seqtrimnext_report 0.0.3 → 0.0.5

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@@ -1,3 +1,11 @@
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+ === 0.0.5 2012-03-01
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+
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+ Fixed bug with report generation
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+
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+ === 0.0.4 2011-07-14
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+
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+ Added extra rejected causes
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+
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  === 0.0.3 2011-06-16
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  Corrected errors with empty plugins
@@ -6,7 +6,6 @@
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  ROOT_PATH=File.dirname(File.dirname(__FILE__))
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  # $: << File.expand_path(File.join(ROOT_PATH, 'lib','seqtrimnext_report','classes'))
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  # $: << File.expand_path(File.join(ROOT_PATH, 'lib'))
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-
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  # $: << '/Users/dariogf/progs/ruby/gems/seqtrimnext/lib'
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  #---------------------------------------------- gems
@@ -47,6 +46,7 @@ end
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  #---------------------------------------------- check if files exists
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  output_files=ARGV.shift
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+
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  if !Dir.exists?(output_files)
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  puts "Directory #{output_files} doesn't exists"
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  exit(-1)
@@ -8,5 +8,5 @@ ROOT_PATH=File.join(File.dirname(__FILE__),'seqtrimnext_report')
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  $: << File.expand_path(File.join(ROOT_PATH, 'classes'))
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  module SeqtrimnextReport
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- VERSION = '0.0.3'
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+ VERSION = '0.0.5'
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  end
@@ -32,8 +32,7 @@ class RejectedReport
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  rejected_hash['rejected']=data_hash
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  if (!stats['sequences']['rejected'].nil?)
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- rejected_hash = load_plugins_info(stats, rejected_hash, input_seqs, plugin_fix_hash)
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-
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+ rejected_hash2 = load_plugins_info(stats, rejected_hash, input_seqs, plugin_fix_hash)
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  #-------------------------------------------------- build table
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  output3.puts '\begin{table}[H]'
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  output3.puts '\begin{center}'
@@ -66,7 +65,7 @@ class RejectedReport
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  output3.puts '\hline'
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  #the hash of hashes is ordered by value (number of sequences rejected)
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- rejected_ordered = rejected_hash.sort {|a,b| b[1]['value']<=>a[1]['value']}
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+ rejected_ordered = rejected_hash2.sort {|a,b| b[1]['value']<=>a[1]['value']}
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  rejected_ordered.each do |plugin|
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@@ -75,12 +74,7 @@ class RejectedReport
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  my_percent = plugin[1]['percent']
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  my_warning = plugin[1]['warning']
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- if (plugin[0] != 'rejected')
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- if (plugin[0] == 'Indeterminations in middle of sequence')
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- plugin[0] = plugin[0].sub(' in middle of sequence','')
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- end
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- output3.puts "#{my_name}&#{my_value}&#{my_percent} \\%&#{my_warning}\\\\"
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- end
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+ output3.puts "#{my_name}&#{my_value}&#{my_percent} \\%&#{my_warning}\\\\"
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  end
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  output3.puts '\hline'
@@ -94,8 +88,10 @@ class RejectedReport
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  rejected_ordered.each do |plugin|
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  if (plugin[1]['warning'] != 'OK')
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- plugin[1]['warning_msg'].gsub!('my_percent',"#{rejected_hash["#{plugin[0]}"]['percent']}")
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- output3.puts '\noindent\fcolorbox{black}{yellow}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{'+"#{plugin[1]['warning']} #{plugin[1]['warning_msg']}"+'}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
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+ if (!rejected_hash2[plugin[0]].nil?)
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+ plugin[1]['warning_msg'].gsub!('my_percent',"#{rejected_hash2["#{plugin[0]}"]['percent']}")
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+ output3.puts '\noindent\fcolorbox{black}{yellow}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{'+"#{plugin[1]['warning']} #{plugin[1]['warning_msg']}"+'}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
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+ end
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  end
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  end
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  else
@@ -128,7 +124,6 @@ class RejectedReport
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  rejected_hash[key]['warning_msg'] = plugin_fix_hash[key]['msg']
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  end
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  end
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-
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  return rejected_hash
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  end
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@@ -193,6 +188,13 @@ class RejectedReport
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  plugin_fix_hash['Indeterminations in middle of sequence'] = msgs_hash
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  msgs_hash = {}
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+ msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are too big or too small"
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+ msgs_hash['threshold'] = 1
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+ msgs_hash['warning'] = 'W9'
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+
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+ plugin_fix_hash['size out of limits'] = msgs_hash
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+ msgs_hash = {}
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+
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  msgs_hash['msg'] = "WT Warning!, a my_percent \\% of your sequences were rejected!"
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  msgs_hash['threshold'] = 25
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  msgs_hash['warning'] = 'WT'
@@ -60,6 +60,12 @@
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  "threshold": 0.01,
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  "warning": "rdW7"
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  },
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+ "size out of limits": {
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+ "name": "Size Out Of Limits",
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+ "msg": "Warning!, a my_percent \\% of your sequences are too big or too small",
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+ "threshold": 1,
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+ "warning": "rdW9"
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+ },
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  "rejected": {
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  "name": "Total Rejected",
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  "msg": "Warning!, a my_percent \\% of your sequences were rejected!",
metadata CHANGED
@@ -2,7 +2,7 @@
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  name: seqtrimnext_report
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  version: !ruby/object:Gem::Version
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  prerelease:
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- version: 0.0.3
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+ version: 0.0.5
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  platform: ruby
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  authors:
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  - Noe Fernandez & Dario Guerrero
@@ -10,7 +10,7 @@ autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2011-06-16 00:00:00 Z
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+ date: 2012-03-01 00:00:00 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: seqtrimnext