Fixed regression tests

Gemfile

@@ -8,6 +8,7 @@ gem "bio-logger", "> 0.8.0"
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
+  gem "rake", ">= 0.9.2"
   gem "shoulda", ">= 0"
   gem "bundler", "~> 1.0.0"
   gem "jeweler", "~> 1.5.2"

Gemfile.lock

@@ -32,6 +32,7 @@ DEPENDENCIES
   bundler (~> 1.0.0)
   jeweler (~> 1.5.2)
   log4r (> 1.1.6)
+  rake (>= 0.9.2)
   rcov
   rspec (>= 2.3.0)
   shoulda

Rakefile

@@ -30,13 +30,13 @@ Support for external FASTA files.
 end
 Jeweler::RubygemsDotOrgTasks.new
 
-# require 'rake/testtask'
-# Rake::TestTask.new(:test) do |test|
-#   test.libs << 'lib' << 'test'
-#   test.pattern = 'test/**/test_*.rb'
-#   test.verbose = true
-#   Kernel.system('rspec spec/*.rb')
-# end
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  Kernel.system('rspec spec/*.rb')
+end
 
 #require 'spec/rake/spectask'
 #Spec::Rake::SpecTask.new(:spec) do |t|

test/data/regression/test_ext_gff3.rtest

@@ -1,4 +1,3 @@
- INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash <>
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -42,8 +41,6 @@
  INFO bio-gff3: Adding CDS <cds1> <>
  INFO bio-gff3: Adding CDS <cds1> <>
  INFO bio-gff3: Adding CDS <cds2> <>
- INFO bio-gff3: Memory used After reading GFF RAM 10M, VMEM 14M
- INFO bio-gff3: Memory used After reading FASTA RAM 10M, VMEM 14M
  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:AL12345.2>
  WARN bio-gff3: No sequence information for <mRNA:trans-8>
  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:ABC123>
@@ -56,5 +53,4 @@ GAAGATTTGTAT
 TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTC
  INFO bio-gff3: find_component: Matched seqname <test01>
 >mrna01a Sequence:test01_1:400 (101:280)
-TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
- INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
+TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT

test/data/regression/test_gff3.rtest

@@ -1,4 +1,3 @@
- INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash <>
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -44,8 +43,6 @@
  INFO bio-gff3: Adding CDS <cds1> <>
  INFO bio-gff3: Adding CDS <cds1> <>
  INFO bio-gff3: Adding CDS <cds2> <>
- INFO bio-gff3: Memory used After reading GFF RAM 10M, VMEM 14M
- INFO bio-gff3: Memory used After reading FASTA RAM 10M, VMEM 14M
  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Transcript:trans-1>
  WARN bio-gff3: No sequence information for <Transcript:trans-1>
  INFO bio-gff3: find_component: Matched (long search) column 0 and location <Clone:AL12345.2>
@@ -60,5 +57,4 @@ GAAGATTTGTAT
 TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
  INFO bio-gff3: find_component: Matched seqname <test01>
 >cds2 Sequence:test01_1:400 (192:200)
-TTCATGGGC
- INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
+TTCATGGGC

test/data/regression/test_lrucache_ext_gff3.rtest

@@ -1,4 +1,3 @@
- INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -60,5 +59,4 @@ TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGA
 TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
  INFO bio-gff3: Cache calls After iterating  = 54 <>
  INFO bio-gff3: Cache hits After iterating   = 37 <>
- INFO bio-gff3: Cache misses After iterating = 17 <>
- INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
+ INFO bio-gff3: Cache misses After iterating = 17 <>

test/data/regression/test_lrucache_gff3.rtest

@@ -1,4 +1,3 @@
- INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (LruCache) <>
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -64,5 +63,4 @@ TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
 TTCATGGGC
  INFO bio-gff3: Cache calls After iterating  = 76 <>
  INFO bio-gff3: Cache hits After iterating   = 52 <>
- INFO bio-gff3: Cache misses After iterating = 24 <>
- INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
+ INFO bio-gff3: Cache misses After iterating = 24 <>

test/data/regression/test_nocache_ext_gff3.rtest

@@ -1,4 +1,3 @@
- INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -54,5 +53,4 @@ GAAGATTTGTAT
 TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTC
  INFO bio-gff3: find_component: Matched seqname <test01>
 >mrna01a Sequence:test01_1:400 (101:280)
-TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
- INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
+TATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACACCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGATAATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT

test/data/regression/test_nocache_gff3.rtest

@@ -1,4 +1,3 @@
- INFO bio-gff3: Memory used BaseLine RAM 10M, VMEM 14M
  INFO bio-gff3: ---- Digest DB and store data in mRNA Hash (NoCache) <>
  INFO bio-gff3: Added transcript with component ID Transcript:trans-1 <>
  INFO bio-gff3: Adding exon <Transcript:trans-1> <>
@@ -58,5 +57,4 @@ GAAGATTTGTAT
 TGGCGACTATCGGTCGAAGTTAAGACATTCATGGGC
  INFO bio-gff3: find_component: Matched seqname <test01>
 >cds2 Sequence:test01_1:400 (192:200)
-TTCATGGGC
- INFO bio-gff3: Memory used Done RAM 10M, VMEM 14M
+TTCATGGGC

test/regressiontest.rb

@@ -16,7 +16,7 @@ def RegressionTest.create b
 	#  in test/regression with +filename+. When +create+ is +true+ the file
 	#  will be created/overwritten. Otherwise it is tested against returning
 	#  whether it has equal or not. When a test fails both test file and new
-	#  file exist in the regrssion directory - so you can execute a diff.
+	#  file exist in the regression directory - so you can execute a diff.
 	#
 	#  Example:
 	#    RegressionTest.test `#{cfrubybin} --help`,'cfruby_helptext',$test_create

test/test_bio-gff3.rb

@@ -1,3 +1,7 @@
+# To recreate the regression files:
+#
+#   ruby -Itest test/test_bio-gff3.rb --create
+
 $: << '.'
 do_create = if ARGV[0] == '-c' or ARGV[0] == '--create'
               ARGV.shift
@@ -38,5 +42,7 @@ def this_method
 def single_run opts, name
   cmd = "#{BIN} --logger stdout #{opts}"
   # p cmd
-  RegressionTest.test `#{cmd}`,name,"#{DAT}/regression"
+  text = `#{cmd}`.split(/\n/).delete_if { | s | s =~ /Memory/ }.join("\n")
+
+  RegressionTest.test text,name,"#{DAT}/regression"
 end