rbbt-util 5.19.29 → 5.19.30

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: dcf03395fb6992f9b928709c4c1a5b62bc8409f8
-  data.tar.gz: 3d06adac3fe7750350c7185c93f61afae8f0b09e
+  metadata.gz: 3184d37817097198d31ebdd2af78c95b51bf1784
+  data.tar.gz: cc4c9a849005583c40a3009e6eb57a6fca0990fd
 SHA512:
-  metadata.gz: 06501f7fca063beaff2358c021a46d14a93630d9ab3fd0b68c1df4e4f98e5c810916168401d2dd79d8e3b835b50a5907ac4cf41bae2bce7e18b28f7e9ef1245b
-  data.tar.gz: 91ee3cf063dc7b645b28c3005ee911d5a51d5f1eaf6d78b10a1fd19ebbf64e73d7a95e8793328883febfa67bfee7ee1a6ae77b41c57272432d2e0e98187a9a68
+  metadata.gz: 27bd364fec2ac63ff3b61167579be2d26aa4f2617481559e199128ee118fb200b0bc71cbb432c59bb505d4719d70d613997baaee2a5448568101d927a73f7beb
+  data.tar.gz: 057a24eccb91df8d925adc264c4b20d7c2613a655b125415bbcf7fdefb3e7cb45723eea5ba42948762d742066876cfcf7cfdbd080f0e40e5f82566f7eb44e411

data/lib/rbbt/tsv/attach.rb

@@ -197,6 +197,7 @@ module TSV
 
     if complete
       fill = TrueClass === complete ? nil : complete
+      field_length = self.fields.length 
       missing = other.keys - self.keys
       case type
       when :single

data/lib/rbbt/tsv/attach/util.rb

@@ -4,6 +4,7 @@ module TSV
     fields = other.fields - [key_field].concat(self.fields) if fields.nil?
 
     fields = [fields].compact unless Array === fields
+    num_fields = fields.length
 
     field_positions = fields.collect{|field| other.identify_field field}
     other.with_unnamed do
@@ -37,9 +38,9 @@ module TSV
             self[key] = current + new_values
           else
             if type == :double
-              self[key] = current + [[]] * fields.length
+              self[key] = current + [[]] * num_fields
             else
-              self[key] = current + [nil] * fields.length
+              self[key] = current + [nil] * num_fields
             end
           end
         end

data/lib/rbbt/tsv/change_id.rb

@@ -53,9 +53,17 @@ module TSV
     identifiers, persist_input, compact = Misc.process_options options, :identifiers, :persist, :compact
     identifiers = tsv.identifier_files.first if identifiers.nil?
     identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace and Organism.identifiers(tsv.namespace).exists?
+    identifiers.namespace ||= tsv.namespace
 
     fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 
-    index = identifiers.index :target => format, :fields => fields, :persist => persist_input
+    #index = identifiers.index :target => format, :fields => fields, :persist => persist_input, :order => true
+
+    grep = Organism.blacklist_genes(tsv.namespace).list  if identifiers.namespace and Organism.blacklist_genes(tsv.namespace).exists?
+    if fields.nil?
+      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :persist => true, :order => true, :unnamed => true, :data_persist => true)
+    else
+      index = identifiers.index(:data_tsv_grep => grep, :data_invert_grep => true, :target => format, :fields => fields, :order => true, :unnamed => true, :persist => true, :data_persist => true)
+    end
 
     orig_type = tsv.type 
     tsv = tsv.to_double if orig_type != :double

data/lib/rbbt/tsv/index.rb

@@ -129,6 +129,7 @@ module TSV
     Log.debug "Static Index: #{ file } - #{Misc.fingerprint options}"
     Persist.persist_tsv nil, file, options, persist_options do |data|
       data_options = Misc.pull_keys options, :data
+      data_options[:grep] ||= data_options[:tsv_grep] if data_options[:tsv_grep]
       identifiers = TSV.open(file, data_options)
       identifiers.with_monitor :desc => "Creating Index for #{ file }" do
         identifiers.index(options.merge :persist_data => data, :persist => persist_options[:persist])

data/lib/rbbt/util/misc/pipes.rb

@@ -353,14 +353,16 @@ module Misc
 
         current_parts = []
         while line 
-          key, *parts = line.strip.split(sep, -1)
-          current_key ||= key
+          key, *parts = line.chomp.split(sep, -1)
           case
           when key.nil?
+          when current_parts.nil?
+            current_parts = parts
+            current_key = key
           when current_key == key
             parts.each_with_index do |part,i|
               if current_parts[i].nil?
-                current_parts[i] = part
+                current_parts[i] = "|" << part
               else
                 current_parts[i] = current_parts[i] << "|" << part
               end

data/share/color/diverging_colors.hex

@@ -0,0 +1,12 @@
+#a6cee3
+#1f78b4
+#b2df8a
+#33a02c
+#fb9a99
+#e31a1c
+#fdbf6f
+#ff7f00
+#cab2d6
+#6a3d9a
+#ffff99
+#b15928

data/share/rbbt_commands/app/start

@@ -18,6 +18,7 @@ $ rbbt app start [options] <app_name>
 -s--server* Server type:  thin, webrick, unicorn, etc
 -f--finder Start server with finder functionality
 -R--Rserve_session* Rserve session to use, otherwise start new one
+-wd--workdir* Change the working directory of the workflow
 --views* Directory with view templates
 EOF
 
@@ -30,6 +31,11 @@ if options[:help]
   exit 0
 end
 
+if options[:workdir]
+  require 'rbbt/workflow'
+  Workflow.workdir = options[:workdir]
+end
+
 options[:Port] ||= options[:port]
 options[:Host] ||= "0.0.0.0"
 options[:Bind] ||= "0.0.0.0"

data/test/rbbt/util/misc/test_pipes.rb

@@ -19,6 +19,34 @@ row2 aa bb cc
     assert_equal ["BB", "bb"], tsv["row2"][1]
   end
 
+  def test_collapse_stream_gap
+    text=<<-EOF
+row2 AA BB 
+row2 aa bb cc
+    EOF
+
+    s = StringIO.new text
+    assert Misc.collapse_stream(s, nil, " ").read =~  /\|cc$/
+    
+    text=<<-EOF
+row2 aa bb cc
+row2 AA BB 
+    EOF
+
+    s = StringIO.new text
+    assert Misc.collapse_stream(s, nil, " ").read =~  /cc\|$/
+
+    text=<<-EOF
+row2 AA BB
+row2 aa bb cc
+    EOF
+
+    s = StringIO.new text
+    assert Misc.collapse_stream(s, nil, " ").read =~  /\|cc$/
+
+  end
+
+
   def test_paste_stream
     text1=<<-EOF
 row1 A B C

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.29
+  version: 5.19.30
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-30 00:00:00.000000000 Z
+date: 2016-04-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -294,6 +294,7 @@ files:
 - share/Rlib/plot.R
 - share/Rlib/svg.R
 - share/Rlib/util.R
+- share/color/diverging_colors.hex
 - share/config.ru
 - share/install/software/HTSLIB
 - share/install/software/lib/install_helpers