seqtrimnext_report 0.0.3 → 0.0.5

data/History.txt

@@ -1,3 +1,11 @@
+=== 0.0.5 2012-03-01
+
+Fixed bug with report generation
+
+=== 0.0.4 2011-07-14
+
+Added extra rejected causes
+
 === 0.0.3 2011-06-16
 
 Corrected errors with empty plugins

data/bin/generate_report.rb

@@ -6,7 +6,6 @@
 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
@@ -47,6 +46,7 @@ end
 
 #---------------------------------------------- check if files exists
 output_files=ARGV.shift
+
 if !Dir.exists?(output_files)
   puts "Directory #{output_files} doesn't exists"
   exit(-1)

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 = '0.0.3'
+   VERSION = '0.0.5'
 end

data/lib/seqtrimnext_report/classes/rejected_report.rb

@@ -32,8 +32,7 @@ class RejectedReport
     rejected_hash['rejected']=data_hash
 
     if (!stats['sequences']['rejected'].nil?)
-      rejected_hash = load_plugins_info(stats, rejected_hash, input_seqs, plugin_fix_hash)
-
+      rejected_hash2 = load_plugins_info(stats, rejected_hash, input_seqs, plugin_fix_hash)
       #-------------------------------------------------- build table
       output3.puts '\begin{table}[H]'
       output3.puts '\begin{center}'
@@ -66,7 +65,7 @@ class RejectedReport
       output3.puts '\hline'
 
       #the hash of hashes is ordered by value (number of sequences rejected)
-      rejected_ordered = rejected_hash.sort {|a,b| b[1]['value']<=>a[1]['value']}
+      rejected_ordered = rejected_hash2.sort {|a,b| b[1]['value']<=>a[1]['value']}
 
       rejected_ordered.each do |plugin|
 
@@ -75,12 +74,7 @@ class RejectedReport
         my_percent = plugin[1]['percent']
         my_warning = plugin[1]['warning']
 
-        if (plugin[0] != 'rejected')
-          if (plugin[0] == 'Indeterminations in middle of sequence')
-            plugin[0] = plugin[0].sub(' in middle of sequence','')
-          end
-          output3.puts "#{my_name}&#{my_value}&#{my_percent} \\%&#{my_warning}\\\\"
-        end
+        output3.puts "#{my_name}&#{my_value}&#{my_percent} \\%&#{my_warning}\\\\"
       end
 
       output3.puts '\hline'
@@ -94,8 +88,10 @@ class RejectedReport
 
       rejected_ordered.each do |plugin|
         if (plugin[1]['warning'] != 'OK')
-          plugin[1]['warning_msg'].gsub!('my_percent',"#{rejected_hash["#{plugin[0]}"]['percent']}")
-          output3.puts '\noindent\fcolorbox{black}{yellow}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{'+"#{plugin[1]['warning']}   #{plugin[1]['warning_msg']}"+'}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
+					if (!rejected_hash2[plugin[0]].nil?)
+	          plugin[1]['warning_msg'].gsub!('my_percent',"#{rejected_hash2["#{plugin[0]}"]['percent']}")
+	          output3.puts '\noindent\fcolorbox{black}{yellow}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{'+"#{plugin[1]['warning']}   #{plugin[1]['warning_msg']}"+'}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
+					end
         end
       end
     else
@@ -128,7 +124,6 @@ class RejectedReport
         rejected_hash[key]['warning_msg'] = plugin_fix_hash[key]['msg']
       end
     end
-
     return rejected_hash
   end
 
@@ -193,6 +188,13 @@ class RejectedReport
     plugin_fix_hash['Indeterminations in middle of sequence'] = msgs_hash
     msgs_hash = {}
 
+		msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are too big or too small"
+		msgs_hash['threshold'] = 1
+		msgs_hash['warning'] = 'W9'
+
+		plugin_fix_hash['size out of limits'] = msgs_hash
+		msgs_hash = {}
+
     msgs_hash['msg'] = "WT  Warning!, a my_percent \\% of your sequences were rejected!"
     msgs_hash['threshold'] = 25
     msgs_hash['warning'] = 'WT'

data/lib/seqtrimnext_report/config/plugin_seqs.json

@@ -60,6 +60,12 @@
     "threshold": 0.01,
     "warning": "rdW7"
   },
+  "size out of limits": {
+    "name": "Size Out Of Limits",
+    "msg": "Warning!, a my_percent \\% of your sequences are too big or too small",
+    "threshold": 1,
+    "warning": "rdW9"
+  },
   "rejected": {
     "name": "Total Rejected",
     "msg": "Warning!, a my_percent \\% of your sequences were rejected!",

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext_report
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.0.3
+  version: 0.0.5
 platform: ruby
 authors: 
 - Noe Fernandez & Dario Guerrero
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-06-16 00:00:00 Z
+date: 2012-03-01 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: seqtrimnext