seqtrimnext_report 0.0.3 → 0.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
data/History.txt
CHANGED
data/bin/generate_report.rb
CHANGED
@@ -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
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@@ -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)
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data/lib/seqtrimnext_report.rb
CHANGED
@@ -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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-
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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}'
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@@ -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 =
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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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-
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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'
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@@ -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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-
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-
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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
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@@ -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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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'
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@@ -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!",
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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.
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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
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date:
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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
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