seqtrimnext_report 0.0.2 → 0.0.3

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.0.3 2011-06-16
+
+Corrected errors with empty plugins
+
 === 0.0.2 2011-06-15
 
 Some small fixes

data/README.rdoc

@@ -27,7 +27,7 @@ gem install seqtrimnext_report
 
 (The MIT License)
 
-Copyright (c) 2011 FIXME full name
+Copyright (c) 2011 Noe Fernandez & Dario Guerrero
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/bin/generate_report.rb

@@ -3,8 +3,10 @@
 # Noe Fdez Pozo 2011-05-11. To build a PDF with latex parsing SeqTrimNext output files
 
 #---------------------------------------------- para indicar donde estan las clases
-ROOT_PATH=File.dirname(__FILE__)
-# $: << File.expand_path(File.join(ROOT_PATH, "classes"))
+ROOT_PATH=File.dirname(File.dirname(__FILE__))
+# $: << File.expand_path(File.join(ROOT_PATH, 'lib','seqtrimnext_report','classes'))
+# $: << File.expand_path(File.join(ROOT_PATH, 'lib'))
+
 # $: << '/Users/dariogf/progs/ruby/gems/seqtrimnext/lib'
 
 #---------------------------------------------- gems
@@ -51,13 +53,13 @@ if !Dir.exists?(output_files)
 end
 
 if !File.exist?(File.join(output_files,'used_params.txt'))
-  puts "File used_params.txt not found.\n"
+  puts "used_params.txt file not found.\n"
   exit(-1)
 elsif !File.exist?(File.join(output_files,'initial_stats.json'))
-  puts "File initial_stats.json not found.\n"
+  puts "initial_stats.json file not found.\n"
   exit(-1)
 elsif !File.exist?(File.join(output_files,'stats.json'))
-  puts "File stats.json not found.\n"
+  puts "stats.json file not found.\n"
   exit(-1)
 end
 
@@ -76,6 +78,16 @@ begin
   initial_stats = get_json_data(File.join(output_files,'initial_stats.json'))
   stats = get_json_data(File.join(output_files,'stats.json'))
   
+	if (initial_stats.nil?)
+		puts "initial_stats.json info does not exist\n"
+	  exit(-1)
+	end
+	
+	if (stats.nil?)
+		puts "stats.json info does not exist\n"
+	  exit(-1)
+	end
+	
   # load json configuration
   plugin_fix_hash = get_json_data(File.join(File.dirname(__FILE__),'..','lib','seqtrimnext_report','config','plugin_seqs.json'))
   plugin_nts_hash = get_json_data(File.join(File.dirname(__FILE__),'..','lib','seqtrimnext_report','config','plugin_nts.json'))
@@ -110,9 +122,9 @@ begin
     `rm -r #{output_latex}`
   end
 
-rescue
+# rescue
 
-  puts "output PDF couldn't be created for this dataset"
+  # puts "Output PDF couldn't be created for this dataset"
 
 end
 # system(cmd)

data/lib/seqtrimnext_report.rb

@@ -8,5 +8,5 @@ ROOT_PATH=File.join(File.dirname(__FILE__),'seqtrimnext_report')
 $: << File.expand_path(File.join(ROOT_PATH, 'classes'))
 
 module SeqtrimnextReport
-   VERSION = '0.0.2'
+   VERSION = '0.0.3'
 end

data/lib/seqtrimnext_report/classes/stats_report.rb

@@ -5,13 +5,19 @@ class StatsReport
 		output2=File.open(File.join(output_latex,'stats.tex'), 'w')
 		output2.puts "%!TEX root = FinalReport.tex"
 		
+		if (stats['sequences'].nil?) || (stats['sequences']['count'].nil?)
+			puts "sequences info does not exist in stats.json\n"
+		  exit(-1)
+		end
+		
 		input_seqs = stats['sequences']['count']['input_count'].to_i
 		rejected_seqs = stats['sequences']['count']['rejected'].to_i
 		output_seqs = stats['sequences']['count']['output_seqs'].to_i
 
+		#------------------------------------------------------------------------------------------ solo cuando hay pareadas
 		output_seqs_paired = 0
 		total_output_seqs = 0
-		#------------------------------------------------------------------------------------------ solo cuando hay pareadas
+
 		if (!stats['sequences']['count']['output_seqs_paired'].nil?)
 			output_seqs_paired = stats['sequences']['count']['output_seqs_paired'].to_i
 			total_output_seqs = output_seqs_paired+output_seqs
@@ -44,9 +50,15 @@ class StatsReport
 		output2.puts '\begin{center}'
 		output2.puts '\begin{tabular}{l r r}'
 		output2.puts " \\hline"
-		output2.puts "Input reads: & total & #{input_seqs} \\\\"
-		output2.puts " & Smallest read (bp) & #{initial_stats['smallest_sequence_size'].to_i} \\\\"
-		output2.puts " & Largest read (bp)& #{initial_stats['biggest_sequence_size'].to_i} \\\\"
+		if (!input_seqs.nil?)
+			output2.puts "Input reads: & total & #{input_seqs} \\\\"
+		end
+		if (!initial_stats['smallest_sequence_size'].nil?)
+			output2.puts " & Smallest read (bp) & #{initial_stats['smallest_sequence_size'].to_i} \\\\"
+		end
+		if (!initial_stats['biggest_sequence_size'].nil?)
+			output2.puts " & Largest read (bp)& #{initial_stats['biggest_sequence_size'].to_i} \\\\"
+		end
 		output2.puts " & Mode (bp) & #{input_mode} \\\\"
 		output2.puts " & Mean (bp)& #{input_mean} \\\\"
 
