full_lengther_next 0.6.2 → 0.9.8

data/lib/full_lengther_next/classes/fln_stats.rb

@@ -1,641 +0,0 @@
-require 'types.rb'
-
-module FlnStats
-	def initialize_stats_hash
-		stats_hash = {}
-		stats_hash['input_seqs'] = 0
-		stats_hash['output_seqs'] = 0
-		stats_hash['failed'] = 0
-		stats_hash['sequences_>200'] = 0
-		stats_hash['sequences_>500'] = 0
-		stats_hash['longest_unigene'] = 0
-		stats_hash['good_seqs'] = 0	
-		stats_hash['artifacts'] = 0
-		stats_hash['misassembled'] = 0
-		stats_hash['chimeras'] = 0
-		stats_hash['other_artifacts'] = 0
-		stats_hash['unknown'] = 0
-		stats_hash['unknown_>200'] = 0
-		stats_hash['unknown_>500'] = 0
-		stats_hash['prot_annotated'] = 0
-		stats_hash['complete'] = 0
-		stats_hash['complete_sure'] = 0
-		stats_hash['complete_putative'] = 0
-		stats_hash['n_terminal'] = 0
-		stats_hash['n_terminal_sure'] = 0
-		stats_hash['n_terminal_putative'] = 0
-		stats_hash['c_terminal'] = 0
-		stats_hash['c_terminal_sure'] = 0
-		stats_hash['c_terminal_putative'] = 0
-		stats_hash['internal'] = 0
-		stats_hash['swissprot'] = 0
-		stats_hash['trembl'] = 0
-		stats_hash['userdb'] = 0
-		stats_hash['ncrna'] = 0
-		stats_hash['coding'] = 0
-		stats_hash['coding_sure'] = 0
-		stats_hash['coding_putative'] = 0
-		stats_hash['coding_>200'] = 0
-		stats_hash['coding_>500'] = 0
-		stats_hash['different_orthologues'] = 0
-		stats_hash['different_completes'] = 0
-		stats_hash['BA_index'] = 0
-
-		return stats_hash
-	end
-
-	def get_taxonomy(name, taxonomy)
-		organism = nil
-		if name.include?('OS=')
-			fields = name.split('OS=',2)
-			organism = fields.last.split(' GN=').first.strip
-		elsif name[0..2] = 'sp=' || name[0..2] = 'tr='
-			name =~ /(\w+ \w+) \(([\w ]+)\) \(([\w ]+)\)/
-			if !$1.nil?
-				organism = $1
-			else
-				name =~ /(\w+ \w+) \(([\w ]+)\)/
-				if !$1.nil?
-					organism = $1  
-				end
-			end
-		else
-			organism = name.split(";",2).last
-			organism = organism.split('.', 2).first
-			organism.gsub!(/\(\D+\)/,'')
-			if organism.split(' ').length > 1
-				organism.gsub!('.','')
-				organism.gsub!(/^ /,'')
-				organism.gsub!('  ','')
-				organism.strip!
-			end
-		end
-		if !organism.nil?
-			organism = organism.split(' ')[0..1].join(' ')
-			if taxonomy[organism].nil?
-				taxonomy[organism] = 1
-			else
-				taxonomy[organism] += 1
-			end	
-		end
-	end
-
-	def initialize_stats_hash_reptrans
-		stats_hash = {}
-		stats_hash['prot_annotated'] = 0
-		stats_hash['est_annotated'] = 0
-		stats_hash['coding_>1'] = 0
-		stats_hash['coding_>0.94'] = 0
-		stats_hash['coding_>0.84'] = 0
-		stats_hash['coding_>0.73'] = 0
-		stats_hash['coding_>0'] = 0
-		return stats_hash
-	end
-
-	def summary_stats(seqs, stats_hash, diff_ids_array, diff_ids_complete_array)
-		low_limit = 200
-		upper_limit = 500
-		#All seqs
-		#-----------
-		stats_hash['output_seqs'] += seqs.length
-		good_seqs = seqs.select{|s| s.type >= UNKNOWN}
-		stats_hash['good_seqs'] += good_seqs.length
-
-		#Longest_unigene
-		current_longest_unigene = seqs.map{|s| s.fasta_length}.max
-		if current_longest_unigene > stats_hash['longest_unigene']
-			stats_hash['longest_unigene'] = current_longest_unigene
-		end
-
-		#Load ids
-		seqs.map{|s| 
-			if s.type > UNKNOWN && s.type < NCRNA
-				diff_ids_array << s.hit.acc
-			end}
-		diff_ids_array.uniq!
-
-		#By Length
-		stats_hash['sequences_>200'] += good_seqs.select{|s| s.fasta_length > low_limit}.length
-		stats_hash['sequences_>500'] += good_seqs.select{|s| s.fasta_length > upper_limit}.length
-
-		stats_hash['failed'] += seqs.select{|s| s.type == FAILED}.length
-
-		#Unknown
-		#-----------------------------
-		all_unknown = seqs.select{|s| s.type == UNKNOWN}
-		stats_hash['unknown'] += all_unknown.length
-
-		#By Length
-		stats_hash['unknown_>200'] += all_unknown.select{|s| s.fasta_length > low_limit}.length
-		stats_hash['unknown_>500'] += all_unknown.select{|s| s.fasta_length > upper_limit}.length
-
-		#Artifacts
-		#----------------
-		stats_hash['artifacts'] += seqs.select{|s| s.type < UNKNOWN && s.type > FAILED}.length
-		stats_hash['misassembled'] += seqs.select{|s| s.type == MISASSEMBLED}.length
-		stats_hash['chimeras'] += seqs.select{|s| s.type == CHIMERA && !s.seq_name.include?('_split_')}.length # We don't want count a multiple chimera
-		stats_hash['other_artifacts'] += seqs.select{|s| s.type == OTHER}.length
-		
-		#Annotated with prot
-		#---------------------
-		prot_annotated = seqs.select{|s| s.type >= COMPLETE && s.type <= INTERNAL}
-		stats_hash['prot_annotated'] += prot_annotated.length
-
-		#By annotation
-		stats_hash['internal'] += seqs.select{|s| s.type == INTERNAL}.length
-		complete = seqs.select{|s| s.type == COMPLETE}
-		n_terminal = seqs.select{|s| s.type == N_TERMINAL}
-		c_terminal = seqs.select{|s| s.type == C_TERMINAL}
-
-		stats_hash['complete'] += complete.length
-		stats_hash['n_terminal'] += n_terminal.length
-		stats_hash['c_terminal'] += c_terminal.length
-
-		#Load  complete ids
-		complete.map{|s| diff_ids_complete_array << s.hit.acc}
-		diff_ids_complete_array.uniq!
-
-		#----> By Status
-		stats_hash['complete_sure'] += complete.select{|s| s.status}.length
-		stats_hash['n_terminal_sure'] += n_terminal.select{|s| s.status}.length
-		stats_hash['c_terminal_sure'] += c_terminal.select{|s| s.status}.length
-		stats_hash['complete_putative'] += complete.select{|s| !s.status}.length
-		stats_hash['n_terminal_putative'] += n_terminal.select{|s| !s.status}.length
-		stats_hash['c_terminal_putative'] += c_terminal.select{|s| !s.status}.length
-			
-		#By database
-		swissprot = prot_annotated.select{|s| s.db_name =~ /^sp_/}.length
-		trembl = prot_annotated.select{|s| s.db_name =~ /^tr_/}.length
-		stats_hash['swissprot'] += swissprot
-		stats_hash['trembl'] += trembl
-		stats_hash['userdb'] += prot_annotated.length - swissprot - trembl
-
-		#ncRNA
-		#----------------
-		stats_hash['ncrna'] += seqs.select{|s| s.type == NCRNA}.length
-
-		#Coding sequences
-		#----------------
-		coding = seqs.select{|s| s.type == CODING}
-		stats_hash['coding'] += coding.length
-
-		#By Status
-		stats_hash['coding_sure'] += coding.select{|s| s.status}.length
-		stats_hash['coding_putative'] += coding.select{|s| !s.status}.length
-
-		#By Length
-		stats_hash['coding_>200'] += coding.select{|s| s.fasta_length > low_limit}.length
-		stats_hash['coding_>500'] += coding.select{|s| s.fasta_length > upper_limit}.length
-
-
-		return stats_hash, diff_ids_array, diff_ids_complete_array
-	end
-
-	def last_stats(stats_hash, diff_ids_array, diff_ids_complete_array)
-		stats_hash['different_orthologues'] = diff_ids_array.length
-		stats_hash['different_completes'] = diff_ids_complete_array.length
-        #BA index
-	    if stats_hash['prot_annotated'] > 0 && 
-	    	stats_hash['complete'] > 0 && 
