macroape 3.3.6 → 3.3.7

data/test/data/short_motif.pat

@@ -0,0 +1,7 @@
+short_motif_name
+0.30861857265872605 -2.254321000121579 0.13505703522674192 0.3285194224375633 
+-1.227018967707036 -4.814127713368663 1.3059890687390967 -4.908681463544344 
+-2.443469374521196 -4.648238485031404 1.3588686548279805 -4.441801801188402 
+-2.7177827948276123 -3.8073538975356565 1.356272809724262 -3.504104725510225 
+-0.5563232977367343 0.5340697765121405 -3.61417723090579 0.5270259776377405 
+-1.8687622060887386 -4.381483976582316 1.337932245336098 -3.815629658877517 

data/test/data/test_collection.yaml

@@ -1,6 +1,17 @@
---- &18156900 !ruby/object:Bioinform::Collection
+--- &19230696 !ruby/object:Bioinform::Collection
 collection:
 - - !ruby/object:Bioinform::PWM
+    parameters: !ruby/object:OpenStruct
+      table:
+        :name: GABPA_f1
+        :tags:
+        - *19230696
+        :background: &19231104
+        - 1
+        - 1
+        - 1
+        - 1
+      modifiable: true
     matrix:
     - - -0.1106670158341858
       - 0.013801606113892391
@@ -54,14 +65,6 @@ collection:
       - -0.01814819455289191
       - 0.4381106695354074
       - -1.0304105539540915
-    name: GABPA_f1
-    tags:
-    - *18156900
-    background: &18124572
-    - 1
-    - 1
-    - 1
-    - 1
     max_hash_size: 1000000
   - !ruby/object:OpenStruct
     table:
@@ -74,6 +77,13 @@ collection:
         0.0001: 7.609999999999999
         0.0005: 4.51
 - - !ruby/object:Bioinform::PWM
+    parameters: !ruby/object:OpenStruct
+      table:
+        :name: KLF4_f2
+        :tags:
+        - *19230696
+        :background: *19231104
+      modifiable: true
     matrix:
     - - 0.30861857265872605
       - -2.254321000121579
@@ -115,10 +125,6 @@ collection:
       - 0.8982415633049462
       - -0.8080773665408135
       - -0.18161647647456935
-    name: KLF4_f2
-    tags:
-    - *18156900
-    background: *18124572
     max_hash_size: 1000000
   - !ruby/object:OpenStruct
     table:
@@ -131,6 +137,13 @@ collection:
         0.0001: 7.909999999999999
         0.0005: 5.8100000000000005
 - - !ruby/object:Bioinform::PWM
+    parameters: !ruby/object:OpenStruct
+      table:
+        :name: SP1_f1
+        :tags:
+        - *19230696
+        :background: *19231104
+      modifiable: true
     matrix:
     - - -0.24435707885585292
       - -0.674823404693731
@@ -176,10 +189,6 @@ collection:
       - 0.7641033353626657
       - -0.2862677570028208
       - -0.68254820978656
-    name: SP1_f1
-    tags:
-    - *18156900
-    background: *18124572
     max_hash_size: 1000000
   - !ruby/object:OpenStruct
     table:
@@ -195,7 +204,7 @@ parameters: !ruby/object:OpenStruct
   table:
     :rough_discretization: 1
     :precise_discretization: 10
-    :background: *18124572
+    :background: *19231104
     :pvalues:
     - 0.0005
     - 0.0001

data/test/eval_alignment_test.rb

@@ -1,4 +1,4 @@
-require 'test_helper'
+require_relative 'test_helper'
 
 class TestEvalAlignment < Test::Unit::TestCase
   def test_process_pcm_files

data/test/eval_similarity_test.rb

@@ -1,4 +1,4 @@
-require 'test_helper'
+require_relative 'test_helper'
 
 class TestEvalSimilarity < Test::Unit::TestCase
   def test_process_pair_of_pcms

data/test/find_pvalue_test.rb

@@ -1,4 +1,4 @@
-require 'test_helper'
+require_relative 'test_helper'
 
 class FindPvalueTest < Test::Unit::TestCase
   def test_process_pcm

data/test/find_threshold_test.rb

@@ -1,4 +1,4 @@
-require 'test_helper'
+require_relative 'test_helper'
 
 class FindThresholdTest < Test::Unit::TestCase
   def test_process_several_pvalues

data/test/preprocess_collection_test.rb

@@ -1,48 +1,70 @@
-require 'test_helper'
+require_relative 'test_helper'
 require 'yaml'
-require 'macroape'
+
+# Don't use YAML.load_file() instead of YAML.load(File.read()) because in ruby before v1.93 p194
+# it doesn't immediately release file descriptor (if I understood error right way) so File.delete fails
 
 class TestPreprocessCollection < Test::Unit::TestCase
-  def test_multipvalue_preproceessing
-    Helpers.run_preprocess_collection('test/data/test_collection -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
-    # Don't use YAML.load_file() instead of YAML.load(File.read()) because in ruby before v1.93 p194 
-    # it doesn't immediately release file descriptor (if I understood error right way) so File.delete fails
-    assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
-    File.delete 'test/data/test_collection.yaml.tmp'
-  end
-  
-  def test_preproceessing_collection_from_a_single_file
-    Helpers.run_preprocess_collection('test/data/test_collection_single_file.txt -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
-    assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
-    File.delete 'test/data/test_collection.yaml.tmp'
-  end
-  
-  def test_preproceessing_collection_from_stdin
-    Helpers.provide_stdin(File.read('test/data/test_collection_single_file.txt')){
-      Helpers.run_preprocess_collection('.stdin -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+  def setup
+    @start_dir = Dir.pwd
+    Dir.chdir File.join(File.dirname(__FILE__), 'data')
+  end
+  def teardown
+    File.delete('test_collection.yaml.tmp')  if File.exist? 'test_collection.yaml.tmp'
+    Dir.chdir(@start_dir)
+  end
+
+  def test_multipvalue_preprocessing
+    Helpers.run_preprocess_collection('test_collection -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
+  end
+
+  def test_preprocessing_collection_from_a_single_file
+    Helpers.run_preprocess_collection('test_collection_single_file.txt -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
+  end
+
+  def test_preprocessing_collection_from_stdin
+    Helpers.provide_stdin('test_collection/GABPA_f1.pat  test_collection/KLF4_f2.pat  test_collection/SP1_f1.pat'){
+      Helpers.run_preprocess_collection('.stdin -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
     }
-    assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
-    File.delete 'test/data/test_collection.yaml.tmp'
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
 
-  def test_preproceessing_folder_pcm
-    Helpers.run_preprocess_collection('test/data/test_collection_pcm -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
-    assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
-    File.delete 'test/data/test_collection.yaml.tmp'
+  def test_preprocessing_folder_pcm
+    Helpers.run_preprocess_collection('test_collection_pcm -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
-  
-  def test_preproceessing_collection_from_a_single_file_pcm
-    Helpers.run_preprocess_collection('test/data/test_collection_single_file_pcm.txt -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
-    assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
-    File.delete 'test/data/test_collection.yaml.tmp'
+
+  def test_preprocessing_collection_from_a_single_file_pcm
+    Helpers.run_preprocess_collection('test_collection_single_file_pcm.txt -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
+  end
+
+  def test_preprocessing_collection_from_a_collection
+    Helpers.run_preprocess_collection('collection_without_thresholds.yaml -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
+  end
+  def test_preprocessing_collection_from_a_pcm_collection
+    Helpers.run_preprocess_collection('collection_pcm_without_thresholds.yaml -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
   end
-  
-  def test_preproceessing_collection_from_stdin_pcm
-    Helpers.provide_stdin(File.read('test/data/test_collection_single_file_pcm.txt')){
-      Helpers.run_preprocess_collection('.stdin -o test/data/test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
+
+  def test_preprocessing_collection_from_stdin_pcm
+    Helpers.provide_stdin('test_collection_pcm/GABPA_f1.pcm  test_collection_pcm/KLF4_f2.pcm  test_collection_pcm/SP1_f1.pcm'){
+      Helpers.run_preprocess_collection('.stdin -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent --pcm')
     }
-    assert_equal YAML.load(File.read('test/data/test_collection.yaml')), YAML.load(File.read('test/data/test_collection.yaml.tmp'))
-    File.delete 'test/data/test_collection.yaml.tmp'
+    assert_equal YAML.load(File.read('test_collection.yaml')), YAML.load(File.read('test_collection.yaml.tmp'))
+  end
+
+  def test_with_name_specified
+    Helpers.run_preprocess_collection('test_collection -n my_collection -p 0.0005 0.0001 0.00005 --silent')
+    assert_equal YAML.load(File.read('test_collection.yaml')).set_parameters(name:'my_collection'), YAML.load(File.read('my_collection.yaml'))
+    File.delete('my_collection.yaml')
   end
 
