From: martinahansen Date: Tue, 29 Mar 2011 10:14:12 +0000 (+0000) Subject: fixed Rakefile X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=d69b157181bcfdea35734d49402c81b3747aed60;p=biopieces.git fixed Rakefile git-svn-id: http://biopieces.googlecode.com/svn/trunk@1308 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/code_ruby/Maasha/Rakefile b/code_ruby/Maasha/Rakefile index 97902c2..8f5b25f 100644 --- a/code_ruby/Maasha/Rakefile +++ b/code_ruby/Maasha/Rakefile @@ -1,7 +1,5 @@ require 'rake/testtask' -test_dir = File.expand_path('test') - Rake::TestTask.new("test") do |t| t.pattern = "test/test_*.rb" t.warning = true diff --git a/code_ruby/Maasha/lib/biopieces.rb b/code_ruby/Maasha/lib/biopieces.rb index 2f98fe9..37edd66 100644 --- a/code_ruby/Maasha/lib/biopieces.rb +++ b/code_ruby/Maasha/lib/biopieces.rb @@ -134,7 +134,7 @@ class Casts < Array ubiquitous check long_to_sym - self.push *@cast_list + self.push(*@cast_list) end private diff --git a/code_ruby/Maasha/lib/bitarray.rb b/code_ruby/Maasha/lib/bitarray.rb index c6a1ebb..8113621 100644 --- a/code_ruby/Maasha/lib/bitarray.rb +++ b/code_ruby/Maasha/lib/bitarray.rb @@ -130,7 +130,7 @@ class BitArray string end - alias :to_s :to_string + alias :to_string :to_s private diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb index 18a0958..e68888f 100644 --- a/code_ruby/Maasha/lib/seq.rb +++ b/code_ruby/Maasha/lib/seq.rb @@ -151,7 +151,7 @@ class Seq seq = self.seq unless wrap.nil? - seq.gsub! /(.{#{wrap}})/ do |match| + seq.gsub!(/(.{#{wrap}})/) do |match| match << "\n" end @@ -384,7 +384,7 @@ class Seq # Method to convert the quality scores from a specified base # to another base. def convert_phred2illumina! - self.qual.gsub! /./ do |score| + self.qual.gsub!(/./) do |score| score_phred = score.ord - SCORE_PHRED raise SeqError, "Bad Phred score: #{score} (#{score_phred})" unless (0 .. 40).include? score_phred score_illumina = score_phred + SCORE_ILLUMINA @@ -395,7 +395,7 @@ class Seq # Method to convert the quality scores from Solexa odd/ratio to # Illumina format. def convert_solexa2illumina! - self.qual.gsub! /./ do |score| + self.qual.gsub!(/./) do |score| score = solexa_char2illumina_char(score) end end diff --git a/code_ruby/Maasha/test/test_biopieces.rb b/code_ruby/Maasha/test/test_biopieces.rb index ec781d1..be702b5 100755 --- a/code_ruby/Maasha/test/test_biopieces.rb +++ b/code_ruby/Maasha/test/test_biopieces.rb @@ -26,7 +26,6 @@ $:.unshift File.join(File.dirname(__FILE__),'..','lib') # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< require 'test/unit' -require 'mocha' require 'biopieces' require 'pp' @@ -305,10 +304,11 @@ class BiopiecesTest < Test::Unit::TestCase # TODO replace the absolute part below the file location with File.dirname(__FILE__) def test_Biopieces_parse_with_glob_argument_expands_correctly + flunk("This test is weird") argv = ["--foo", "/Users/maasha/unit_test/foo*,/Users/maasha/unit_test/my_dir/*.fna", "-I", DUMMY_FILE] casts = [{:long=>"foo", :short=>"f", :type=>"files!", :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}] options = @bp.parse(argv, casts, SCRIPT_PATH) - assert_equal(options[:foo], ["/Users/maasha/unit_test/foo.fna", "/Users/maasha/unit_test/my_dir/bar.fna"]) + assert_equal(["/Users/maasha/unit_test/foo.fna", "/Users/maasha/unit_test/my_dir/bar.fna"], options[:foo]) end def test_Biopieces_parse_with_dir_cast_and_dir_dont_exists_raises diff --git a/code_ruby/Maasha/test/test_genbank.rb b/code_ruby/Maasha/test/test_genbank.rb index b6ceb63..3c46386 100755 --- a/code_ruby/Maasha/test/test_genbank.rb +++ b/code_ruby/Maasha/test/test_genbank.rb @@ -33,33 +33,32 @@ require 'pp' class TestGenbank < Test::Unit::TestCase def setup - seq = Seq.new(nil, "tcatgatcaagatctaacagcagaagtacacttctattta", "dna") - @loc = Locator.new("", seq) + @seq = Seq.new(nil, "tcatgatcaagatctaacagcagaagtacacttctattta", "dna") end def test_Locator_with_single_position_returns_correctly - @loc.locator = "10" - assert_equal("a", @loc.subseq.seq) + loc = Locator.new("10", @seq) + assert_equal("a", loc.subseq.seq) end def test_Locator_with_single_interval_returns_correctly - @loc.locator = "5..10" - assert_equal("gatca", @loc.subseq.seq) + loc = Locator.new("5..10", @seq) + assert_equal("gatca", loc.subseq.seq) end def test_Locator_with_multiple_intervals_return_correctly - @loc.locator = "5..10,15..20" - assert_equal("gatcataaca", @loc.subseq.seq) + loc = Locator.new("5..10,15..20", @seq) + assert_equal("gatcataaca", loc.subseq.seq) end def test_Locator_with_join_multiple_intervals_return_correctly - @loc.locator = "join(5..10,15..20)" - assert_equal("gatcataaca", @loc.subseq.seq) + loc = Locator.new("join(5..10,15..20)", @seq) + assert_equal("gatcataaca", loc.subseq.seq) end def test_Locator_with_complement_and_single_interval_return_correctly - @loc.locator = "complement(5..10)" - assert_equal("tgatc", @loc.subseq.seq) + loc = Locator.new("complement(5..10)", @seq) + assert_equal("tgatc", loc.subseq.seq) end end diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/Maasha/test/test_seq.rb index 5caed92..d785c8c 100755 --- a/code_ruby/Maasha/test/test_seq.rb +++ b/code_ruby/Maasha/test/test_seq.rb @@ -266,7 +266,7 @@ class TestSeq < Test::Unit::TestCase assert_equal("CG", @entry.seq) end - def test_Seq_subseq_bang_returns_correct_qual + def test_Seq_subseq_bang_with_pos_and_len_returns_correct_qual @entry.seq = "ATCG" @entry.qual = "abcd" @entry.subseq!(0, 2) @@ -277,7 +277,7 @@ class TestSeq < Test::Unit::TestCase assert_equal("cd", @entry.qual) end - def test_Seq_subseq_bang_returns_correct_qual + def test_Seq_subseq_bang_with_pos_returns_correct_qual @entry.seq = "ATCG" @entry.qual = "abcd" @entry.subseq!(0) @@ -333,12 +333,14 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_adaptor_locate_right_with_bad_hamming_dist_raises + flunk("adaptor location needs updating") @entry.seq = "ATCG" assert_raise(SeqError) { @entry.adaptor_locate_right("ATCG", -1) } assert_raise(SeqError) { @entry.adaptor_locate_right("ATCG", 101) } end def test_Seq_adaptor_locate_right_with_ok_hamming_dist_dont_raise + flunk("adaptor location needs updating") @entry.seq = "ATCG" assert_nothing_raised { @entry.adaptor_locate_right("ATCG", 0) } assert_nothing_raised { @entry.adaptor_locate_right("ATCG", 50.5) } @@ -346,6 +348,7 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_adaptor_locate_right_returns_correctly + flunk("adaptor location needs updating") @entry.seq = "nnnnncgat" assert_equal(-1, @entry.adaptor_locate_right("X")) assert_equal(8, @entry.adaptor_locate_right("TX")) @@ -356,18 +359,21 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_adaptor_locate_right_with_hd_returns_correctly + flunk("adaptor location needs updating") @entry.seq = "nnnnncgat" assert_equal(5, @entry.adaptor_locate_right("XGAT", 25)) assert_equal(5, @entry.adaptor_locate_right("XXAT", 50)) end def test_Seq_adaptor_locate_left_with_bad_hamming_dist_raises + flunk("adaptor location needs updating") @entry.seq = "ATCG" assert_raise(SeqError) { @entry.adaptor_locate_left("ATCG", -1) } assert_raise(SeqError) { @entry.adaptor_locate_left("ATCG", 101) } end def test_Seq_adaptor_locate_left_with_ok_hamming_dist_dont_raise + flunk("adaptor location needs updating") @entry.seq = "ATCG" assert_nothing_raised { @entry.adaptor_locate_left("ATCG", 0) } assert_nothing_raised { @entry.adaptor_locate_left("ATCG", 50.5) } @@ -375,6 +381,7 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_adaptor_locate_left_returns_correctly + flunk("adaptor location needs updating") @entry.seq = "cgatnnnnn" assert_equal(-1, @entry.adaptor_locate_left("X")) assert_equal(0, @entry.adaptor_locate_left("XC")) @@ -385,24 +392,28 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_adaptor_locate_left_with_hd_returns_correctly + flunk("adaptor location needs updating") @entry.seq = "cgatnnnnn" assert_equal(3, @entry.adaptor_locate_left("XGAT", 25)) assert_equal(3, @entry.adaptor_locate_left("XXAT", 50)) end def test_Seq_adaptor_clip_right_returns_correct_sequence + flunk("adaptor location needs updating") @entry.seq = "nnnnncgat" @entry.adaptor_clip_right("cgat") assert_equal( "nnnnn", @entry.seq) end def test_Seq_adaptor_clip_right_with_hd_returns_correct_sequence + flunk("adaptor location needs updating") @entry.seq = "nnnnncgat" @entry.adaptor_clip_right("xgat", 25) assert_equal( "nnnnn", @entry.seq) end def test_Seq_adaptor_clip_right_returns_correct_qual + flunk("adaptor location needs updating") @entry.seq = "nnnnncgat" @entry.qual = "abcdefghi" @entry.adaptor_clip_right("cgat") @@ -410,6 +421,7 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_adaptor_clip_right_with_hd_returns_correct_qual + flunk("adaptor location needs updating") @entry.seq = "nnnnncgat" @entry.qual = "abcdefghi" @entry.adaptor_clip_right("xgat", 25) @@ -417,25 +429,29 @@ class TestSeq < Test::Unit::TestCase end def test_Seq_adaptor_clip_left_returns_correct_sequence + flunk("adaptor location needs updating") @entry.seq = "cgatnnnnn" @entry.adaptor_clip_left("cgat") assert_equal( "nnnnn", @entry.seq) end def test_Seq_adaptor_clip_left_with_hd_returns_correct_sequence + flunk("adaptor location needs updating") @entry.seq = "cgatnnnnn" @entry.adaptor_clip_left("cgax", 25) assert_equal( "nnnnn", @entry.seq) end def test_Seq_adaptor_clip_left_returns_correct_qual + flunk("adaptor location needs updating") @entry.seq = "cgatnnnnn" @entry.qual = "abcdefghi" @entry.adaptor_clip_left("cgat") assert_equal( "efghi", @entry.qual) end - def test_Seq_adaptor_clip_left_returns_correct_qual + def test_Seq_adaptor_clip_left_with_len_returns_correct_qual + flunk("adaptor location needs updating") @entry.seq = "cgatnnnnn" @entry.qual = "abcdefghi" @entry.adaptor_clip_left("cgax", 25)