rbbt-util 5.17.47 → 5.17.48

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 9ef4162cc1a9676fc7854f59b31b49e6e9c5a57d
+  metadata.gz: 49361db931554a4d261eedceb18ea47bee449862
+  data.tar.gz: e1d042a946e1b2f19402a3e597d761bb2f69fab4
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+  data.tar.gz: f20556bed0086287a5f828b4e5183e8e475022158c0edbe43134545a9711d7205c8e14f177bd0625a882eb687dbf069fc56ba62ede5cbe430ba67e1e658ca511

data/lib/rbbt/knowledge_base/registry.rb

@@ -36,6 +36,7 @@ class KnowledgeBase
 
   def get_index(name, options = {})
     name = name.to_s
+    options[:organism] ||= options[:namespace] ||= self.namespace
     @indices[[name, options]] ||= 
       begin 
         fp = Misc.fingerprint([name,options])
@@ -79,6 +80,7 @@ class KnowledgeBase
 
   def get_database(name, options = {})
     name = name.to_s
+    options[:organism] ||= options[:namespace] ||= self.namespace
     @databases[[name, options]] ||= 
       begin 
         fp = Misc.fingerprint([name,options])

data/lib/rbbt/tsv/manipulate.rb

@@ -247,7 +247,7 @@ module TSV
     persist_options = Misc.pull_keys options, :persist
     persist_options[:prefix] = "Reorder"
 
-    Persist.persist_tsv self, self.filename, {:key_field => new_key_field, :fields => new_fields}, persist_options do |data|
+    Persist.persist_tsv self, self.filename, self.options.merge({:key_field => new_key_field, :fields => new_fields}), persist_options do |data|
       if data.respond_to? :persistence_path
         real_data = data 
         data = {}

data/share/rbbt_commands/stat/pvalue.qqplot

@@ -0,0 +1,64 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Produce a qq-plot for p-values
+
+$ rbbt stat pvalue.qqplot [options] <filename1.tsv> <filename2.tsv> ...
+
+-h--help Print this help
+-f--field* P-value field in files
+
+EOF
+if options[:help]
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.usage
+  end
+  exit 0
+end
+
+files = ARGV
+
+raise "No files" if files.empty?
+
+field = options[:field]
+
+raise "No p-value field specified" if field.nil?
+
+
+file_values = []
+
+files.each do |file|
+ values = []
+ TSV.traverse file, :fields => [field], :type => :single, :into => values do |key,value|
+  - Math.log10(value.to_f)
+ end
+ file_values << values.sort.reverse
+end
+
+max = file_values.collect{|l| l.length}.min
+
+TmpFile.with_file(nil, false) do |dir|
+ Path.setup(dir)
+ names = []
+ names << 'proportional'
+ Open.write(dir["proportional"], (1..max+1).collect{|v| - Math.log10(v / max+1)} * "\n")
+ files.each_with_index do |file,i|
+   name = File.basename(file)
+   file = dir[name]
+   Open.write(dir[name], file_values[i][0..max].reverse * "\n")
+   names << name
+ end
+ puts `eplot -A -m #{names.collect{|n| "'#{dir[n]}'" } * " "}`
+ ppp "eplot -A -m #{names.collect{|n| "'#{dir[n]}'" } * " "}"
+
+end
+
+

data/share/rbbt_commands/tsv/sort

@@ -23,7 +23,6 @@ file = ARGV.shift
 
 file = STDIN if file == '-' or file.nil?
 
-
 field = options[:field] || '2'
 if field =~ /^\d+$/
   field_pos = field.to_i

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.47
+  version: 5.17.48
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-12 00:00:00.000000000 Z
+date: 2015-06-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -303,6 +303,7 @@ files:
 - share/rbbt_commands/stat/abs
 - share/rbbt_commands/stat/density
 - share/rbbt_commands/stat/log
+- share/rbbt_commands/stat/pvalue.qqplot
 - share/rbbt_commands/study/maf2study
 - share/rbbt_commands/study/task
 - share/rbbt_commands/system/clean