rbbt-util 5.19.28 → 5.19.29

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2149fa7923fc0214ca857eec7d13d18f386b3e9e
-  data.tar.gz: ed588eb8da4eb1868e2bdfb4a7211ff282c1ce3d
+  metadata.gz: dcf03395fb6992f9b928709c4c1a5b62bc8409f8
+  data.tar.gz: 3d06adac3fe7750350c7185c93f61afae8f0b09e
 SHA512:
-  metadata.gz: 9c1709fc586ddeb17dc5c13485a6c10c8655db5d36bfc59ff2098bd3059b874bac079814a3ab2dd24368834d4b0060d8616c9d268736e5502c9a412d8ac22f43
-  data.tar.gz: 34f31ba40eccf2bc78f83332374217a52177f1e43dfa15be80cff52c1c80fe2f2ff76e27b99bac38cae2d276c930390263409ff208cfab25742115401cee4357
+  metadata.gz: 06501f7fca063beaff2358c021a46d14a93630d9ab3fd0b68c1df4e4f98e5c810916168401d2dd79d8e3b835b50a5907ac4cf41bae2bce7e18b28f7e9ef1245b
+  data.tar.gz: 91ee3cf063dc7b645b28c3005ee911d5a51d5f1eaf6d78b10a1fd19ebbf64e73d7a95e8793328883febfa67bfee7ee1a6ae77b41c57272432d2e0e98187a9a68

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

@@ -29,7 +29,7 @@ module TSV
               end
             end
 
-            new_values.collect!{|v| [v]}     if     type == :double and not other.type == :double
+            new_values.collect!{|v| [v]}     if     type == :double and not (other.type == :double or other.type == :flat)
             new_values.collect!{|v| v.nil? ? nil : (other.type == :single ? v : v.first)} if not type == :double and     other.type == :double
 
             new_values.flatten if type == :flat

data/lib/rbbt/tsv/change_id.rb

@@ -51,8 +51,10 @@ module TSV
     options = Misc.add_defaults options, :persist => false, :identifiers => tsv.identifiers, :compact => true
 
     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?
 
-    fields = identifiers.all_fields.include?(field)? [field] : nil
+    fields = (identifiers and identifiers.all_fields.include?(field))? [field] : nil 
     index = identifiers.index :target => format, :fields => fields, :persist => persist_input
 
     orig_type = tsv.type 

data/lib/rbbt/tsv/stream.rb

@@ -18,7 +18,7 @@ module TSV
  
   def self.paste_streams(streams, options = {})
     options = Misc.add_defaults options, :sep => "\t", :sort => true
-    sort, sep, preamble, header, same_fields, fix_flat = Misc.process_options options, :sort, :sep, :preamble, :header, :same_fields, :fix_flat
+    sort, sep, preamble, header, same_fields, fix_flat, all_match = Misc.process_options options, :sort, :sep, :preamble, :header, :same_fields, :fix_flat, :all_match
 
     out = Misc.open_pipe do |sin|
 
@@ -127,6 +127,9 @@ module TSV
           min = keys.compact.sort.first
           break if min.nil?
           str = []
+
+          skip = all_match && keys.uniq != [min]
+
           keys.each_with_index do |key,i|
             case key
             when min
@@ -161,6 +164,8 @@ module TSV
             end
           end
 
+          next if skip
+
           if same_fields
 
             values = nil

data/lib/rbbt/tsv/util.rb

@@ -292,7 +292,7 @@ module TSV
         through do |k,v| new[k] = v[pos] end
       end
     when :flat
-      self
+      return self
     when :single
       through do |k,v|
         new[k] = [v]

data/lib/rbbt/util/log.rb

@@ -247,8 +247,8 @@ module Log
 
   def self.tsv(tsv)
     STDERR.puts Log.color :magenta, "TSV log: " << Log.last_caller(caller)
-    puts Log.color(:blue, "=> "<< Misc.fingerprint(tsv), true) 
-    puts Log.color(:cyan, "=> " << tsv.summary)
+    STDERR.puts Log.color(:blue, "=> "<< Misc.fingerprint(tsv), true) 
+    STDERR.puts Log.color(:cyan, "=> " << tsv.summary)
   end
 
   def self.stack(stack)

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

@@ -365,6 +365,10 @@ module Misc
                 current_parts[i] = current_parts[i] << "|" << part
               end
             end
+
+            (parts.length..current_parts.length-1).to_a.each do |pos|
+              current_parts[pos] = current_parts[pos] << "|" << ""
+            end
           when current_key != key
             sin.puts [current_key, current_parts].flatten * sep
             current_key = key

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.28
+  version: 5.19.29
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-29 00:00:00.000000000 Z
+date: 2016-03-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake