rbbt-util 5.6.1 → 5.6.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3656ab04698a077becda559ac837570042688fa8
-  data.tar.gz: f54aa65f719933df04767b54e896c74adb805e34
+  metadata.gz: 7529a3f61ee17378eae98591577b9a39f9a64fd8
+  data.tar.gz: 21485c3f12ae2823f13e7a7f098d242dac15c0c1
 SHA512:
-  metadata.gz: 929e4be6771df3db4f8507a9af317cb9bd841107d4170ec2ff198f1e1ed2aca0762e5b32851b1653336afdae49dc2729b0143fd65938cedd11660db2a5d687fc
-  data.tar.gz: 63ce2e0a7e12c9e6c6204a5d79764e9691ff781ae68e27586b135c524710ce557ce89a958aff4b7c101aa3cfd67897fdcb0ec415b5b09f315dad8a27ce437199
+  metadata.gz: 73f9e121eb79a0c91b92dd5474f04508771230d8451178cf348d6fb3f920d89518491106c7a051f95bd28d94bb59884aa20491b3d8dd1839786603eecb2efc41
+  data.tar.gz: 39c04b2dff5c9fd798c2cb45cb432395d627b60f1ff2bf9483e5602035ab8e36ccd5847e75b03eec3c0cd4b61ee0a2c4c5bdb804d2776f031708babee6303289

data/lib/rbbt/resource/path.rb

@@ -199,7 +199,9 @@ module Path
   end
 
   def yaml
-    YAML.load self.open
+    self.open do |f|
+      YAML.load f
+    end
   end
 
   def pipe_to(cmd, options = {})

data/lib/rbbt/tsv/accessor.rb

@@ -547,5 +547,28 @@ Example:
     ENTRY_KEYS.each{|entry| new.delete entry}
     new
   end
+
+  def unzip(field = 0)
+    new = {}
+    field_pos = self.identify_field field
+
+    self.through do |key,values|
+      field_values = values.delete_at field_pos
+      zipped = values.zip_fields
+      field_values.zip(zipped) do |value, *rest|
+        new[[key,value]*":"] = Misc.zip_fields(rest)
+      end
+    end
+
+    self.annotate new
+    new.type = :list
+
+    new.key_field = [self.key_field, self.fields[field_pos]] * ":"
+    new_fields = self.fields.dup
+    new_fields.delete_at field_pos
+    new.fields = new_fields
+
+    new
+  end
 end
 

data/lib/rbbt/tsv/parser.rb

@@ -25,7 +25,7 @@ module TSV
 
       if line and line =~ /^#{@header_hash}: (.*)/
         options = Misc.string2hash $1
-        line = stream.gets
+        line = Misc.fixutf8 stream.gets
       end
 
       # Determine separator
@@ -34,14 +34,17 @@ module TSV
 
       # Process fields line
 
-      while line and Misc.fixutf8(line) =~ /^#{@header_hash}/
+      while line and Misc.fixutf8(line) =~ /^#{@header_hash}/ 
         line.chomp!
         @fields = line.split(@sep)
         @key_field = @fields.shift
         @key_field = @key_field[(0 + header_hash.length)..-1] # Remove initial hash character
-        line = stream.gets
+
+        line = @header_hash != "" ?  Misc.fixutf8(stream.gets) : nil
       end
 
+      line ||= stream.gets
+
       @first_line = line
 
       options

data/lib/rbbt/util/filecache.rb

@@ -21,7 +21,7 @@ module FileCache
     filename.match(/(.+)\.(.+)/)
 
     base = filename.sub(/\..+/,'')
-    dirs = base.scan(/./).values_at(0,1,2,3,4).compact.reverse
+    dirs = base.scan(/./).reverse.values_at(0,1,2,3,4).compact
 
     File.join(File.join(CACHEDIR, *dirs), filename) 
   end
@@ -75,13 +75,6 @@ module FileCache
       filename = pattern ? pattern.sub("{ID}", id.to_s) : id.to_s
       path = FileCache.path(filename)
       Open.write(path, content)
-      result_files[id] = content
-    end
-
-    missing.each do |id|
-      filename = pattern ? pattern.sub("{ID}", id.to_s) : id.to_s
-      result = yield id
-      File.open{|f| f.write(path = FileCache.path(filename)) }
       result_files[id] = path
     end
 

data/lib/rbbt/util/misc.rb

@@ -29,7 +29,7 @@ module Misc
   def self.correct_icgc_mutation(pos, ref, mut_str)
     mut = mut_str
     mut = '-' * (mut_str.length - 1) if mut =~/^-[ACGT]/
-      mut = "+" << mut if ref == '-'
+    mut = "+" << mut if ref == '-'
     [pos, [mut]]
   end
 