-	    	stats_hash['sequences_>500'] > 0 && 
-	    	stats_hash['different_orthologues'] > 0 && 
-	    	stats_hash['different_completes'] > 0
-	        coef_anot_geom = (stats_hash['prot_annotated'] * stats_hash['complete'] * 1.0)/(stats_hash['sequences_>500']*10000)
-	        coef_mejora = (stats_hash['different_orthologues']*1.0 + stats_hash['different_completes'])/(stats_hash['prot_annotated'] + stats_hash['complete'])
-	   		stats_hash['BA_index'] = Math.sqrt(coef_anot_geom*coef_mejora)
-	   	end
-
-		return stats_hash
-	end
-
-	def coding_stats_reptrans(coding_seq, stats_hash)
-		group = nil
-		if coding_seq.t_code > 1
-			group = 'coding_>1'
-		elsif coding_seq.t_code > 0.95
-			group = 'coding_>0.94'
-		elsif coding_seq.t_code > 0.85
-			group = 'coding_>0.84'
-		elsif coding_seq.t_code > 0.73
-			group = 'coding_>0.73'
-		elsif coding_seq.t_code > 0
-			group = 'coding_>0'
-		end
-		if !group.nil?
-			stats_hash[group] += 1
-		end
-	end
-
-	def write_summary_stats(stats_hash, stats_taxonomy, diff_ids_array, diff_ids_complete_array, txt_file, html_file)
-		stats_hash = last_stats(stats_hash, diff_ids_array, diff_ids_complete_array)
-		write_txt(stats_hash, txt_file)
-		write_html(stats_hash, html_file, stats_taxonomy)
-	end
-
-	def write_reptrans_stats(stats_hash, html_file, txt_file)
-		html = File.open(html_file,'w')
-		txt = File.open(txt_file,'w')
-		write_txt(stats_hash, txt)
-		write_html_reptrans(stats_hash, html)
-	end
-
-	def write_html_reptrans(stats_hash, html_file)
-		html_file.puts '<html>'
-		header(html_file)
-		body_reptrans(html_file, stats_hash)
-		html_file.puts '</html>'
-	end
-
-	def write_txt(stats_hash, file)
-		stats_hash.each do |key, value|
-			file.puts "#{value}\t#{key}"
-		end
-	end
-
-	def write_html(stats_hash, html_file, stats_taxonomy)
-		js_path = File.dirname(html_file.to_path)
-		system("unzip -qq #{File.join(File.dirname(__FILE__), '..', '..', 'expresscanvas.zip')} -d #{js_path}") if !File.exists?(File.join(js_path, 'expresscanvas'))
-		html_file.puts '<html>'
-		html_header(html_file, stats_hash, stats_taxonomy)
-		body(html_file, stats_hash)
-		html_file.puts '</html>'
-	end
-
-	def header(html_file)
-		html_file.puts 	'<head>',
-						'<title>FLN Summary</title>',
-						'</head>'
-	end
-
-	def html_header(html_file, stats_hash, stats_taxonomy)
-    	structural_data_sure = []
-    	structural_data_sure << stats_hash['unknown']
-    	structural_data_sure << stats_hash['complete_sure']
-    	structural_data_sure << stats_hash['n_terminal_sure']
-    	structural_data_sure << stats_hash['c_terminal_sure']
-    	structural_data_sure << stats_hash['internal']
-    	structural_data_sure << stats_hash['ncrna']
-    	structural_data_sure << stats_hash['coding']
-
-    	structural_data_putative = []
-    	structural_data_putative << 0
-    	structural_data_putative << stats_hash['complete_putative']
-    	structural_data_putative << stats_hash['n_terminal_putative']
-    	structural_data_putative << stats_hash['c_terminal_putative']
-    	structural_data_putative << 0
-    	structural_data_putative << 0
-    	structural_data_putative << stats_hash['coding_putative']
-
-    	values_structural_sure = "[#{structural_data_sure.map{|stat| stat*100.0/stats_hash['good_seqs']}.join(', ')}]"
-    	values_structural_putative = "[#{structural_data_putative.map{|stat| stat*100.0/stats_hash['good_seqs']}.join(', ')}]"
-
-    	data = stats_taxonomy.to_a.sort{|s2, s1| s1.last <=> s2.last}[0..20]
-    	smps_taxonomy = "['#{data.map{|tax| tax.first}.join("', '")}']"
-    	values_taxonomy = "[#{data.map{|tax| tax.last}.join(', ')}]"
-
-		html_file.puts 	'<head>
-			<title>FLN Summary</title>
-			<meta http-equiv="CACHE-CONTROL" CONTENT="NO-CACHE">
-			<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
-    		<!--[if lt IE 9]><script type="text/javascript" src="./expresscanvas/js/flashcanvas.js"></script><![endif]-->
-    		<script type="text/javascript" src="./expresscanvas/js/canvasXpress.min.js"></script>
-
-    		<script id=\'demoScript\'>
-    			var showDemo = function () {'
-
-		#'smpTitle': 'Status',
-		
-		html_file.puts "new CanvasXpress('profile',
-					  {
-						'y' : {
-						  'vars' : ['Sure', 'Putative'],
-						  'smps' : ['Unknown', 'Complete', 'N-terminal', 'C-terminal', 'Internal', 'ncrna', 'Coding'],
-						  'data' : [#{values_structural_sure}, 
-						  			#{values_structural_putative}],
-						},
-						'a' : {
-						  'xAxis' : ['Sure', 'Putative']
-						},
-					  },
-
-					  {'gradient': false,
-					  'toolbarPermanent': true,
-					  'graphOrientation': 'vertical',
-					  'graphType': 'Stacked',
-					  'legendBackgroundColor': false,
-					  'smpLabelScaleFontFactor': 0.8,
-					  'xAxisTitle': '% sequences',
-					  'xAxis2Show': false,
-					  'xAxisExact': true,
-					  'setMaxX': 80,
-					  'setMinX': 0,
-					  'axisTitleScaleFontFactor': 2,
-					  'smpTitleFontStyle': 'italic',
-					  'titleHeight': 60
-					  }
-					);
-
-					new CanvasXpress('taxonomy',
-					  {
-						'y' : {
-						  'vars' : ['Annotations'],
-						  'smps' : #{smps_taxonomy},
-						  'data' : [#{values_taxonomy}],
-						},
-						'a' : {
-						  'xAxis' : ['Sure', 'Putative']
-						},
-					  },
-
-					  {'gradient': false,
-					  'toolbarPermanent': true,
-					  'graphOrientation': 'horizontal',
-					  'showLegend': false,
-					  'smpLabelScaleFontFactor': 1.5,
-					  'xAxisTitle': 'Number of sequences',
-					  'xAxis2Show': false,
-					  'titleHeight': 60
-					  }
-					);
-				}
-   			</script>
-		</head>"
-							  
-	end
-
-	def body_reptrans(html_file, stats_hash)
-		html_file.puts '<body bgcolor="#FFFFFF" >', '<center>' # Start body
-		html_file.puts '<div style="float:center; font-size:30; margin:10px"><b>', 'Full-LengtherNEXT Representative Transcriptome Summary', '</b></div>'
-		# TABLES
-		html_file.puts '<div style=" width: 850px; height: 350px; padding: 10 ">'
-		reptrans_report(html_file, stats_hash, 'left')
-		reptrans_acumulative_report(html_file, stats_hash, 'rigth')
-		html_file.puts '</div>'
-		# END TABLES
-		html_file.puts '</center>', '</body>' # End body
-	end
-
-	def body(html_file, stats_hash)
-		html_file.puts '<body bgcolor="#FFFFFF" onload="showDemo(); id=demo">', '<center>' # Start body
-		html_file.puts '<div style="float:center; font-size:30; margin:10px"><b>', 'Full-LengtherNEXT Summary', '</b></div>'
-
-		# TABLES
-		html_file.puts '<div style="overflow: hidden; width: 950px; height: 550px; padding: 10 ">'
-		general_report(html_file, stats_hash, 'left')
-		assembly_report(html_file, stats_hash, 'right')
-		html_file.puts '</div>'
-		html_file.puts '<div style="overflow: hidden; width: 950px; height: 550px; padding: 10 ">'
-		status_graph(html_file, 'left')
-		status_report(html_file, stats_hash, 'rigth')
-		html_file.puts '</div>'
-		html_file.puts '<div style="overflow: hidden; width: 950px; height: 750px; padding: 10 ">'
