From d69b157181bcfdea35734d49402c81b3747aed60 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 29 Mar 2011 10:14:12 +0000
Subject: [PATCH] fixed Rakefile
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1308 74ccb610-7750-0410-82ae-013aeee3265d
---
code_ruby/Maasha/Rakefile | 2 --
code_ruby/Maasha/lib/biopieces.rb | 2 +-
code_ruby/Maasha/lib/bitarray.rb | 2 +-
code_ruby/Maasha/lib/seq.rb | 6 +++---
code_ruby/Maasha/test/test_biopieces.rb | 4 ++--
code_ruby/Maasha/test/test_genbank.rb | 23 +++++++++++------------
code_ruby/Maasha/test/test_seq.rb | 22 +++++++++++++++++++---
7 files changed, 37 insertions(+), 24 deletions(-)
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)
--
2.39.5