@@ -93,12 +105,10 @@ class StatsReport
 				end
 			end
 		end
-		#-----------------------------------------------------------------------------
+		#--------------------------------------------------- end pareadas
 		
 		output2.puts "\\hline"
 		
-		
-
 		output2.puts '\end{tabular}'
 		output2.puts '\label{table:nonlin}'
 		output2.puts '\end{center}'
@@ -141,10 +151,12 @@ class StatsReport
 		
 		# en las pareadas añadimos el inserto de izq y derecha ------------------------------------- solo cuando hay pareadas
 		paired_nts=0
-		if (stats['PluginExtractInserts']['left_insert_size']) || (stats['PluginExtractInserts']['right_insert_size'])
+		if (stats['PluginExtractInserts']['left_insert_size'])
 			stats['PluginExtractInserts']['left_insert_size'].each do |element|
 				paired_nts += element[0].to_i*element[1].to_i
 			end
+		end
+		if (stats['PluginExtractInserts']['right_insert_size'])
 			stats['PluginExtractInserts']['right_insert_size'].each do |element|
 				paired_nts += element[0].to_i*element[1].to_i
 			end
@@ -163,18 +175,27 @@ class StatsReport
 	def get_mode(initial_stats,stats)
 		output_mode = 0
 		mode_array = []
+		
 		# take the mode from initial_stats.json
-		input_mode = initial_stats['mode_of_sizes']
+		if (!initial_stats.nil? and !initial_stats.empty?)
+			input_mode = initial_stats['mode_of_sizes']
+		else
+			input_mode = 0
+		end
 		
 		# calculate the mode using data from stats.json
-		stats['PluginExtractInserts']['insert_size'].each do |key,value|
-			mode_array[key.to_i]=value
-		end
+		if (!stats['PluginExtractInserts']['insert_size'].nil?)
+			stats['PluginExtractInserts']['insert_size'].each do |key,value|
+				mode_array[key.to_i]=value
+			end
 		
-		mode_array.map!{|e| e || 0}
-		s=ScbiStats.new(mode_array)
+			mode_array.map!{|e| e || 0}
+			s=ScbiStats.new(mode_array)
 		
-		output_mode = s.fat_mode
+			output_mode = s.fat_mode
+		else
+			output_mode = 0
+		end
 		
 		return [input_mode, output_mode]
 	end
@@ -183,21 +204,29 @@ class StatsReport
 		output_mean = 0
 
 		# take the mean from initial_stats.json
-		input_mean = sprintf("%0.1f", (initial_stats['mean_of_sequence_sizes']))
-		# input_mean = sprintf("%0.2f", (initial_stats['mean_of_sequence_sizes']))
-
+		if (!initial_stats.nil? and !initial_stats.empty?)
+			input_mean = sprintf("%0.1f", (initial_stats['mean_of_sequence_sizes']))
+		else
+			input_mean = 0
+		end
+			
 		# calculate the mean using data from stats.json
 		nts_count = 0
 		seqs_count = 0
-		stats['PluginExtractInserts']['insert_size'].each do |key,value|
-			seqs_count += value.to_i
-			nts_count += (key.to_f*value)
-			# nts_count += (key.to_f*value.to_f)
-		end
-		
+		if (!stats['PluginExtractInserts']['insert_size'].nil?)
+			stats['PluginExtractInserts']['insert_size'].each do |key,value|
+				seqs_count += value.to_i
+				nts_count += (key.to_f*value)
+			end
 		
-		output_mean = sprintf("%0.1f", (nts_count/seqs_count))
-		# output_mean = sprintf("%0.2f", (nts_count/seqs_count))
+			if (nts_count == 0 || seqs_count == 0)
+				output_mean = 0
+			else
+				output_mean = sprintf("%0.1f", (nts_count/seqs_count))
+			end
+		else
+			output_mean = 0
+		end
 		
 		return [input_mean, output_mean]
 	end
@@ -236,7 +265,7 @@ class StatsReport
 		nts_table_hash = {}
 		insert_array = []
 		warning_array = []
-
+		
 		plugin_nts_hash.each do |plugin|
 			
 			my_name = plugin[0]
@@ -302,7 +331,9 @@ class StatsReport
 		end
 		
 		output2.puts '\hline'
-		output2.puts nts_table_hash['insert_size'][0]
+		if (!nts_table_hash['insert_size'].nil?)
+			output2.puts nts_table_hash['insert_size'][0]
+		end
 		output2.puts '\hline'
 		output2.puts '\end{tabular}'
 		output2.puts '\label{table:nonlin}'

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext_report
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors: 
 - Noe Fernandez & Dario Guerrero
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-06-15 00:00:00 Z
+date: 2011-06-16 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: seqtrimnext