-		taxonomy_graph(html_file, 'left')
-		database_report(html_file, stats_hash, 'rigth')
-		html_file.puts '</div>'
-		# END TABLES
-		html_file.puts '</center>', '</body>' # End body
-	end
-
-
-
-	def reptrans_report(html_file, stats_hash, align)
-		html = []
-		all_seqs = 0
-		stats_hash.values.map{|v| all_seqs += v}
-		html << '<div style=" margin: 0; float:'+align+'">'
-		html << table_title('Sequences info')
-		html.concat(table_header(['', 'Sequences', '%'], 0))
-		html.concat(single_row('Output', all_seqs, all_seqs))
-		html.concat(single_row('Annotated with protein', stats_hash['prot_annotated'], all_seqs))
-		html.concat(single_row('Annotated with EST', stats_hash['est_annotated'], all_seqs))
-		html.concat(single_row('Coding test-code > 1', stats_hash['coding_>1'], all_seqs))
-		html.concat(single_row('Coding test-code > 0.94', stats_hash['coding_>0.94'], all_seqs))
-		html.concat(single_row('Coding test-code > 0.84', stats_hash['coding_>0.84'], all_seqs))
-		html.concat(single_row('Coding test-code > 0.73', stats_hash['coding_>0.73'], all_seqs))
-		html.concat(single_row('Coding test-code > 0', stats_hash['coding_>0'], all_seqs))
-		html << '</table>'
-		html << '</div>'
-		write_array_html(html, html_file)
-	end
-
-	def reptrans_acumulative_report(html_file, stats_hash, align)
-		html = []
-		all_seqs = 0
-		stats_hash.values.map{|v| all_seqs += v}
-		html << '<div style=" margin: 0; float:'+align+'">'
-		html << table_title('Sequences summary (Acumulative)')
-		html.concat(table_header(['', 'Sequences', '%'], 0))
-		acumulative = 0
-		html.concat(single_row('Annotated with protein', stats_hash['prot_annotated'], all_seqs))
-		acumulative += stats_hash['prot_annotated']
-		html.concat(single_row('Annotated with EST', stats_hash['est_annotated'] + acumulative, all_seqs))
-		acumulative += stats_hash['est_annotated']
-		html.concat(single_row('Coding test-code > 1', stats_hash['coding_>1'] + acumulative, all_seqs))
-		acumulative += stats_hash['coding_>1']
-		html.concat(single_row('Coding test-code > 0.94', stats_hash['coding_>0.94'] + acumulative, all_seqs))
-		acumulative += stats_hash['coding_>0.94']
-		html.concat(single_row('Coding test-code > 0.84', stats_hash['coding_>0.84'] + acumulative, all_seqs))
-		acumulative += stats_hash['coding_>0.84']
-		html.concat(single_row('Coding test-code > 0.73', stats_hash['coding_>0.73'] + acumulative, all_seqs))
-		html << '</table>'
-		html << '</div>'
-		write_array_html(html, html_file)
-	end
-
-	def general_report(html_file, stats_hash, align)
-		html = []
-		html << '<div  style="margin: 0; float:'+align+'">'
-		html << table_title('General info')
-		html.concat(table_header(['', 'Sequences', '%'], 0))
-		html.concat(single_row('Input', stats_hash['input_seqs'], stats_hash['input_seqs']))
-		html.concat(single_row('Failing sequences', stats_hash['failed'], stats_hash['output_seqs']))
-		html.concat(single_row('Artifacts <sup>1</sup>', stats_hash['artifacts'], stats_hash['output_seqs']))
-		html.concat(single_row('Misassembled', stats_hash['misassembled'], stats_hash['artifacts'], TRUE))
-		html.concat(single_row('Chimeras', stats_hash['chimeras'], stats_hash['artifacts'], TRUE))
-		html.concat(single_row('Other', stats_hash['other_artifacts'], stats_hash['artifacts'], TRUE))
-		html.concat(single_row('Sequences with resolved chimeras', stats_hash['output_seqs'], stats_hash['input_seqs']))
-		html.concat(single_row('Sequences without artifacts', stats_hash['good_seqs'], stats_hash['output_seqs']))