data/lib/rbbt/util/open.rb

@@ -216,9 +216,13 @@ module Open
       save_content_in_repo(*dir_sub_path)
     else
       File.open(file, mode) do |f|
-        f.flock(File::LOCK_EX)
-        f.write content 
-        f.flock(File::LOCK_UN)
+        begin
+          f.flock(File::LOCK_EX)
+          f.write content 
+          f.flock(File::LOCK_UN)
+        ensure
+          f.close unless f.closed?
+        end
       end
     end
   end
@@ -359,21 +363,18 @@ module Open
   end
 
   def self.read(file, options = {}, &block)
-    f = open(file, options)
-
-    if block_given?
-      res = []
-      while not f.eof?
-        l = f.gets
-        l = Misc.fixutf8(l) 
-        res << yield(l)
+    open(file, options) do |f|
+      if block_given?
+        res = []
+        while not f.eof?
+          l = f.gets
+          l = Misc.fixutf8(l) 
+          res << yield(l)
+        end
+        res
+      else
+        Misc.fixutf8(f.read)
       end
-      f.close
-      res
-    else
-      text = Misc.fixutf8(f.read)
-      f.close unless f.closed?
-      text 
     end
   end
 

data/share/rbbt_commands/tsv/info

@@ -7,6 +7,8 @@ options = SOPT.get("-tch--tokyocabinet:-tcb--tokyocabinet_bd")
 
 file = ARGV.shift
 
+file = STDIN if file == '-'
+
 case
 when options[:tokyocabinet]
   tsv = Persist.open_tokyocabinet(file, false)
@@ -18,6 +20,7 @@ else
   header = TSV.parse_header(Open.open(file))
 
   puts "File: #{ file }"
+  puts "Type: #{header.type}"
   puts "Key: #{header.key_field}"
   puts "Fields: "
   header.fields.each_with_index do |f,i|

data/share/rbbt_commands/tsv/unzip

@@ -0,0 +1,25 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+options = SOPT.get("-tch--tokyocabinet:-tcb--tokyocabinet_bd")
+
+file = ARGV.shift
+
+file = STDIN if file == '-'
+
+case
+when options[:tokyocabinet]
+  tsv = Persist.open_tokyocabinet(file, false)
+when options[:tokyocabinet_bd]
+  tsv = Persist.open_tokyocabinet(file, false, nil, TokyoCabinet::BDB)
+else
+  if String === file
+    file = file.dup
+    Path.setup(File.expand_path(file))
+  end
+  tsv = TSV.open(file)
+end
+
+puts tsv.unzip.to_s

data/share/rbbt_commands/tsv/values

@@ -0,0 +1,25 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+options = SOPT.get("-tch--tokyocabinet:-tcb--tokyocabinet_bd")
+
+file = ARGV.shift
+
+file = STDIN if file == '-'
+
+case
+when options[:tokyocabinet]
+  tsv = Persist.open_tokyocabinet(file, false)
+when options[:tokyocabinet_bd]
+  tsv = Persist.open_tokyocabinet(file, false, nil, TokyoCabinet::BDB)
+else
+  if String === file
+    file = file.dup
+    Path.setup(File.expand_path(file))
+  end
+  tsv = TSV.open(file)
+end
+
+tsv.each{|k,v| puts (Array === v ? v.flatten*"\t" : v.to_s ) }

data/share/rbbt_commands/workflow/task

@@ -112,10 +112,11 @@ options = SOPT.get <<EOF
 -cl--clean Clean the last step of the job so that it gets recomputed:
 -rcl--recursive_clean Clean the last step and its dependencies to recompute the job completely:
 -jn--jobname* Job name to use. The name 'Default' is used by default:
--pn--printname Print the name of the job and exit without starting it:
--jf--job_file* Output one of the job produced files:
 -wd--workdir* Change the working directory of the workflow:
 -O--output* Save job result into file:
+-pn--printname Print the name of the job and exit without starting it:
+-jf--job_file* Output one of the job produced files:
+--info Show the job info:
 --provenance Report the jobs provenance:
 --fork Run job asyncronously:
 EOF
@@ -193,8 +194,14 @@ if recursive_clean
   job = workflow.job(task.name, name, job_options)
 end
 
+require 'pp'
+
 # run
 begin
+  if options[:info]
+    pp job.info
+    exit 0
+  end
   if do_exec
     res = job.exec
     case
@@ -225,7 +232,6 @@ begin
 
 
   if options.delete(:provenance)
-    require 'pp'
     pp job.provenance
     exit 0
   end

data/test/rbbt/util/test_open.rb

@@ -1,6 +1,7 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'rbbt/util/open'
 require 'rbbt/util/tmpfile'
+require 'rbbt/persist'
 require 'test/unit'
 require 'iconv'
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.1
+  version: 5.6.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-13 00:00:00.000000000 Z
+date: 2014-02-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -231,6 +231,8 @@ files:
 - share/rbbt_commands/tsv/get
 - share/rbbt_commands/tsv/info
 - share/rbbt_commands/tsv/json
+- share/rbbt_commands/tsv/unzip
+- share/rbbt_commands/tsv/values
 - share/rbbt_commands/workflow/cmd
 - share/rbbt_commands/workflow/install
 - share/rbbt_commands/workflow/monitor