_parent_entries.first
+			gff_cds_entries = gffdb.get_cds_by_parent_id(parsed_name_for_gffid)
+
+			# Account for sixframe case. Parent is CDS and there are no children
+			#
+			gff_cds_entries=[gff_parent_entry] if gff_cds_entries.nil? && gff_parent_entry.feature=="CDS"
+
+			peptides = tool.stack_charge_states ? protein.peptides : protein.representative_peptides
+
+			peptides.each do |peptide|
+				if peptide.nsp_adjusted_probability >= tool.peptide_probability_threshold
+					peptide_entries = peptide.to_gff3_records(protein_entry.aaseq,gff_parent_entry,gff_cds_entries)
+					peptide_entries.each do |peptide_entry|
+						output_fh.write peptide_entry.to_s
+					end
+				end
 			end
-		end
 
-	rescue NoGFFEntryFoundError
-		$protk.log "No gff entry for #{parsed_name_for_gffid}", :info
-		num_missing_gff_entries+=1
-	rescue ProteinNotInDBError
-		$protk.log "No entry for #{parsed_name_for_protdb}", :info
-	rescue MultipleGFFEntriesForProteinError
-		$protk.log "Multiple entries in gff file for #{parsed_name_for_gffid}", :info
-	rescue PeptideNotInProteinError
-		$protk.log "A peptide was not found in its parent protein #{protein.protein_name}" , :warn
+		rescue NoGFFEntryFoundError
+			$protk.log "No gff entry for #{parsed_name_for_gffid}", :info
+			num_missing_gff_entries+=1
+		rescue ProteinNotInDBError
+			$protk.log "No entry for #{parsed_name_for_protdb}", :info
+		rescue MultipleGFFEntriesForProteinError
+			$protk.log "Multiple entries in gff file for #{parsed_name_for_gffid}", :info
+		rescue PeptideNotInProteinError
+			$protk.log "A peptide was not found in its parent protein #{protein.protein_name}" , :warn
+		end
 	end
 end
 

data/bin/protxml_to_psql.rb

@@ -24,7 +24,7 @@ def prepare_fasta(database_path,type)
   when Pathname.new(database_path).exist? # It's an explicitly named db  
     db_filename = Pathname.new(database_path).expand_path.to_s
   else
-    db_filename=Constants.new.current_database_for_name(database_path)
+    db_filename=Constants.instance.current_database_for_name(database_path)
   end
 
   db_indexfilename = "#{db_filename}.pin"

data/bin/protxml_to_table.rb

@@ -20,6 +20,7 @@ tool=Tool.new([:explicit_output])
 tool.option_parser.banner = "Convert a protXML file to a tab delimited table.\n\nUsage: protxml_to_table.rb [options] file1.protXML"
 
 tool.add_boolean_option(:groups,false,["--groups","Print output by groups rather than for each protein"])
+tool.add_boolean_option(:invert_probabilities,false,["--invert-probabilities","Output 1-p instead of p for all probability values"])
 
 exit unless tool.check_options(true)
 
@@ -78,12 +79,20 @@ protein_groups.each do |protein_group|
 		column_values=[]
 
 		column_values << protein_group.attributes['group_number']
-		column_values << protein_group.attributes['probability']
+
+		grp_prob = protein_group.attributes['probability']
+		grp_prob = (1.0-grp_prob.to_f).round(3) if tool.invert_probabilities
+		column_values << grp_prob
 
 		column_values << protein.attributes['protein_name']
 		column_values << protein_id
 		column_values << indis_proteins_summary
-		column_values << protein.attributes['probability']
+
+		prt_prob = protein.attributes['probability']
+		prt_prob = (1.0-prt_prob.to_f).round(3) if tool.invert_probabilities		
+		column_values << prt_prob
+
+
 		column_values << protein.attributes['percent_coverage']
 		column_values << protein.attributes['unique_stripped_peptides']
 		column_values << protein.attributes['total_number_peptides']
@@ -96,7 +105,11 @@ protein_groups.each do |protein_group|
 	end
 
 	group_column_values=[protein_group.attributes['group_number']]
-	group_column_values<<protein_group.attributes['probability']
+
+	grp_prob = protein_group.attributes['probability']
+	grp_prob = (1.0-grp_prob.to_f).round(3) if tool.invert_probabilities
+	group_column_values<<grp_prob
+
 	group_column_values<<group_members.join(" ")
 
 	if tool.groups

data/bin/repair_run_summary.rb

@@ -17,7 +17,7 @@ include LibXML
 
 # Environment with global constants
 #
-genv=Constants.new
+genv=Constants.instance
 
 
 # Setup specific command-line options for this tool. Other options are inherited from Tool

data/bin/sixframe.rb

@@ -28,7 +28,7 @@ tool.option_parser.banner = "Create a sixframe translation of a genome.\n\nUsage
 
 tool.add_boolean_option(:print_coords,false,['--coords', 'Write genomic coordinates in the fasta header'])
 tool.add_boolean_option(:keep_header,true,['--strip-header', 'Dont write sequence definition'])
-tool.add_value_option(:min_len,20,['--min-len','Minimum ORF length to keep'])
+tool.add_value_option(:min_len,20,['--min-len l','Minimum ORF length to keep'])
 tool.add_boolean_option(:write_gff,false,['--gff3','Output gff3 instead of fasta'])
 
 exit unless tool.check_options(true)
@@ -58,7 +58,7 @@ file.each do |entry|
     oi=0
     orfs.each do |orf|
       oi+=1
-      if ( orf.length > tool.min_len )
+      if ( orf.length > tool.min_len.to_i )
 
         position_start = position
         position_end = position_start + orf.length*3 -1

data/bin/swissprot_to_table.rb

@@ -61,7 +61,7 @@ end
 exit unless tool.check_options(true,[:database])
 
 
-$protk = Constants.new
+$protk = Constants.instance
 log_level = tool.debug ? :debug : :fatal
 $protk.info_level= log_level
 

data/bin/tandem_search.rb

@@ -15,7 +15,7 @@ include LibXML
 
 # Environment with global constants
 #
-genv=Constants.new
+genv=Constants.instance
 search_tool=TandemSearchTool.new()
 
 exit unless search_tool.check_options(true)

data/bin/tandem_to_pepxml.rb

@@ -12,7 +12,7 @@ require 'protk/search_tool'
 
 # Environment with global constants
 #
-genv=Constants.new
+genv=Constants.instance
 
 tool=SearchTool.new([:explicit_output,:over_write,:prefix])
 tool.option_parser.banner = "Convert tandem files to pep.xml files.\n\nUsage: tandem_to_pepxml.rb [options] file1.dat file2.dat ... "

data/lib/protk/constants.rb

@@ -7,9 +7,10 @@
 require 'yaml'
 require 'logger'
 require 'pathname'
+require 'singleton'
 
 class Constants
-
+  include Singleton
   # A Hash holding all the constants
   #
   @env

data/lib/protk/convert_util.rb

@@ -11,7 +11,7 @@ class ConvertUtil
 
   def self.index_mzml(mzml_file)
     Dir.mktmpdir do |tmpdir|
-      genv=Constants.new
+      genv=Constants.instance
       %x["#{genv.msconvert} -o #{tmpdir} #{mzml_file}"]
       indexed_file = Dir["#{tmpdir}/*"][0]
       FileUtils.mv(indexed_file, mzml_file)

