rbbt-util 5.6.16 → 5.6.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 24c17a9f2dd891d8f1921bfc2b0b2df3c32bffa1
-  data.tar.gz: 2fec2a54a9f0f343efd5baf1a400ce884cb25fe2
+  metadata.gz: 9cd5bcdf21e90d1e62413b0c5f05c2fe92cd43cc
+  data.tar.gz: 0e5f75492b51edf63e76b32624d4a4dc39092a6e
 SHA512:
-  metadata.gz: 34feb9cc1d573271d7228a53683574eb036d4cb8f2067f5e9b316ba8b76243a45d0289788b47bbd497e58e3cd2fccbe1424444a3fbfea75312a6eb1cd56aa101
-  data.tar.gz: 2083c933319a679c82b25c00033423283d81f3bde77eff41d6162b3e8e6590c81762b31270ed390ce987e9654a356f6f9ba53d8212b61eebb70834862c93e2e2
+  metadata.gz: e2b471f1a98ae3ddfe81fd90675cc05a8d1cbbd24da1ce2d08955f476038681f87bebfd979d9798241c0cee531e28c1c18e4faa868a9d7f7c24dfc2831742bdf
+  data.tar.gz: 4db6e2a91bc5c1cf7370feba6494ffef580f80b4b0d67d7c27be5b8f83a2a9f429e73244001541a40252ca9c7a218eaae8c75a46e76352b20e0deb5f565d145f

data/lib/rbbt/util/misc.rb

@@ -1,7 +1,6 @@
 require 'lockfile'
 require 'net/smtp'
 require 'digest/md5'
-require 'narray'
 require 'cgi'
 require 'zlib'
 require 'rubygems/package'
@@ -506,80 +505,82 @@ end
     "val" =>   "V"
   }
 
-  def self.fast_align(reference, sequence)
-    init_gap = -1
-    gap = -2
-    diff = -2
-    same = 2
-
-    cols = sequence.length + 1
-    rows = reference.length + 1
-
-    a = NArray.int(cols, rows)
-
-    for spos in 0..cols-1 do a[spos, 0] = spos * init_gap end
-    for rpos in 0..rows-1 do a[0, rpos] = rpos * init_gap end
-
-    spos = 1
-    while spos < cols do
-      rpos = 1
-      while rpos < rows do
-        match = a[spos-1,rpos-1] + (sequence[spos-1] != reference[rpos-1] ? diff : same)
-        skip_sequence = a[spos-1,rpos] + gap
-        skip_reference = a[spos,rpos-1] + gap
-        a[spos,rpos] = [match, skip_sequence, skip_reference].max
-        rpos += 1
-      end
-      spos += 1
-    end
-
-    start = Misc.max(a[-1,0..rows-1])
-    start_pos = a[-1,0..rows-1].to_a.index start
-
-    ref = ''
-    seq = ''
-    rpos = start_pos
-    spos = cols - 1
-
-    while spos > 0 and rpos > 0
-      score = a[spos,rpos]
-      score_match = a[spos-1,rpos-1]
-      score_skip_reference = a[spos,rpos-1]
-      score_skip_sequence = a[spos-1,rpos]
+  #def self.fast_align(reference, sequence)
+  #
+  #require 'narray'
+  #  init_gap = -1
+  #  gap = -2
+  #  diff = -2
+  #  same = 2
+
+  #  cols = sequence.length + 1
+  #  rows = reference.length + 1
+
+  #  a = NArray.int(cols, rows)
+
+  #  for spos in 0..cols-1 do a[spos, 0] = spos * init_gap end
+  #  for rpos in 0..rows-1 do a[0, rpos] = rpos * init_gap end
+
+  #  spos = 1
+  #  while spos < cols do
+  #    rpos = 1
+  #    while rpos < rows do
+  #      match = a[spos-1,rpos-1] + (sequence[spos-1] != reference[rpos-1] ? diff : same)
+  #      skip_sequence = a[spos-1,rpos] + gap
+  #      skip_reference = a[spos,rpos-1] + gap
+  #      a[spos,rpos] = [match, skip_sequence, skip_reference].max
+  #      rpos += 1
+  #    end
+  #    spos += 1
+  #  end
 
