macroape 4.0.0 → 4.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3037e164fd1b1c23bf40a9fca1d1da39737934a5
-  data.tar.gz: 4d4482d00ce0c76cbb47fe9d9eff53b48c1d2741
+  metadata.gz: 4499602694103f438e53430766a1b5bad85baf61
+  data.tar.gz: e95adc086488900be4e0f0654da3543a8ea6a8c2
 SHA512:
-  metadata.gz: cc4176fe2b1d2f7b5bf4835b3612d316797f378dbf036bf0bba3135effe1cf9cbba1037ef87c7cffc24d0d2ef8d2ebf16fe5d585780445a1492fa795df44cb48
-  data.tar.gz: d86983eeb148235e1470dbfa7f674cf0e395129bd1836e34256b42bba06525f0881961cd8c6ca0e5e09df520786a8735e1ec2e10e76c4e59b8cfddb38b151685
+  metadata.gz: 42fa7ba9a07625432176831623549395695aa936f19efcfd62e9282f1dc6bb5b93359103b7e84de6d3fcda4686dc5f8f1264756a050e0b1f2fb433c4b96809bb
+  data.tar.gz: d4e94f5384e9e1cf4d34d777349b2d4e64e780f7b8ad9a5c71228c4b83b0b791165499c7bdc8c6c84a0a8d384bd617e9c312e68cb27e32713cd0be79a34cf879

data/lib/macroape/cli/align_motifs.rb

@@ -18,6 +18,8 @@ module Macroape
           Usage:
             #{run_tool_cmd} [options] <leader pm> <rest pm files>...
               or
+            ls rest_pms/*.pm | #{run_tool_cmd} [options]
+              or
             ls rest_pms/*.pm | #{run_tool_cmd} [options] <leader pm>
 
           Options:
@@ -28,8 +30,8 @@ module Macroape
             [-b <background probabilities] ACGT - 4 numbers, comma-delimited(spaces not allowed), sum should be equal to 1, like 0.25,0.24,0.26,0.25
         EOS
 
-        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+        if (argv.empty? && $stdin.tty?) || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
+          $stderr.puts doc
           exit
         end
 
@@ -65,17 +67,20 @@ module Macroape
           end
         end
 
-        leader_pwm_file = argv.shift
-        rest_pwms_file = argv
-        rest_pwms_file += $stdin.read.shellsplit  unless $stdin.tty?
-        rest_pwms_file.reject!{|filename| File.expand_path(filename) == File.expand_path(leader_pwm_file)}
+        pwm_files = argv
+        pwm_files += $stdin.read.shellsplit  unless $stdin.tty?
+        leader_pwm_file = pwm_files.first
+        rest_pwm_files = pwm_files[1..-1]
+        rest_pwm_files.reject!{|filename| File.expand_path(filename) == File.expand_path(leader_pwm_file)}
+
+        raise 'Specify leader file'  unless leader_pwm_file
 
         shifts = []
         shifts << [leader_pwm_file, 0, :direct]
         pwm_first = data_model.new(File.read(leader_pwm_file)).to_pwm
         pwm_first.set_parameters(background: leader_background, max_hash_size: max_hash_size).discrete!(discretization)
 
-        rest_pwms_file.each do |motif_name|
+        rest_pwm_files.each do |motif_name|
           pwm_second = data_model.new(File.read(motif_name)).to_pwm
           pwm_second.set_parameters(background: rest_motifs_background, max_hash_size: max_hash_size).discrete!(discretization)
           cmp = Macroape::PWMCompare.new(pwm_first, pwm_second).set_parameters(max_pair_hash_size: max_pair_hash_size)
@@ -87,7 +92,7 @@ module Macroape
           puts "#{motif_name}\t#{shift}\t#{orientation}"
         end
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end

data/lib/macroape/cli/eval_alignment.rb

@@ -24,7 +24,7 @@ module Macroape
         EOS
 
         if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+          $stderr.puts doc
           exit
         end
 
@@ -148,7 +148,7 @@ module Macroape
         puts Helper.similarity_info_string(info)
 
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end

data/lib/macroape/cli/eval_similarity.rb

@@ -23,7 +23,7 @@ module Macroape
         EOS
 
         if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+          $stderr.puts doc
           exit
         end
 
@@ -129,7 +129,7 @@ module Macroape
         puts Helper.similarity_info_string(info)
 
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end

data/lib/macroape/cli/find_pvalue.rb

@@ -20,7 +20,7 @@ module Macroape
         EOS
 
         if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+          $stderr.puts doc
           exit
         end
 
@@ -79,7 +79,7 @@ module Macroape
                                             {discretization: discretization,
                                             background: background} )
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end

data/lib/macroape/cli/find_threshold.rb

@@ -21,7 +21,7 @@ module Macroape
         EOS
 
         if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+          $stderr.puts doc
           exit
         end
 
@@ -88,7 +88,7 @@ module Macroape
                                           background: background,
                                           pvalue_boundary: pvalue_boundary} )
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end

data/lib/macroape/cli/preprocess_collection.rb

@@ -26,7 +26,7 @@ module Macroape
         EOS
 
         if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+          $stderr.puts doc
           exit
         end
 
@@ -99,7 +99,7 @@ module Macroape
         pwms = motifs.map(&:to_pwm)
 
         pwms.each_with_index do |pwm,index|
-          STDERR.puts "Motif #{pwm.name}, length: #{pwm.length} (#{index+1} of #{pwms.size}, #{index*100/pwms.size}% complete)"  unless silent
+          $stderr.puts "Motif #{pwm.name}, length: #{pwm.length} (#{index+1} of #{pwms.size}, #{index*100/pwms.size}% complete)"  unless silent
 
           # When support of onefile collections is introduced - then here should be check if name exists.
           # Otherwise it should skip motif and tell you about this
@@ -140,7 +140,7 @@ module Macroape
           end
           collection.add_pm(pwm, info)  unless skip_motif
         end
-        STDERR.puts "100% complete. Saving results"  unless silent
+        $stderr.puts "100% complete. Saving results"  unless silent
         File.open(output_file, 'w') do |f|
           f.puts(collection.to_yaml)
         end
@@ -152,7 +152,7 @@ module Macroape
           infos.background_parameter('B', 'background', background)
         }.result
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end

data/lib/macroape/cli/scan_collection.rb

@@ -29,7 +29,7 @@ module Macroape
         EOS
 
         if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
-          STDERR.puts doc
+          $stderr.puts doc
           exit
         end
 
@@ -123,7 +123,7 @@ module Macroape
 
         collection.each_with_index do |motif, index|
           name = motif.name
-          STDERR.puts "Testing motif #{name} (#{index+1} of #{collection.size}, #{index*100/collection.size}% complete)"  unless silent
+          $stderr.puts "Testing motif #{name} (#{index+1} of #{collection.size}, #{index*100/collection.size}% complete)"  unless silent
           motif.set_parameters(background: collection_background, max_hash_size: max_hash_size)
           if motif.rough[pvalue]
             collection_pwm_rough = motif.pwm.discrete(rough_discretization)
@@ -141,7 +141,7 @@ module Macroape
           similarities[name] = info
         end
 
-        STDERR.puts "100% complete"  unless silent
+        $stderr.puts "100% complete"  unless silent
 
         similarities_to_output = similarities.sort_by{|name, info| info[:similarity] }.reverse.select{|name,info| info[:similarity] >= cutoff }.map{|name,info|info}
         puts Helper.scan_collection_infos_string( similarities_to_output,
@@ -155,7 +155,7 @@ module Macroape
                                                   collection_background: collection_background,
                                                   query_background: query_background} )
       rescue => err
-        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
+        $stderr.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse --help option for help\n\n#{doc}"
       end
 
     end

data/lib/macroape/version.rb

@@ -1,4 +1,4 @@
 module Macroape
-  VERSION = "4.0.0"
+  VERSION = "4.0.1"
   STANDALONE = false
 end

data/test/align_motifs_test.rb

@@ -21,12 +21,18 @@ class TestAlignmotifs < Test::Unit::TestCase
                   %w[SP1_f1_revcomp.pcm -1 revcomp]],
       Helpers.align_motifs_output('--pcm KLF4_f2.pcm  KLF3_f1.pcm  SP1_f1_revcomp.pcm')
   end
-  def test_names_from_stdin
+  def test_names_from_stdin_leader_specified
     assert_equal [%w[KLF4_f2.pwm 0 direct],
                   %w[KLF3_f1.pwm -4 direct],
                   %w[SP1_f1_revcomp.pwm -1 revcomp]],
       Helpers.provide_stdin('KLF3_f1.pwm  SP1_f1_revcomp.pwm'){ Helpers.align_motifs_output('KLF4_f2.pwm') }
   end
+  def test_names_from_stdin_leader_not_specified
+    assert_equal [%w[KLF4_f2.pwm 0 direct],
+                  %w[KLF3_f1.pwm -4 direct],
+                  %w[SP1_f1_revcomp.pwm -1 revcomp]],
+      Helpers.provide_stdin('KLF4_f2.pwm  KLF3_f1.pwm  SP1_f1_revcomp.pwm'){ Helpers.align_motifs_output('') }
+  end
   def test_names_from_stdin_duplicate_leader
     assert_equal [%w[KLF4_f2.pwm 0 direct],
                   %w[KLF3_f1.pwm -4 direct],

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: macroape
 version: !ruby/object:Gem::Version
-  version: 4.0.0
+  version: 4.0.1
 platform: ruby
 authors:
 - Ilya Vorontsov
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-29 00:00:00.000000000 Z
+date: 2013-05-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bioinform