data/lib/protk/data/tandem-style.css

@@ -0,0 +1,349 @@
+.c {
+	cursor:pointer
+} 
+
+.b {
+	color:red;
+	font-family: Verdana,Arial,Helvetica,sans-serif; 
+	font-weight:bold;
+	Font-size: 8pt;
+	text-decoration:none
+} 
+
+.e{
+	margin-left:1em;
+	text-indent:-1em;
+	margin-right:1em;
+	margin-bottom:3pt
+} 
+
+.k{
+	margin-left:+3em;
+	text-indent:0em;
+	margin-right:1em;
+} 
+
+.fm{
+	font-family:Courier New,Courier,monospace;
+	font-size:11pt;
+	font-style:normal;
+	color:white;
+	font-variant:normal;
+	text-decoration:underline;
+	font-weight:bold;
+	cursor:pointer;
+	background-color:red;
+}
+
+.f{
+	font-family:Courier New,Courier,monospace;
+	font-size:11pt;
+	font-style:normal;
+	color:red;
+	font-variant:normal;
+	text-decoration:none;
+	font-weight:bold;
+	cursor:pointer;
+	background-color:white;
+}
+
+.f1{
+	font-family:Courier New,Courier,monospace;
+	font-size:11pt;
+	font-style:normal;
+	color:red;
+}
+
+.f2{
+	font-family:Courier New,Courier,monospace;
+	font-size:11pt;
+	font-style:normal;
+	color:black;
+}
+
+.db{
+	text-indent:0px;
+	margin-left:1em;
+	margin-top:0px;
+	margin-bottom:0px;
+	padding-left:.3em;
+	border-left:1px solid #CCCCCC;
+	font-family:Courier New,Courier,monospace;
+} 
+
+.di{
+	font-family:Courier New,Courier,monospace;
+} 
+
+.cb{
+	text-indent:0px;
+	margin-left:1em;
+	margin-top:0px;
+	margin-bottom:0px;
+	padding-left:.3em;
+	font-family:Courier New,Courier,monospace;
+	color:#888888
+} 
+
+.ci{
+	font-family:Courier New,Courier,monospace;
+	color:#888888
+} 
+
+PRE {
+	margin:0px;
+	display:inline
+}
+
+.aa_h {
+	color:black;
+	font-weight: normal;
+	font-family: Courier New,Courier,monospace;
+	font-size: 10pt;
+	background-color:#99AAFF;
+}
+
+.aa_s {
+	color:black;
+	font-weight: normal;
+	font-family: Courier New,Courier,monospace;
+	font-size: 8pt;
+}
+
+.residues {
+	color: black; 
+	text-decoration: none;
+	font-family: Courier New,Courier,monospace;
+	font-size: 10pt;
+}
+
+.top_note {
+	color: black; 
+	text-decoration: none;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 10pt;
+}
+
+.top_highlight {
+	color: black; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 10pt;}
+
+.greek {
+	color: black; 
+	text-decoration: none;
+	font-family: Symbol,sans-serif;
+	font-size: 10pt;
+}
+
+.greek_b {
+	color: red; 
+	font-weight: bold;
+	text-decoration: none;
+	font-family: Symbol,sans-serif;
+	font-size: 12pt;
+}
+
+.top_label {
+	color: blue; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 10pt;
+}
+
+.peptide_label {
+	color: black; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 10pt;
+}
+td {
+	color: black; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+p {
+	color: black; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+th {
+	color: black; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+big {
+	color: black; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+h3 {
+	color: black; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 10pt;
+}
+
+.mod {
+	color: white;
+	background-color: blue; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.mut {
+	color: white;
+	background-color: red; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.y0 {	
+	color: red; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.y17 {
+	color: #FF9933; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.b0 {
+	color: blue; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.b17 {
+	color: green; 
+	font-weight: bold;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.small_label {
+	color: black; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.small_link {
+	color: blue; 
+	cursor: pointer;
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.small_value {
+	color: blue; 
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.go_button {
+	color: white; 
+	cursor: pointer;
+	font-weight: normal;
+	font-style: normal;
+	font-family: Trebuchet MS, Verdana, Arial, Helvetica,sans-serif;
+	font-size: 12pt;
+	width: 120px;
+	background-color:#ff9933;
+	border-color: #ffaa44;
+	border-width: 2px;
+	border-style: ridge;
+	height: 30px;
+}
+
+a {
+	color: blue; 
+	cursor: pointer;
+	font-weight: normal;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	text-decoration: none;
+	font-size: 8pt;
+}
+
+a:hover {
+	color: blue; 
+	cursor: pointer;
+	font-weight: normal;
+	font-style: normal;
+	text-decoration: underline;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+a:visited {
+	color: blue; 
+	cursor: pointer;
+	font-weight: normal;
+	font-style: italic;
+	font-variant: small-caps;
+	text-decoration: underline;
+	font-family: Verdana, Arial, Helvetica,sans-serif;
+	font-size: 8pt;
+}
+
+.button {
+	cursor: pointer;
+	border: #FFFFFF thin solid; 
+	border-width: 1px;  
+	font-weight: bold; 
+	font-size: 10px; 
+	color: white; 
+	line-height: 16px; 
+	padding-top: 2px; 
+	padding-right: 2px; 
+	padding-left: 2px; 
+	padding-bottom: 2px;  
+	font-family: Verdana,Arial,Helvetica,sans-serif; 
+	text-decoration: none;
+	background-color: black;
+}
+
+.button:hover {
+	cursor: pointer;
+	border: black thin solid; 
+	border-width: 1px;  
+	font-weight: bold; 
+	font-size: 10px; 
+	color: Blue; 
+	line-height: 16px; 
+	padding-top: 2px; 
+	padding-right: 2px; 
+	padding-left: 2px; 
+	padding-bottom: 2px;  
+	font-family: Verdana,Arial,Helvetica,sans-serif; 
+	text-decoration: none;
+	background-color: silver;
+}
+
+.ensembl {
+	color:#5A85D6;
+	font-weight: bold;
+	text-decoration:none;
+	font-family: Verdana,Arial,Helvetica,sans-serif;
+	font-size: 10pt;
+	background-color:#ffdf27;
+}
+