-      case
-      when score == score_match + (sequence[spos-1] != reference[rpos-1] ? diff : same)
-        ref << reference[rpos-1]
-        seq << sequence[spos-1]
-        spos -= 1
-        rpos -= 1
-      when score == score_skip_reference + gap
-        ref << reference[rpos-1]
-        seq << '-'
-        rpos -= 1
-      when score == score_skip_sequence + gap
-        seq << sequence[spos-1]
-        ref << '-'
-        spos -= 1
-      else
-        raise "stop"
-      end
-    end
+  #  start = Misc.max(a[-1,0..rows-1])
+  #  start_pos = a[-1,0..rows-1].to_a.index start
+
+  #  ref = ''
+  #  seq = ''
+  #  rpos = start_pos
+  #  spos = cols - 1
+
+  #  while spos > 0 and rpos > 0
+  #    score = a[spos,rpos]
+  #    score_match = a[spos-1,rpos-1]
+  #    score_skip_reference = a[spos,rpos-1]
+  #    score_skip_sequence = a[spos-1,rpos]
+
+  #    case
+  #    when score == score_match + (sequence[spos-1] != reference[rpos-1] ? diff : same)
+  #      ref << reference[rpos-1]
+  #      seq << sequence[spos-1]
+  #      spos -= 1
+  #      rpos -= 1
+  #    when score == score_skip_reference + gap
+  #      ref << reference[rpos-1]
+  #      seq << '-'
+  #      rpos -= 1
+  #    when score == score_skip_sequence + gap
+  #      seq << sequence[spos-1]
+  #      ref << '-'
+  #      spos -= 1
+  #    else
+  #      raise "stop"
+  #    end
+  #  end
 
-    while (rpos > 0)
-      ref << reference[rpos-1]
-      seq = seq << '-'
-      rpos -= 1    
-    end
+  #  while (rpos > 0)
+  #    ref << reference[rpos-1]
+  #    seq = seq << '-'
+  #    rpos -= 1    
+  #  end
 
-    while (spos > 0)
-      seq << sequence[spos-1]
-      ref = ref + '-'
-      spos -= 1
-    end
-    
-    [ref.reverse + reference[start_pos..-1], seq.reverse + '-' * (rows - start_pos - 1)]
-  end
+  #  while (spos > 0)
+  #    seq << sequence[spos-1]
+  #    ref = ref + '-'
+  #    spos -= 1
+  #  end
+  #  
+  #  [ref.reverse + reference[start_pos..-1], seq.reverse + '-' * (rows - start_pos - 1)]
+  #end
 
   def self.IUPAC_to_base(iupac)
     IUPAC2BASE[iupac]
@@ -972,6 +973,8 @@ end
     rescue
       Log.warn("Error checking lockfile #{lockfile}: #{$!.message}. Removing. Content: #{begin Open.read(lockfile) rescue "Could not open file" end}")
       FileUtils.rm lockfile if File.exists?(lockfile)
+      lockfile = Lockfile.new(lock_path)
+      retry
     end
 
     begin

metadata

@@ -1,113 +1,99 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.16
+  version: 5.6.17
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
 date: 2014-03-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: progress-monitor
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
   prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: progress-monitor
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: lockfile
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
   prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: lockfile
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: spreadsheet
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
   prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: spreadsheet
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: highline
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
   prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: highline
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: narray
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
   prerelease: false
+  type: :runtime
+- !ruby/object:Gem::Dependency
+  name: term-ansicolor
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: term-ansicolor
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - '>='
       - !ruby/object:Gem::Version
         version: '0'
-  type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+  type: :runtime
 description: Utilities for handling tsv files, caches, etc
 email: miguel.vazquez@cnio.es
 executables:
@@ -288,33 +274,39 @@ homepage: http://github.com/mikisvaz/rbbt-util
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
+rubyforge_project:
 rubygems_version: 2.2.2
-signing_key: 
+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/test_association.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_entity.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/test_fix_width_table.rb
 - test/rbbt/resource/test_path.rb
 - test/rbbt/util/test_cmd.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/test_log.rb
@@ -327,17 +319,13 @@ test_files:
 - test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_tmpfile.rb
-- test/rbbt/test_association.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_entity.rb
-- test/rbbt/test_knowledge_base.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
 - test/rbbt/association/test_index.rb
 - test/rbbt/association/test_item.rb
-- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/workflow/test_step.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
@@ -352,5 +340,3 @@ test_files:
 - test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/test_fix_width_table.rb
-- test/test_helper.rb