-		html.concat(single_row('BA index', "%5.2f" % [stats_hash['BA_index']], nil)) if stats_hash['BA_index'] > 0
-		html << '</table>'
-		html << '</div>'
-		write_array_html(html, html_file)
-	end
-
-	def taxonomy_graph(html_file, align)
-		html_file.puts '<div style=\'float:'+align+'\'>'
-		html_file.puts table_title('Taxonomy distribution on annotations')
-		html_file.puts '<table >
-				<tr>
-					<td>
-						<canvas id=\'taxonomy\' width=\'540\' height=\'640\'></canvas>
-					</td>
-				</tr>
-			</table>
-		</div>'
-
-	end
-
-
-	def database_report(html_file, stats_hash, align)
-		html = []
-		html << '<div style=" margin: 0 float:'+align+'">'
-		html << table_title('Database usage')
-		html.concat(table_header(['', 'Unigenes', '%'], 0))
-		html.concat(single_row('UserDB', stats_hash['userdb'], stats_hash['good_seqs']))
-		html.concat(single_row('SwissProt', stats_hash['swissprot'], stats_hash['good_seqs']))
-		html.concat(single_row('TrEMBL', stats_hash['trembl'], stats_hash['good_seqs']))
-		html.concat(single_row('ncRNA', stats_hash['ncrna'], stats_hash['good_seqs']))
-		html.concat(single_row('None', stats_hash['coding']+ stats_hash['unknown'], stats_hash['good_seqs']))
-		html.concat(single_row('Total', stats_hash['good_seqs'], stats_hash['good_seqs']))
-		html << '</table>'
-		html << '</div>'
-		write_array_html(html, html_file)
-	end
-
-	def assembly_report(html_file, stats_hash, align)
-		html = []
-		html << '<div style=" margin: 0; float:'+align+'">'
-		html << table_title('Report guiding assembly quality')
-		html.concat(table_header(['', 'Unigenes', '%'], 0))
-		html.concat(single_row('Unigenes', stats_hash['good_seqs'], stats_hash['good_seqs']))
-		html.concat(single_row('Unigenes >500pb', stats_hash['sequences_>500'], stats_hash['good_seqs']))
-		html.concat(single_row('Unigenes >200pb', stats_hash['sequences_>200'], stats_hash['good_seqs']))
-		html.concat(single_row('Longest unigene', stats_hash['longest_unigene'], nil))
-		html.concat(single_row('With orthologue <sup>1</sup>', stats_hash['prot_annotated'], stats_hash['good_seqs']))
-		html.concat(single_row('Different orthologue IDs', stats_hash['different_orthologues'], stats_hash['prot_annotated'], TRUE))
-		html.concat(single_row('Complete transcripts', stats_hash['complete'], stats_hash['prot_annotated'], TRUE))
-		html.concat(single_row('Different complete transcripts ', stats_hash['different_completes'], stats_hash['prot_annotated'], TRUE))
-		html.concat(single_row('ncRNA', stats_hash['ncrna'], stats_hash['good_seqs']))
-		without_orthologue = stats_hash['coding']+ stats_hash['unknown']
-		html.concat(single_row('Without orthologue <sup>1</sup>', without_orthologue, stats_hash['good_seqs']))
-		html.concat(single_row('Coding (all)', stats_hash['coding'], without_orthologue, TRUE))
-		html.concat(single_row('Coding > 200bp', stats_hash['coding_>200'], without_orthologue, TRUE))
-		html.concat(single_row('Coding > 500bp', stats_hash['coding_>500'], without_orthologue, TRUE))
-		html.concat(single_row('Unknown (all)', stats_hash['unknown'], without_orthologue, TRUE))
-		html.concat(single_row('Unknown > 200bp', stats_hash['unknown_>200'], without_orthologue, TRUE))
-		html.concat(single_row('Unknown > 500bp', stats_hash['unknown_>500'], without_orthologue, TRUE))
-		html << '</table>'
-		html << '<sup>1</sup> Percents for subclassifications of this category <br> were calculated using this line as 100% reference.'
