@sam = Sam.new(StringIO.new(SAM_DATA))
end
-# def test_Sam_header_without_entry_returns_nil
-# @sam.io = StringIO.new
-# assert_nil(@sam.header)
-# end
-
- def test_Sam_header_parse_with_missing_version_number_raises
+ def test_Sam_new_with_missing_version_number_raises
assert_raise(SamError) { Sam.new(StringIO.new("@HD")) }
end
- def test_Sam_header_parse_with_bad_version_number_raises
+ def test_Sam_new_with_bad_version_number_raises
assert_raise(SamError) { Sam.new(StringIO.new("@HD\tXN:1.3")) }
end
- def test_Sam_header_parse_with_ok_version_number_returns_correctly
+ def test_Sam_new_with_ok_version_number_returns_correctly
sam = Sam.new(StringIO.new("@HD\tVN:1.3"))
assert_equal(1.3, sam.header[:HD][:VN])
end
- def test_Sam_header_parse_with_bad_sort_order_raises
+ def test_Sam_new_with_bad_sort_order_raises
assert_raise(SamError) { Sam.new(StringIO.new("@HD\tVN:1.3\tSO:fish")) }
end
- def test_Sam_header_parse_with_ok_sort_order_returns_correctly
+ def test_Sam_new_with_ok_sort_order_returns_correctly
%w{unknown unsorted queryname coordinate}.each do |order|
sam = Sam.new(StringIO.new("@HD\tVN:1.3\tSO:#{order}"))
assert_equal(order, sam.header[:HD][:SO])
end
end
- def test_Sam_header_parse_with_missing_sequence_name_raises
+ def test_Sam_new_with_missing_sequence_name_raises
assert_raise(SamError) { Sam.new(StringIO.new("@SQ")) }
end
- def test_Sam_header_parse_with_bad_sequence_name_raises
+ def test_Sam_new_with_bad_sequence_name_raises
assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:")) }
end
- def test_Sam_header_parse_with_ok_sequence_name_returns_correctly
+ def test_Sam_new_with_ok_sequence_name_returns_correctly
sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45"))
assert_equal({:LN=>45}, sam.header[:SQ][:SN][:ref])
end
- def test_Sam_header_parse_with_duplicate_sequence_name_raises
+ def test_Sam_new_with_duplicate_sequence_name_raises
assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:ref\n@SQ\tSN:ref")) }
end
- def test_Sam_header_parse_with_missing_sequence_length_raises
+ def test_Sam_new_with_missing_sequence_length_raises
assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:ref")) }
end
- def test_Sam_header_parse_with_bad_sequence_length_raises
+ def test_Sam_new_with_bad_sequence_length_raises
assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:scaffold17_1_MH0083\tLN:x")) }
end
- def test_Sam_header_parse_with_ok_sequence_length_returns_correctly
+ def test_Sam_new_with_ok_sequence_length_returns_correctly
sam = Sam.new(StringIO.new("@SQ\tSN:scaffold17_1_MH0083\tLN:995"))
assert_equal(995, sam.header[:SQ][:SN][:scaffold17_1_MH0083][:LN])
end
- def test_Sam_header_parse_with_full_SQ_dont_raise
+ def test_Sam_new_with_full_SQ_dont_raise
sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\tAS:ident\tM5:87e6b2aedf51b1f9c89becfab9267f41\tSP:E.coli\tUR:http://www.biopieces.org"))
assert_nothing_raised { sam.header }
end
- def test_Sam_header_parse_with_bad_read_group_identifier_raises
+ def test_Sam_new_with_bad_read_group_identifier_raises
assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:")) }
end
- def test_Sam_header_parse_with_missing_read_group_identifier_raises
+ def test_Sam_new_with_missing_read_group_identifier_raises
assert_raise(SamError) { Sam.new(StringIO.new("@RG")) }
end
- def test_Sam_header_parse_with_duplicate_read_group_identifier_raises
+ def test_Sam_new_with_duplicate_read_group_identifier_raises
assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\n@RG\tID:123")) }
end
- def test_Sam_header_parse_with_ok_read_group_identifier_dont_raise
+ def test_Sam_new_with_ok_read_group_identifier_dont_raise
sam = Sam.new(StringIO.new("@RG\tID:123\n@RG\tID:124"))
assert_nothing_raised { sam.header }
end
- def test_Sam_header_parse_with_bad_flow_order_raises
+ def test_Sam_new_with_bad_flow_order_raises
assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\tFO:3")) }
end
- def test_Sam_header_parse_with_ok_flow_order_dont_raise