-end
+  def test_with_name_and_output_specified
+    Helpers.run_preprocess_collection('test_collection -n my_collection -o test_collection.yaml.tmp -p 0.0005 0.0001 0.00005 --silent')
+    assert_equal YAML.load(File.read('test_collection.yaml')).set_parameters(name:'my_collection'), YAML.load(File.read('test_collection.yaml.tmp'))
+  end
+end

data/test/scan_collection_test.rb

@@ -1,4 +1,4 @@
-require 'test_helper'
+require_relative 'test_helper'
 
 class TestScanCollection < Test::Unit::TestCase
   def test_scan_pcm
@@ -24,4 +24,13 @@ class TestScanCollection < Test::Unit::TestCase
                   Helpers.scan_collection_output('.stdin test/data/test_collection.yaml --silent')
                 }
   end
+
+  def test_scan_medium_length_motif
+    assert_match /Query motif medium_motif_name gives 0 recognized words for a given P-value of 0\.0005 with the rough discretization level of 1. Forcing precise discretization level of 10/,
+                 Helpers.scan_collection_stderr('test/data/medium_motif.pat test/data/test_collection.yaml --precise --all --silent').gsub("\r\n", "\n")
+  end
+  def test_scan_short_length_motif
+    assert_match /Query motif short_motif_name gives 0 recognized words for a given P-value of 0\.0005 with the precise discretization level of 10\. It.s impossible to scan collection for this motif/,
+                 Helpers.scan_collection_stderr('test/data/short_motif.pat test/data/test_collection.yaml --precise --all --silent').gsub("\r\n", "\n")
+  end
 end

data/test/test_helper.rb

@@ -1,16 +1,17 @@
-$lib_folder = File.dirname(__FILE__) + '/../lib'
-$LOAD_PATH.unshift $lib_folder
+$bioinform_folder = File.expand_path(File.join(File.dirname(__FILE__), '..', '..', 'bioinform', 'lib'))
+$LOAD_PATH.unshift $bioinform_folder
+
 require 'test/unit'
 require 'stringio'
 require 'shellwords'
 
-require 'macroape/cli/find_threshold'
-require 'macroape/cli/find_pvalue'
-require 'macroape/cli/eval_similarity'
-require 'macroape/cli/eval_alignment'
-require 'macroape/cli/preprocess_collection'
-require 'macroape/cli/scan_collection'
-require 'macroape/cli/align_motifs'
+require_relative '../lib/macroape/cli/find_threshold'
+require_relative '../lib/macroape/cli/find_pvalue'
+require_relative '../lib/macroape/cli/eval_similarity'
+require_relative '../lib/macroape/cli/eval_alignment'
+require_relative '../lib/macroape/cli/preprocess_collection'
+require_relative '../lib/macroape/cli/scan_collection'
+require_relative '../lib/macroape/cli/align_motifs'
  
 module Helpers
   # from minitest
@@ -65,6 +66,9 @@ module Helpers
   def self.scan_collection_output(param_list)
     capture_output{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }
   end
+  def self.scan_collection_stderr(param_list)
+    capture_stderr{ Macroape::CLI::ScanCollection.main(param_list.shellsplit) }
+  end
   def self.run_preprocess_collection(param_list)
     Macroape::CLI::PreprocessCollection.main(param_list.shellsplit)
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: macroape
 version: !ruby/object:Gem::Version
-  version: 3.3.6
+  version: 3.3.7
   prerelease: 
 platform: ruby
 authors:
@@ -9,24 +9,24 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-11 00:00:00.000000000 Z
+date: 2012-09-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bioinform
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
-        version: 0.1.7
+        version: 0.1.8
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - '='
       - !ruby/object:Gem::Version
-        version: 0.1.7
+        version: 0.1.8
 description: Macroape is an abbreviation for MAtrix CompaRisOn by Approximate P-value
   Estimation. It's a bioinformatic tool for evaluating similarity measure and best
   alignment between a pair of Position Weight Matrices(PWM), finding thresholds by
@@ -51,6 +51,7 @@ files:
 - README.md
 - Rakefile.rb
 - TODO.txt
+- benchmark/benchmark_helper.rb
 - benchmark/similarity_benchmark.rb
 - bin/align_motifs
 - bin/eval_alignment
@@ -89,6 +90,10 @@ files:
 - test/data/SP1_f1.pcm
 - test/data/SP1_f1_revcomp.pat
 - test/data/SP1_f1_revcomp.pcm
+- test/data/collection_pcm_without_thresholds.yaml
+- test/data/collection_without_thresholds.yaml
+- test/data/medium_motif.pat
+- test/data/short_motif.pat
 - test/data/test_collection.yaml
 - test/data/test_collection/GABPA_f1.pat
 - test/data/test_collection/KLF4_f2.pat
@@ -145,6 +150,10 @@ test_files:
 - test/data/SP1_f1.pcm
 - test/data/SP1_f1_revcomp.pat
 - test/data/SP1_f1_revcomp.pcm
+- test/data/collection_pcm_without_thresholds.yaml
+- test/data/collection_without_thresholds.yaml
+- test/data/medium_motif.pat
+- test/data/short_motif.pat
 - test/data/test_collection.yaml
 - test/data/test_collection/GABPA_f1.pat
 - test/data/test_collection/KLF4_f2.pat