-		html << '</div>'
-		write_array_html(html, html_file)
-	end
-
-	def status_graph(html_file, align)
-		html_file.puts '<div style=\'float:'+align+'\'>'
-		html_file.puts table_title('Structural profile')
-		html_file.puts '<table >
-				<tr>
-					<td>
-						<canvas id=\'profile\' width=\'500\' height=\'440\'></canvas>
-					</td>
-				</tr>
-			</table>
-		</div>'
-
-	end
-
-	def status_report(html_file, stats_hash, align)
-		html = []
-		html << '<div style=" margin: 0; float:'+align+'">'
-		html << table_title('Status report')				
-		html.concat(table_header(['Status', 'Unigenes', '%'], 2))
-		html.concat(fused_row('Complete', stats_hash['complete_sure'], stats_hash['complete_putative'], stats_hash['good_seqs']))
-		html.concat(fused_row('C-terminus', stats_hash['c_terminal_sure'], stats_hash['c_terminal_putative'], stats_hash['good_seqs']))
-		html.concat(fused_row('N-terminus', stats_hash['n_terminal_sure'], stats_hash['n_terminal_putative'], stats_hash['good_seqs']))
-		html.concat(composed_single_row('Internal', stats_hash['internal'], stats_hash['good_seqs']))
-		html.concat(fused_row('Coding', stats_hash['coding_sure'], stats_hash['coding_putative'], stats_hash['good_seqs']))
-		html.concat(composed_single_row('ncRNA', stats_hash['ncrna'], stats_hash['good_seqs']))
-		html.concat(composed_single_row('Unknown', stats_hash['unknown'], stats_hash['good_seqs']))
-		html.concat(composed_single_row('Total', stats_hash['good_seqs'], stats_hash['good_seqs']))
-		html << '</table>'
-		html << '</div>'
-		write_array_html(html, html_file)
-	end
-
-
-	def table_title(title)
-		html = 	'<div style="font-size:25px; margin: 10"><b>'+title+'</b></div>'
-		return html
-	end
-
-	def table_header(col_array, colspan)
-		html = []
-
-		html << '<table border="2" cellspacing="0" cellpadding="2">'
-		# Table header
-		html << '<tr>'
-		col_array.each_with_index do |col,i|
-			if i == 0 && colspan > 0
-				html <<	'<th colspan="'+colspan.to_s+'">'+col+'</th>'
-			else
-				html <<	'<th>'+col+'</th>'
-			end
-		end
-		html <<	'</tr>'
-		return html
-	end
-
-	def single_row(name, magnitude, total, space = FALSE)
-		if space
-			name = '&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'+ name
-		end
-		html = []
-		html << '<tr>'
-		html << '<td align="left">'+name+'</td>'
-		html.concat(sub_row(magnitude, total))
-		html << '</tr>'
-		return html
-	end
-
-
-	def fused_row(type, sure_magnitude, putative_magnitude, total)
-		html = []
-		html << '<td rowspan="2" align="left">'+type+'</td>'
-		html <<	seq_status('Sure')
-		html.concat(sub_row(sure_magnitude, total)) 
-		html << '</tr>'	
-		html << '<tr>'
-		html <<	seq_status('Putative')
-		html.concat(sub_row(putative_magnitude, total)) 
-		html << '</tr>'
-		return html
-	end
-
-	def seq_status(status)
-		html = '<td align="left">'+status+'</td>'
-		return html
-	end
-
-	def sub_row(magnitude, total)
-		if !total.nil?
-			perc_float = magnitude*100.0/total
-			if !perc_float.nan?
-				percentage = '%.2f' % perc_float.to_s 
-				percentage += '%'
-			else
-				percentage ='-'
-			end
-		else
-			percentage = '-'
-		end	
-		html = []
-		html << '<td align="right">'+magnitude.to_s+'</td>'
-		html << '<td align="right">'+percentage+'</td>'
-		return html
-	end
-
-	def composed_single_row(type, magnitude, total)
-		html = []
-		html <<	'<tr>'
-		html << '<td colspan="2" align="left">'+type+'</td>'
-		html.concat(sub_row(magnitude, total))
-		html <<	'</tr>'
-		return html
-	end
-
-
-	def write_array_html(html, html_file)
-		html.map{|line| html_file.puts line}
-	end
-end