rbbt-util 5.21.90 → 5.21.91

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e68de8ec56241c9fbc4bceed94f7c632a859c930
-  data.tar.gz: 3e4caace384777f8e4ecce35d89c003be40354fc
+  metadata.gz: f563cccf569fa61510d611058e9bbc3f15f4ecca
+  data.tar.gz: 8d11affe29abde8039c69e64c53206a40584bfd0
 SHA512:
-  metadata.gz: 29df479899b22d4577a28714247a80102836b4a63cd97548e3432d3d9cbcf469b13e3211c757ff4f83940e73f8a96696fa9779c0a5b9e43e8272f95b9738d926
-  data.tar.gz: a89236195f0add1240259fac4627a5e51e5808b73548f8d279586e3390688ef0aafc9e1d288f0704e68febbaf48a4159a6f3e86fbf875e836e320b12cccc3fe9
+  metadata.gz: db6be501c52eefb3e8f7a66a494772462fb26652d3ec17f20215da24958f91d17ae5e7fb648c8dd12770cd500eced281fcd4fdbb174e1f9f86705cfd71f01bfe
+  data.tar.gz: ce353bf4de86ec04797f6cf6b839bb6ee7fb19e4ad67e21d481404d34ea253ab0f79e7d09fc436a3c476be27e9ca33618562f2faa8987acfacb3940f5d1f0c26

data/lib/rbbt/tsv/attach.rb

@@ -100,7 +100,7 @@ module TSV
       key1 = key2 = nil
       while key1.nil?
         while (line1 = file1.gets) =~ /^#/
-          key_field1, *fields1 = line1.strip.sub('#','').split(sep)
+          key_field1, *fields1 = line1.chomp.sub('#','').split(sep)
         end
         key1, *parts1 = line1.sub("\n",'').split(sep, -1)
         cols1 = parts1.length
@@ -108,7 +108,7 @@ module TSV
 
       while key2.nil?
         while (line2 = file2.gets) =~ /^#/
-          key_field2, *fields2 = line2.strip.sub('#','').split(sep)
+          key_field2, *fields2 = line2.chomp.sub('#','').split(sep)
         end
         key2, *parts2 = line2.sub("\n",'').split(sep, -1)
         cols2 = parts2.length

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

@@ -76,7 +76,7 @@ module TSV
             if type == :double
               self[key] = values.concat field_positions.collect{|v| []}
             else
-              self[key] = values.concat [nil] * field_positions
+              self[key] = values.concat [nil] * field_positions.length
             end
           when Array === source_keys
             all_new_values = source_keys.collect do |source_key|

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -174,7 +174,7 @@ module TSV
           end
         end
         begin
-          callback.call yield line.strip
+          callback.call yield line.chomp
         ensure
           bar.tick if bar
         end
@@ -183,7 +183,7 @@ module TSV
       bar.init if bar
       while line = io.gets
         begin
-          yield line.strip
+          yield line.chomp
         ensure
           bar.tick if bar
         end

data/lib/rbbt/tsv/stream.rb

@@ -238,12 +238,12 @@ module TSV
   def self.reorder_stream(stream, positions, sep = "\t")
     Misc.open_pipe do |sin|
       line = stream.gets
-      line.strip! unless line.nil?
+      line.chomp! unless line.nil?
 
       while line =~ /^#\:/
         sin.puts line
         line = stream.gets
-        line.strip! unless line.nil?
+        line.chomp! unless line.nil?
       end
 
       while line  =~ /^#/
@@ -255,9 +255,9 @@ module TSV
           end
           positions = new
         end
-        sin.puts "#" + line.sub(/^#/,'').strip.split(sep).values_at(*positions).compact * sep
+        sin.puts "#" + line.sub(/^#/,'').chomp.split(sep).values_at(*positions).compact * sep
         line = stream.gets
-        line.strip! unless line.nil?
+        line.chomp! unless line.nil?
       end
 
       while line
@@ -273,7 +273,7 @@ module TSV
         new_values = values.values_at(*positions)
         sin.puts new_values * sep
         line = stream.gets
-        line.strip! unless line.nil?
+        line.chomp! unless line.nil?
       end
     end
   end

data/lib/rbbt/util/log/progress/report.rb

@@ -48,13 +48,22 @@ module Log
                       else
                         20
                       end
-        max_history = 100 if max_history > 100
+        max_history = 30 if max_history > 30
         @history.shift if @history.length > max_history
       end
 
       @mean_max ||= 0
       if @history.length > 3
-        mean = @mean = Misc.mean(@history)
+
+        w_mean = 0
+        total_w = 0
+        @history.each_with_index do |v,i|
+          c = i ** 10
+          w_mean += v * c
+          total_w += c
+        end
+        mean = @mean = w_mean.to_f / total_w
+
         @mean_max = mean if mean > @mean_max
       end
 

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

@@ -307,7 +307,7 @@ module Misc
   end
 
   def self.intersect_streams_read(io, sep=":")
-    line = io.gets.strip
+    line = io.gets.chomp
     parts = line.split(sep)
     chr, start, eend, *rest = parts
     start = start.to_i

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

@@ -523,7 +523,7 @@ module Misc
           keys[i] = nil
           parts[i] = []
         else
-          key, *p = line.strip.split(sep, -1) 
+          key, *p = line.chomp.split(sep, -1) 
           keys[i] = key
           parts[i] = p
         end
@@ -542,7 +542,7 @@ module Misc
               keys[i] = nil
               parts[i] = nil
             else
-              k, *p = line.strip.split(sep, -1)
+              k, *p = line.chomp.split(sep, -1)
               keys[i] = k
               parts[i] = p
             end

data/lib/rbbt/workflow/step.rb

@@ -121,7 +121,7 @@ class Step
               when :array
                 array = []
                 while line = value.gets
-                  array << line.strip
+                  array << line.chomp
                 end
                 array
               when :tsv

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.90
+  version: 5.21.91
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-07-05 00:00:00.000000000 Z
+date: 2017-07-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -508,83 +508,83 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
+- test/rbbt/test_workflow.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_setup.rb
 - test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/test_chain_methods.rb
 - test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_open.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_pipes.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_association.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_parser.rb
 - test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_excel.rb
+- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/test_persist.rb
+- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
+- test/test_helper.rb