rbbt-util 5.20.12 → 5.20.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: d8d1de6c214c2a8f052d01de4357d50531943eb5
+  metadata.gz: 841046995ec2cd9dda2e965c39eb088c77460d72
+  data.tar.gz: 5f07ff9767eaf96377ff5dc1ed222599e111486d
 SHA512:
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+  metadata.gz: b1f2f171aedb529a94e7d972859f8dcc6b2c152a74e0bbc37e8d3816f1274f9df3e2bbc593d633be412cea27b47c7dcae47e29f2ae8c4d019812b4492a5eea59
+  data.tar.gz: 19e701161b6b0c8b7cf74e508b18365d94c53af2783441145afda1673dd38f45c16a17ef64527a5d99484246c9e80a64ec780edefbe95ed39028812abdd145ca

data/lib/rbbt/persist/tsv.rb

@@ -82,6 +82,7 @@ module Persist
     persist_options[:prefix] ||= "TSV"
 
     if data = persist_options[:data]
+      Log.debug "TSV persistence creating with data: #{ Misc.fingerprint(data) }"
       yield data
       return data 
     end

data/lib/rbbt/tsv/parser.rb

@@ -471,7 +471,6 @@ module TSV
         raise "Unknown TSV type: #{@type.inspect}"
       end
 
-
       @straight = false if @sep != "\t" or not @cast.nil? or merge or (@type == :flat and fields)
     end
 

data/lib/rbbt/tsv/stream.rb

@@ -10,7 +10,7 @@ module TSV
 
     sorted_input_stream = Misc.sort_stream input_stream, header_hash, cmd_args
 
-    parser = TSV::Parser.new sorted_input_stream, options.dup
+    parser = TSV::Parser.new(sorted_input_stream, options.dup)
     dumper = TSV::Dumper.new parser
     header = TSV.header_lines(parser.key_field, parser.fields, parser.options)
     dumper.close_in
@@ -232,4 +232,63 @@ module TSV
     end
     dumper
   end
+
+
+  def self.reorder_stream(stream, positions, sep = "\t")
+    Misc.open_pipe do |sin|
+      line = stream.gets
+      line.strip! unless line.nil?
+
+      while line =~ /^#\:/
+        sin.puts line
+        line = stream.gets
+        line.strip! unless line.nil?
+      end
+
+      while line  =~ /^#/
+        if Hash === positions
+          new = (0..line.split(sep).length-1).to_a
+          positions.each do |k,v|
+            new[k] = v
+            new[v] = k
+          end
+          positions = new
+        end
+        sin.puts "#" + line.sub(/^#/,'').strip.split(sep).values_at(*positions).compact * sep
+        line = stream.gets
+        line.strip! unless line.nil?
+      end
+
+      while line
+        if Hash === positions
+          new = (0..line.split(sep).length-1).to_a
+          positions.each do |k,v|
+            new[k] = v
+            new[v] = k
+          end
+          positions = new
+        end
+        values = line.split(sep)
+        new_values = values.values_at(*positions)
+        sin.puts new_values * sep
+        line = stream.gets
+        line.strip! unless line.nil?
+      end
+    end
+  end
+
+
+  def self.reorder_stream_tsv(stream, key_field, fields)
+    parser = TSV::Parser.new TSV.get_stream(stream), :key_field => key_field, :fields => fields
+    dumper_options = parser.options
+    dumper = TSV::Dumper.new dumper_options
+    dumper.init 
+    TSV.traverse parser, :into => dumper do |key,values|
+      key = key.first if Array === key
+      values = [values] unless Array === values
+      [key, values]
+    end
+    dumper
+  end
+
 end

data/lib/rbbt/tsv/util.rb

@@ -6,48 +6,6 @@ module TSV
     field_matches.sort_by{|field, count| count.to_i}.last
   end
 
-  def self.reorder_stream(stream, positions, sep = "\t")
-    Misc.open_pipe do |sin|
-      line = stream.gets
-      line.strip! unless line.nil?
-
-      while line =~ /^#\:/
-        sin.puts line
-        line = stream.gets
-        line.strip! unless line.nil?
-      end
-
-      while line  =~ /^#/
-        if Hash === positions
-          new = (0..line.split(sep).length-1).to_a
-          positions.each do |k,v|
-            new[k] = v
-            new[v] = k
-          end
-          positions = new
-        end
-        sin.puts "#" + line.sub(/^#/,'').strip.split(sep).values_at(*positions).compact * sep
-        line = stream.gets
-        line.strip! unless line.nil?
-      end
-
-      while line
-        if Hash === positions
-          new = (0..line.split(sep).length-1).to_a
-          positions.each do |k,v|
-            new[k] = v
-            new[v] = k
-          end
-          positions = new
-        end
-        values = line.split(sep)
-        new_values = values.values_at(*positions)
-        sin.puts new_values * sep
-        line = stream.gets
-        line.strip! unless line.nil?
-      end
-    end
-  end
 
   def self.field_match_counts(file, values, options = {})
     options = Misc.add_defaults options, :persist_prefix => "Field_Matches"

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

@@ -201,7 +201,7 @@ module Misc
              when cds =~ />/
                cds.split(">").last
              when cds =~ /del/
-               deletion = cds.split("del").last
+               deletion = cds.split("del").last.chomp
                case
                when deletion =~ /^\d+$/
                  "-" * deletion.to_i

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

@@ -398,11 +398,6 @@ module Misc
   def self.sort_stream(stream, header_hash = "#", cmd_args = "-u")
     Misc.open_pipe do |sin|
       begin
-        #if defined? Step and Step === stream
-        #  step = stream
-        #  stream = stream.get_stream || stream.path.open
-        #end
-
         stream = TSV.get_stream stream
 
         line = stream.gets

data/lib/rbbt/workflow/step/dependencies.rb

@@ -153,8 +153,7 @@ class Step
       Log.error "Interrupted while in dep. #{Log.color :red, dependency.task_name.to_s}"
       raise $!
     rescue Exception
-      Log.error "Exception in dep. #{ Log.color :red, dependency.task_name.to_s }"
-      Log.exception $!
+      Log.error "Exception in dep. #{ Log.color :red, dependency.task_name.to_s } -- #{$!.message}"
       raise $!
     end
   end

data/test/rbbt/tsv/test_stream.rb

@@ -217,4 +217,20 @@ row2 a|aa|aaa
     assert_equal text2, s2.stream.read
   end
 
+  def test_reorder_stream
+    text=<<-EOF
+#: :sep=" "
+#Row LabelA LabelB LabelC
+row1 A B C
+row1 a b c
+row2 AA BB CC
+row2 aa bb cc
+row4  BBB CC
+    EOF
+
+    s = StringIO.new text
+    dumper = TSV.reorder_stream_tsv(s, "LabelC", %w(Row LabelA))
+    tsv = TSV.open TSV.collapse_stream(dumper.stream).stream.read
+    assert_equal %w(row2 row4), tsv["CC"]["Row"]
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.20.12
+  version: 5.20.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-16 00:00:00.000000000 Z
+date: 2016-06-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake