rbbt-util 5.19.12 → 5.19.13

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 31f019642b140c119e08c2e4eb465b6775f4e89b
+  metadata.gz: 5f75831f4615a7e138d5b695bbea6517b889124a
+  data.tar.gz: ccdb744d5b4fcbdecd7123b2ef7be14d4a5ba554
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+  data.tar.gz: 0cdc819b514319fe59d065d29220eac6f5179c287df8cbca1c9e8ce7d29d2068dc83f726a59794d7c33f69ecebdec660f16a8701cdda34eab285e93845997db0

data/lib/rbbt/persist/tsv.rb

@@ -6,31 +6,31 @@ require 'rbbt/persist/tsv/packed_index'
 begin
   require 'rbbt/persist/tsv/tokyocabinet'
 rescue Exception
-  Log.warn "The tokyocabinet gem could not be loaded: persistence over TSV files will fail"
+  Log.warn "The tokyocabinet gem could not be loaded. Persistence using this engine will fail."
 end
 
 begin
   require 'rbbt/persist/tsv/lmdb'
 rescue Exception
-  Log.debug "The lmdb gem could not be loaded. Persistance using this engine will fail."
+  Log.debug "The lmdb gem could not be loaded. Persistence using this engine will fail."
 end
 
 begin
   require 'rbbt/persist/tsv/leveldb'
 rescue Exception
-  Log.debug "The LevelDB gem could not be loaded. Persistance using this engine will fail."
+  Log.debug "The LevelDB gem could not be loaded. Persistence using this engine will fail."
 end
 
 begin
   require 'rbbt/persist/tsv/cdb'
 rescue Exception
-  Log.debug "The CDB gem could not be loaded. Persistance using this engine will fail."
+  Log.debug "The CDB gem could not be loaded. Persistence using this engine will fail."
 end
 
 begin
   require 'rbbt/persist/tsv/kyotocabinet'
 rescue Exception
-  Log.debug "The kyotocabinet gem could not be loaded. Persistance using this engine will fail."
+  Log.debug "The kyotocabinet gem could not be loaded. Persistence using this engine will fail."
 end
 
 module Persist

data/lib/rbbt/util/cmd.rb

@@ -3,78 +3,78 @@ require 'stringio'
 
 module CMD
 
-  module SmartIO 
-    attr_accessor :pid, :cmd, :post, :in, :out, :err, :log
-    def self.tie(io, pid = nil, cmd = "",  post = nil, sin = nil, out = nil, err = nil, log = true)
-      io.extend SmartIO
-      io.pid = pid
-      io.cmd = cmd
-      io.in  = sin 
-      io.out  = out 
-      io.err  = err 
-      io.post = post
-      io.log = log
-
-      io.class.send(:alias_method, :original_close, :close)
-      io.class.send(:alias_method, :original_read, :read)
-      io
-    end
-
-    def wait_and_status
-      if @pid
-        begin
-          Process.waitpid(@pid)
-        rescue
-        end
-
-        Log.debug{"Process #{ cmd } succeded" if $? and $?.success? and log}
-
-        if $? and not $?.success?
-          Log.debug{"Raising exception" if log}
-          exception = ProcessFailed.new "Command [#{@pid}] '#{@cmd}' failed with error status #{$?.exitstatus}"
-          begin
-            original_close
-          ensure
-            raise exception
-          end
-        end
-      end
-    end
-
-    def close
-      self.original_read unless self.closed? or self.eof?
-
-      wait_and_status
-
-      @post.call if @post
-
-      original_close unless self.closed?
-    end
-
-    def force_close
-      if @pid
-        Log.debug{"Forcing close by killing '#{@pid}'" if log}
-        begin
-          Process.kill("KILL", @pid)
-          Process.waitpid(@pid)
-        rescue
-          Log.low{"Exception in forcing close of command [#{ @pid }, #{cmd}]: #{$!.message}"}
-        end
-      end
-
-      @post.call if @post
-
-      original_close unless self.closed?
-    end
-
-    def read(*args)
-      data = original_read(*args) unless self.closed? #or self.eof?
-
-      self.close if not self.closed? and self.eof?
-
-      data #|| ""
-    end
-  end
+  #module SmartIO 
+  #  attr_accessor :pid, :cmd, :post, :in, :out, :err, :log
+  #  def self.tie(io, pid = nil, cmd = "",  post = nil, sin = nil, out = nil, err = nil, log = true)
+  #    io.extend SmartIO
+  #    io.pid = pid
+  #    io.cmd = cmd
+  #    io.in  = sin 
+  #    io.out  = out 
+  #    io.err  = err 
+  #    io.post = post
+  #    io.log = log
+
+  #    io.class.send(:alias_method, :original_close, :close)
+  #    io.class.send(:alias_method, :original_read, :read)
+  #    io
+  #  end
+
+  #  def wait_and_status
+  #    if @pid
+  #      begin
+  #        Process.waitpid(@pid)
+  #      rescue
+  #      end
+
+  #      Log.debug{"Process #{ cmd } succeded" if $? and $?.success? and log}
+
+  #      if $? and not $?.success?
+  #        Log.debug{"Raising exception" if log}
+  #        exception = ProcessFailed.new "Command [#{@pid}] '#{@cmd}' failed with error status #{$?.exitstatus}"
+  #        begin
+  #          original_close
+  #        ensure
+  #          raise exception
+  #        end
+  #      end
+  #    end
+  #  end
+
+  #  def close
+  #    self.original_read unless self.closed? or self.eof?
+
+  #    wait_and_status
+
+  #    @post.call if @post
+
+  #    original_close unless self.closed?
+  #  end
+
+  #  def force_close
+  #    if @pid
+  #      Log.debug{"Forcing close by killing '#{@pid}'" if log}
+  #      begin
+  #        Process.kill("KILL", @pid)
+  #        Process.waitpid(@pid)
+  #      rescue
+  #        Log.low{"Exception in forcing close of command [#{ @pid }, #{cmd}]: #{$!.message}"}
+  #      end
+  #    end
+
+  #    @post.call if @post
+
+  #    original_close unless self.closed?
+  #  end
+
+  #  def read(*args)
+  #    data = original_read(*args) unless self.closed? #or self.eof?
+
+  #    self.close if not self.closed? and self.eof?
+
+  #    data #|| ""
+  #  end
+  #end
 
