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restandardise method name
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Ben J Woodcroft committed Apr 3, 2011
1 parent d733dc9 commit c798b7d
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Showing 2 changed files with 23 additions and 23 deletions.
8 changes: 4 additions & 4 deletions lib/bio/sequence/emboss_six_frame_nucleotide_sequences.rb
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Expand Up @@ -8,10 +8,10 @@ class NA
# sequence. The frame returned aligns with the frames that are generated by
# bioruby itself and the EMBOSS package program transeq.
#
# Bio::Sequence::NA.new('ATGATG').transeq_nucleotide_sequence(1) => Bio::Sequence::NA.new('ATGATG')
# Bio::Sequence::NA.new('ATGATG').transeq_nucleotide_sequence(2) => Bio::Sequence::NA.new('TGATG')
# Bio::Sequence::NA.new('ATGATG').transeq_nucleotide_sequence(4) => Bio::Sequence::NA.new('CATCAT')
def nucleotide_sequence_of_translation(frame)
# Bio::Sequence::NA.new('ATGATG').nucleotide_sequence_of_transeq_translation(1) => Bio::Sequence::NA.new('ATGATG')
# Bio::Sequence::NA.new('ATGATG').nucleotide_sequence_of_transeq_translation(2) => Bio::Sequence::NA.new('TGATG')
# Bio::Sequence::NA.new('ATGATG').nucleotide_sequence_of_transeq_translation(4) => Bio::Sequence::NA.new('CATCAT')
def nucleotide_sequence_of_transeq_translation(frame)
unless [-1,-2,-3,1,2,3,4,5,6].include?(frame) #error checking
raise Exception, "unexpected frame for translation: `#{frame.inspect}'"
end
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38 changes: 19 additions & 19 deletions test/test_bio-emboss_six_frame_nucleotide_sequences.rb
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Expand Up @@ -12,9 +12,9 @@ class TestBioEmbossSixFrameNucleotideSequences < Test::Unit::TestCase
# >9nt_3
# DDX
a = na.new('ATGATGATG')
assert_equal na.new('ATGATGATG').downcase, a.transeq_nucleotide_sequence(1)
assert_equal na.new('TGATGATG').downcase, a.transeq_nucleotide_sequence(2)
assert_equal na.new('GATGATG').downcase, a.transeq_nucleotide_sequence(3)
assert_equal na.new('ATGATGATG').downcase, a.nucleotide_sequence_of_transeq_translation(1)
assert_equal na.new('TGATGATG').downcase, a.nucleotide_sequence_of_transeq_translation(2)
assert_equal na.new('GATGATG').downcase, a.nucleotide_sequence_of_transeq_translation(3)
end

# >9nt_4
Expand All @@ -25,9 +25,9 @@ class TestBioEmbossSixFrameNucleotideSequences < Test::Unit::TestCase
# IIX
should "test length divisible by 3 backwards" do
a = na.new('ATGATGATG')
assert_equal na.new('CATCATCAT').downcase, a.transeq_nucleotide_sequence(4)
assert_equal na.new('TCATCAT').downcase, a.transeq_nucleotide_sequence(5)
assert_equal na.new('ATCATCAT').downcase, a.transeq_nucleotide_sequence(6)
assert_equal na.new('CATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(4)
assert_equal na.new('TCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(5)
assert_equal na.new('ATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(6)
end

should "test length divisible by 3 remainder 1 forwards" do
Expand All @@ -38,9 +38,9 @@ class TestBioEmbossSixFrameNucleotideSequences < Test::Unit::TestCase
# >10nt_3
# DDX
a = na.new('ATGATGATGA')
assert_equal na.new('ATGATGATGA').downcase, a.transeq_nucleotide_sequence(1)
assert_equal na.new('TGATGATGA').downcase, a.transeq_nucleotide_sequence(2)
assert_equal na.new('GATGATGA').downcase, a.transeq_nucleotide_sequence(3)
assert_equal na.new('ATGATGATGA').downcase, a.nucleotide_sequence_of_transeq_translation(1)
assert_equal na.new('TGATGATGA').downcase, a.nucleotide_sequence_of_transeq_translation(2)
assert_equal na.new('GATGATGA').downcase, a.nucleotide_sequence_of_transeq_translation(3)
end

# >10nt_4
Expand All @@ -51,9 +51,9 @@ class TestBioEmbossSixFrameNucleotideSequences < Test::Unit::TestCase
# IIX
should "test length divisible by 3 remainder 1 backwards" do
a = na.new('ATGATGATGA')
assert_equal na.new('CATCATCAT').downcase, a.transeq_nucleotide_sequence(4)
assert_equal na.new('TCATCATCAT').downcase, a.transeq_nucleotide_sequence(5)
assert_equal na.new('ATCATCAT').downcase, a.transeq_nucleotide_sequence(6)
assert_equal na.new('CATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(4)
assert_equal na.new('TCATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(5)
assert_equal na.new('ATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(6)
end

should "test length divisible by 3 remainder 2 forwards" do
Expand All @@ -64,9 +64,9 @@ class TestBioEmbossSixFrameNucleotideSequences < Test::Unit::TestCase
# >11nt_3
# DDD
a = na.new('ATGATGATGAT')
assert_equal na.new('ATGATGATGAT').downcase, a.transeq_nucleotide_sequence(1)
assert_equal na.new('TGATGATGAT').downcase, a.transeq_nucleotide_sequence(2)
assert_equal na.new('GATGATGAT').downcase, a.transeq_nucleotide_sequence(3)
assert_equal na.new('ATGATGATGAT').downcase, a.nucleotide_sequence_of_transeq_translation(1)
assert_equal na.new('TGATGATGAT').downcase, a.nucleotide_sequence_of_transeq_translation(2)
assert_equal na.new('GATGATGAT').downcase, a.nucleotide_sequence_of_transeq_translation(3)
end

# >11nt_4
Expand All @@ -77,9 +77,9 @@ class TestBioEmbossSixFrameNucleotideSequences < Test::Unit::TestCase
# IIIX
should "test length divisible by 3 remainder 2 backwards" do
a = na.new('ATGATGATGAT')
assert_equal na.new('CATCATCAT').downcase, a.transeq_nucleotide_sequence(4)
assert_equal na.new('TCATCATCAT').downcase, a.transeq_nucleotide_sequence(5)
assert_equal na.new('ATCATCATCAT').downcase, a.transeq_nucleotide_sequence(6)
assert_equal na.new('CATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(4)
assert_equal na.new('TCATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(5)
assert_equal na.new('ATCATCATCAT').downcase, a.nucleotide_sequence_of_transeq_translation(6)
end

# in test/data, 3 nucleotide sequences have been translated by transeq into
Expand All @@ -104,7 +104,7 @@ class TestBioEmbossSixFrameNucleotideSequences < Test::Unit::TestCase
if matches = pname.match(/(.*)_([1-6])/)
pseq.gsub!(/X/,'') #remove hanging Xs cos bioruby and transeq do that
# differently
assert_equal pseq, na.new(nucleotide_sequences[matches[1]]).transeq_nucleotide_sequence(matches[2].to_i).translate
assert_equal pseq, na.new(nucleotide_sequences[matches[1]]).nucleotide_sequence_of_transeq_translation(matches[2].to_i).translate
else
raise
end
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