+ def test_Sam_new_with_ok_flow_order_dont_raise
sam = Sam.new(StringIO.new("@RG\tID:123\tFO:*"))
assert_nothing_raised { sam.header }
sam = Sam.new(StringIO.new("@RG\tID:123\tFO:ACMGRSVTWYHKDBN"))
assert_nothing_raised { sam.header }
end
- def test_Sam_header_parse_with_bad_platform_raises
+ def test_Sam_new_with_bad_platform_raises
assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\tPL:maersk")) }
end
- def test_Sam_header_parse_with_ok_platform_dont_raise
+ def test_Sam_new_with_ok_platform_dont_raise
sam = Sam.new(StringIO.new("@RG\tID:123\tPL:ILLUMINA"))
assert_nothing_raised { sam.header }
end
- def test_Sam_header_parse_with_bad_program_identifier_raises
+ def test_Sam_new_with_bad_program_identifier_raises
assert_raise(SamError) { Sam.new(StringIO.new("@PG\tID:")) }
end
- def test_Sam_header_parse_with_missing_program_identifier_raises
+ def test_Sam_new_with_missing_program_identifier_raises
assert_raise(SamError) { Sam.new(StringIO.new("@PG")) }
end
- def test_Sam_header_parse_with_duplicate_program_identifier_raises
+ def test_Sam_new_with_duplicate_program_identifier_raises
assert_raise(SamError) { Sam.new(StringIO.new("@PG\tID:123\n@PG\tID:123")) }
end
- def test_Sam_header_parse_with_bad_comment_raises
+ def test_Sam_new_with_bad_comment_raises
assert_raise(SamError) { Sam.new(StringIO.new("@CO\t")) }
end
- def test_Sam_header_parse_with_ok_comment_dont_raise
+ def test_Sam_new_with_ok_comment_dont_raise
sam = Sam.new(StringIO.new("@CO\tfubar"))
assert_nothing_raised { sam.header }
end
assert_nothing_raised { sam.each }
end
- def test_Sam_each_with_bad_cigar_raises
- sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24\t*\t*\t*\t*\t*\n"))
- assert_raise(SamError) { sam.each }
- end
-
- def test_Sam_each_with_ok_cigar_dont_raise
- sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24M2I3D\t*\t*\t*\t*\t*\n"))
- assert_nothing_raised { sam.each }
-
- sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
- assert_nothing_raised { sam.each }
- end
-
def test_Sam_each_with_bad_rnext_raises
sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t \t*\t*\t*\t*\n"))
assert_raise(SamError) { sam.each }
assert_raise(SamError) { sam.each }
end
- def test_Sam_each_wtih_rname_present_in_header_dont_raise
+ def test_Sam_each_with_rname_present_in_header_dont_raise
sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\tref\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
assert_nothing_raised { sam.each }
sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
assert_nothing_raised { sam.each }
end
+
+ def test_Sam_each_with_rnext_missing_from_header_raises
+ sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\tMIS\t*\t\*\t*\t*\n"))
+ assert_raise(SamError) { sam.each }
+ end
+
+ def test_Sam_each_with_rnext_present_in_header_dont_raise
+ sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
+ assert_nothing_raised { sam.each }
+
+ sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\t=\t*\t\*\t*\t*\n"))
+ assert_nothing_raised { sam.each }
+
+ sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\tref\t*\t\*\t*\t*\n"))
+ assert_nothing_raised { sam.each }
+ end
+
+ def test_Sam_to_bp_returns_correctly
+ string = "ID00036734\t0\tgi48994873\t366089\t37\t37M1I62M\t*\t0\t0\tGTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG\t*\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:1\tXG:i:1\tMD:Z:99\n"
+
+ sam = Sam.new(StringIO.new(string))
+
+ sam.each do |s|
+ assert_equal("SAM", Sam.to_bp(s)[:REC_TYPE])
+ assert_equal("ID00036734", Sam.to_bp(s)[:Q_ID])
+ assert_equal("-", Sam.to_bp(s)[:STRAND])
+ assert_equal("gi48994873", Sam.to_bp(s)[:S_ID])
+ assert_equal(366089, Sam.to_bp(s)[:S_BEG])
+ assert_equal(37, Sam.to_bp(s)[:MAPQ])
+ assert_equal("37M1I62M", Sam.to_bp(s)[:CIGAR])
+ assert_equal("GTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG", Sam.to_bp(s)[:SEQ])
+ assert_equal("37:->T", Sam.to_bp(s)[:ALIGN])
+ end
+ end
end
projects / biopieces.git / blobdiff