 
   def self.process_cmd_options(options = {})
@@ -105,6 +105,7 @@ module CMD
     post       = options.delete(:post)
     log        = options.delete(:log)
     no_fail    = options.delete(:no_fail)
+    no_wait    = options.delete(:no_wait)
     dont_close_in  = options.delete(:dont_close_in)
 
     log = true if log.nil?
@@ -132,15 +133,9 @@ module CMD
 
         io = in_content
         while IO === io
-          if SmartIO === io
-            io.original_close unless io.closed?
-            io.out.close unless io.out.nil? or io.out.closed?
-            io.err.close unless io.err.nil? or io.err.closed?
-            io = io.in
-          else
-            io.close unless io.closed?
-            io = nil
-          end
+          io.join if io.respond_to?(:join) and not io.joined?
+          io.close if io.respond_to?(:close) and not io.closed?
+          io = nil
         end
 
         STDIN.reopen sin.first
@@ -206,7 +201,7 @@ module CMD
       end
 
       #SmartIO.tie sout, pid, cmd, post, in_content, sin, serr
-      ConcurrentStream.setup sout, :pids => [pid], :autojoin => true, :no_fail => no_fail
+      ConcurrentStream.setup sout, :pids => [pid], :autojoin => true, :no_fail => no_fail unless no_wait
 
       sout
     else

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

@@ -1,9 +1,23 @@
+
 require 'rbbt/persist'
 require 'set'
 
 module Bgzf
   attr_accessor :data_offset, :compressed_stream, :block_cache_size
 
+  def self.bgzip_cmd
+    @@bgzip_cmd ||= begin
+                      path = `bash -c "type -p bgzips"`.strip
+                      if path.empty?
+                        Rbbt.claim Rbbt.software.opt.htslib, :install, Rbbt.share.install.software.HTSLIB
+                        Rbbt.software.opt.htslib.produce
+                        Rbbt.software.opt.htslib.bin.bgzip.find
+                      else
+                        path
+                      end
+                    end
+  end
+
   def self.setup(compressed_stream)
     require 'bio-bgzf'
     reader = Bio::BGZF::Reader.new(compressed_stream)

data/lib/rbbt/util/open.rb

@@ -294,7 +294,7 @@ module Open
    
   def self.gunzip(stream)
     #Zlib::GzipReader.new(stream)
-    CMD.cmd('zcat', :in => stream, :pipe => true)
+    CMD.cmd('zcat', :in => stream, :pipe => true, :no_fail => true, :no_wait => true)
   end
 
   def self.unzip(stream)

data/lib/rbbt/workflow/usage.rb

@@ -44,7 +44,7 @@ module Task
     puts
     
     if selects.any?
-      puts Log.color(:magenta, "Input options: ") << Log.color(:blue, result_type.to_s) << "\n"
+      puts Log.color(:magenta, "Input select options")
       puts
       selects.each do |input,options|
         puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| o.to_s} * ", ") << "\n"

data/share/rbbt_commands/system/optimize

@@ -35,13 +35,15 @@ raise ParameterException, "Not a valid directory" unless File.directory? directo
 directory = Path.setup directory.dup
 keep = options[:keep]
 
+require 'rbbt/util/misc/bgzf'
+
 Log.info Log.color(:magenta, "Processing chromosomes")
 chromosome_files = directory.glob('**/chromosome_*')
 TSV.traverse chromosome_files, :type => :array, :bar => "Processing chromosomes" do |chr_file|
   next if chr_file =~ /.bgz$/
   compressed_file = chr_file + '.bgz'
   Log.info "Compressing #{ chr_file } into #{ compressed_file }"
-  CMD.cmd("bgzip '#{ chr_file }' -c > #{ compressed_file }")
+  CMD.cmd("#{Bgzf.bgzip_cmd} '#{ chr_file }' -c > #{ compressed_file }")
   begin
     Open.read(compressed_file)
     if keep

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

@@ -2,7 +2,7 @@ require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_he
 require 'rbbt/util/misc/bgzf'
 
 class TestBgzf < Test::Unit::TestCase
-  def _test_Bgzf
+  def test_Bgzf
     content = "1234567890" * 1000000
     TmpFile.with_file(content) do |file|
       compressed = file + '.gz'
@@ -35,5 +35,10 @@ class TestBgzf < Test::Unit::TestCase
       end
     end
   end
+
+  def test_bgzip
+    assert File.exists?(Bgzf.bgzip_cmd)
+    assert 'bgzip', File.basename(Bgzf.bgzip_cmd)
+  end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.12
+  version: 5.19.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-01-27 00:00:00.000000000 Z
+date: 2016-02-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake