bio-sam-mutation 0.4.1

data/test/test_mutation_array.rb

@@ -0,0 +1,13 @@
+require 'helper'
+class MutationArrayTest < Test::Unit::TestCase
+  def test_hgvs
+		sub_del_ins = Bio::DB::Alignment.new "OR1FQ:00021:00043	0	ENST00000366794	936	70	128M1D16M1I38M	*	0	0	ACTCATCTTCAACAAGCAGCAAGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCCGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGTGCCTATTACTGCACTGGGGGACGTCACTGCCTGGACCAAGTGTATGGTCAAGAC	CCCCCCCDB@?=<B7;;<<<A7?@FCDDABBCCD;C???BAB?@@?CAC@CC>??C@;;;7;;;/8/000+.;;8/@7<;;;1;;7;7;;1>BBCCDAD;???;;;C:;;C;;;?@@BC=;;7;;<00...)-55357DC<<6;;;;;,66;;;;;;6606606<:@@;5;44--)--.)---	PG:Z:novoalign	AS:i:121	UQ:i:121	NM:i:3	MD:Z:60T67^A54"
+		# Using MutationArray collection method:
+		assert_equal "ENST00000366794:c.[996T>C;1064delA;1080_1081insG]", sub_del_ins.mutations.to_hgvs("c")
+  end
+
+  def test_vep
+    del = Bio::DB::Alignment.new "MLF7W:00035:00652\t0\tENST00000366794\t361\t70\t141M3D68M8S\t*\t0\t0\tGGGTTCTCTGAGCTTCGGTGGGATGACCAGCAGAAAGTCAAGAAGACAGCGGAAGCTGGAGGAGTGACAGGCAAAGGCCAGGATGGAATTGGTAGCAAGGCAGAGAAGACTCTGGGTGACTTTGCAGCAGAGTATGCCAAGAACAGAAGTACGTGCAAGGGGTGTATGGAGAAGATAGAAAAGGGCCAGGTGCGCCTGTCCAAGAAGATGGCTGAGG\tEE?E?@@CCBB??>@CCACCC?CBCAA<?ACDCDE?CD@.)-/8/--;;;A6;=???DADD@BACCCDCCACCC?CACA>?>?CC@CAC@C@CCCBC@CACCCBCC@??>CCBBC=B@ACCC?CCCDDCCCCCCADDAD<??BCCCCADDCCDCDCCACCC:CCCCCCACCC@ACA:::::.:C;CACCACCDDB>BCCC@CACCA???CACCCCC@\tPG:Z:novoalign\tAS:i:135\tUQ:i:135\tNM:i:3\tMD:Z:141^TCC68"
+    assert_equal "TCC/-", del.mutations(1,nil,145).vep[0]["allele_string"]
+  end
+end

data/test/test_sam.rb

@@ -0,0 +1,160 @@
+require 'helper'
+class SAMTest < Test::Unit::TestCase
+	def test_split_types
+		sam = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	112767204	37	60M1D7M2I6M	*	0	0	GCAGTAATTTCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:60^G13")
+		assert(sam.qname.is_a? String)
+		assert(sam.flag.is_a? Integer) # DB::Alignment only supports integer FLAG
+		assert(sam.rname.is_a? String)
+		assert(sam.pos.is_a? Integer)
+		assert(sam.mapq.is_a? Integer)
+		assert(sam.cigar.is_a? String)
+		assert(sam.mrnm.is_a?(String) || sam.mrnm.nil?)
+		assert(sam.mpos.is_a?(Integer) || sam.mpos.nil?)
+		assert(sam.isize.is_a?(Integer) || sam.isize.nil?)
+		assert(sam.seq.is_a? String)
+		assert(sam.qual.is_a? String)
+		assert(sam.tags.is_a? Hash)
+
+	end
+	def test_split
+		sam = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	112767204	37	60M1D7M2I6M	*	0	0	GCAGTAATTTCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:60^G13")
+		assert_equal(sam.qname,"DKNQZ:00025:00303","ID not as expected")
+		assert_equal(sam.flag,0,"Flag not as expected")
+		assert_equal(sam.rname,"5","Chr not as expected")
+		assert_equal(sam.pos,112767204,"Position not as expected")
+		assert_equal(sam.mapq,37,"Quality not as expected")
+		assert_equal("60M1D7M2I6M", sam.cigar)
+		assert_equal("*",sam.mrnm)
+		assert_equal(0,sam.mpos)
+		assert_equal(0,sam.isize)
+		assert_equal(sam.seq,"GCAGTAATTTCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA")
+		assert_equal(sam.qual,"CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112","Base quality string not as expected")
+		assert_equal("60^G13",sam.tags["MD"].value)
+
+	end
+
+	def test_aliases
+		sam = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	1	37	60M1D7M2I6M	*	0	0	GCAGTAATTTCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:60^G13")
+		assert_equal(sam.chr,sam.rname)
+		assert_equal(sam.tags,sam.opt)
+	end
+
+	def test_insertion_mutation
+		insertion = Bio::DB::Alignment.new("I2M5K:00253:00406	0	5	112839854	70	63M2I138M1D27M7S	*	0	0	CAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCATACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTATTACATTTTGCCACGGAAAGTACTGCTGAGG	@CDDDCCCCACACCCCCCCC?CCACCCC>A6;;;;7;;6;6;BC;;6;;;;;.;;>ADDA??;;;;;?CCACCCD>C??@CCCC>C@C;>?CCCC@C=::@:::::+:::/:CCC?>>>>CCCCDDD9CCCC@AB????=AB>??;?BB>@@@AA???CC<@@?????BB>??;;;B<BC;??8;6:A=@=@BBB;;;?<77//*08*088888*8=9=?B7;;4;??????????<	PG:Z:novoalign	AS:i:183	UQ:i:183	NM:i:3	MD:Z:201^T27")
+		assert_equal 112839916, insertion.mutations[0].position
+		assert_nil insertion.mutations[0].reference
+		assert_equal "AT", insertion.mutations[0].mutant
+		assert_equal :insertion, insertion.mutations[0].type
+		assert_equal 112839916, insertion.mutations(60,10)[0].position
+	end
+  def test_ins_with_offset
+		insertion = Bio::DB::Alignment.new("I2M5K:00253:00406	0	5	112839854	70	63M2I138M1D27M7S	*	0	0	CAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCATACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTATTACATTTTGCCACGGAAAGTACTGCTGAGG	@CDDDCCCCACACCCCCCCC?CCACCCC>A6;;;;7;;6;6;BC;;6;;;;;.;;>ADDA??;;;;;?CCACCCD>C??@CCCC>C@C;>?CCCC@C=::@:::::+:::/:CCC?>>>>CCCCDDD9CCCC@AB????=AB>??;?BB>@@@AA???CC<@@?????BB>??;;;B<BC;??8;6:A=@=@BBB;;;?<77//*08*088888*8=9=?B7;;4;??????????<	PG:Z:novoalign	AS:i:183	UQ:i:183	NM:i:3	MD:Z:201^T27")
+		assert_equal 112839916, insertion.mutations(60,10)[0].position
+	end
+	def test_sorting
+		insertion_and_deletion = Bio::DB::Alignment.new("I2M5K:00253:00406	0	5	1	70	63M2I138M1D27M7S	*	0	0	CAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCCACCATACCTCCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTATTACATTTTGCCACGGAAAGTACTGCTGAGG	@CDDDCCCCACACCCCCCCC?CCACCCC>A6;;;;7;;6;6;BC;;6;;;;;.;;>ADDA??;;;;;?CCACCCD>C??@CCCC>C@C;>?CCCC@C=::@:::::+:::/:CCC?>>>>CCCCDDD9CCCC@AB????=AB>??;?BB>@@@AA???CC<@@?????BB>??;;;B<BC;??8;6:A=@=@BBB;;;?<77//*08*088888*8=9=?B7;;4;??????????<	PG:Z:novoalign	AS:i:183	UQ:i:183	NM:i:3	MD:Z:201^T27")
+		assert_equal :insertion, insertion_and_deletion.mutations[0].type
+		assert_equal :deletion, insertion_and_deletion.mutations[1].type
+	end
+
+	def test_deletion_mutation
+		deletion = Bio::DB::Alignment.new("I2M5K:00271:01406	0	5	112839854	70	55M12D162M7S	*	0	0	CAGTGATCTTCCAGATAGCCCTGGACAAACCATGCCACCAAGCAGAAGTAAAACACCTCAAACAGCTCAAACCAAGCGAGAAGTACCTAAAAATAAAGCACCTACTGCTGAAAAGAGAGAGAGTGGACCTAAGCAAGCTGCAGTAAATGCTGCAGTTCAGAGGGTCCAGGTTCTTCCAGATGCTGATACTTTATTACATTTTGCCACGGAAAGTACTGCTGAGG	ACHECCC@???ACCCCCCDC>CC@CDCC>C>>?CC=>?ACADCCCCACCCCC:AAA<=CCC??<>CDCDE?C@C>=;CC=>>>@@@>:::::+:::/:@@@<>>?CCCD=>>=7:D???AAAAAB8;;>??;?@@=?;;;???@@@:@B;;;;GBB?BBAAAA9??=@@;?<?A>B?C@@@@@CBBB?;;;4;C?BB;;;:1:B>BBB=AA;A@@???A>?::2	PG:Z:novoalign	AS:i:194	UQ:i:194	NM:i:12	MD:Z:55^CCTCCACCACCT162")
+		assert_equal deletion.mutations[0].type, :deletion
+		assert_equal deletion.mutations[0].reference, "CCTCCACCACCT"
+		assert_equal deletion.mutations[0].mutant, nil
+		assert_equal deletion.mutations(50,40)[0].position, 112839909
+		assert_equal "5", deletion.mutations[0].seqname
+	end
+	def test_substitution_mutation
+		substitution = Bio::DB::Alignment.new("OR1FQ:00462:02257	0	ENST00000366794	936	70	193M43S	*	0	0	ACTCATCTTCAACAAGCAGCAAGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCCGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGATGCCTATTACTGCACTGGGGACGTCACTGCCTGGACCAAGTGTATGGTCAAGACACAGACACCCTCCACAGCCTCGGCTCCTGCTGCTGTGAACTCCTCTGCTGAGG	@BCACC@@@@DAFFADCCCCDEID@@?@ACCCDD:@??;<8<1..=>=<1111@@CD??@@CC@C@CFDCACCCADDABCCD?DD@CACD?CC??>C6;6;>>???E?C@??CCDACCC@CD@CCC><?A>>7;<<7<<<??;BBBBB/;;;;;BBBCC@CCACC=@7;;;;;;;6;@@7?@CCCCCC111<6<<+00>>>=CCD;??C@CCCC?????CCAC????CCECDDCDB	PG:Z:novoalign	AS:i:328	UQ:i:328	NM:i:1	MD:Z:60T132")
+		assert_equal substitution.mutations[0].type, :substitution
+		assert_equal substitution.mutations[0].reference, "T"
+		assert_equal substitution.mutations[0].mutant, "C"
+		assert_equal 996, substitution.mutations[0].position
+		assert_equal "ENST00000366794", substitution.mutations[0].seqname
+	end
+	def test_substitution_mutation_with_translation_pos
+		substitution = Bio::DB::Alignment.new("OR1FQ:00462:02257	0	ENST00000366794	936	70	193M43S	*	0	0	ACTCATCTTCAACAAGCAGCAAGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCCGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGATGCCTATTACTGCACTGGGGACGTCACTGCCTGGACCAAGTGTATGGTCAAGACACAGACACCCTCCACAGCCTCGGCTCCTGCTGCTGTGAACTCCTCTGCTGAGG	@BCACC@@@@DAFFADCCCCDEID@@?@ACCCDD:@??;<8<1..=>=<1111@@CD??@@CC@C@CFDCACCCADDABCCD?DD@CACD?CC??>C6;6;>>???E?C@??CCDACCC@CD@CCC><?A>>7;<<7<<<??;BBBBB/;;;;;BBBCC@CCACC=@7;;;;;;;6;@@7?@CCCCCC111<6<<+00>>>=CCD;??C@CCCC?????CCAC????CCECDDCDB	PG:Z:novoalign	AS:i:328	UQ:i:328	NM:i:1	MD:Z:60T132")
+		# offset, length, reference start, translation start
+		assert_equal 852, substitution.mutations(55,20,145)[0].position
+		assert_equal "ENST00000366794", substitution.mutations[0].seqname
+	end
+
+	def test_cdna_mutation
+	parp1	=	Bio::DB::Alignment.new("OR1FQ:00028:00030	0	ENST00000366794	342	70	66M1D88M6D70M8S	*	0	0	CCCTGACGTTGAGGTGGATGGGTTCTCTGAGCTTCGGTGGGATGATCAGCAGAAAGTCAAGAAGACGCGGAAGCTGGAGGAGTGACAGGCAAAGGCCAGGATGGAATTGGTAGCAAGGCAGAGAAGACTCTGGGTGACTTTGCAGCAGAGTATGCCAACAGAAGTACGTGCAAGGGGTGTATGGAGAAGATAGAAAAGGGCCAGGTGCGCCTGTCCAAGAAGATGGCTGAGG	;;1;;;;6606660;B?A<<<1?ACCDC?@;;;A<;7;<<16B==BDB@@@;;;1;@@@:;/*/;/0--)-)-C660>B@=?@D?;;;7;;;1;7;@;;7;;;64.4.4.454;;6;=@CFDCC@?>;@A;;>:;CACCC>CCCCCCCCCCCCCC@C>@@CCACCCCECC@@6:::.::::>D>?>CACEC?>1<<(00*0*0/6777?A??C??6;?;;6;@::;?CDCD>	PG:Z:novoalign	AS:i:234	UQ:i:234	NM:i:8	MD:Z:45C20^A88^CCAAGT70")
+		response = parp1.mutations(140,40,145).vep("human","c")
+		assert_equal "ENST00000366794:c.353_358delCCAAGT", parp1.mutations(140,40,145).first.to_hgvs("c")
+		assert_equal "CCAAGT/-", response.first["allele_string"]
+		assert_equal 226392243, response.first["start"]
+	end
+
+	def test_nil_if_no_mutation
+		no_mut = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	1	37	75M	*	0	0	GCAGTAATTTCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:75")
+	  assert_nil no_mut.mutations
+	end
+
+	def test_query_no_mutation
+		no_mut = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	1	37	75M	*	0	0	GCAGTAATTTCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:75")
+		assert_equal "TTTCCCTGGA", no_mut.query(8,10)
+	end
+	def test_query_deletion
+		del_mut = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	100000	37	9M1D65M	*	0	0	GCAGTAATTCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:9^T65")
+		assert_equal "TT-CCCTGGA", del_mut.query(8,10)
+	end
+	def test_query_insertion
+		ins_mut = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	100000	37	10M2I65M	*	0	0	GCAGTAATTTGGCCCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:75")
+		assert_equal "TTT_gg_CCCTGGA", ins_mut.query(8,10)
+	end
+	def test_query_substitution
+		sub_mut = Bio::DB::Alignment.new("DKNQZ:00025:00303	0	5	100000	37	75M	*	0	0	GCAGTAATTTCGCTGGAGTAAAACTGCGGTCAAAAATGTCCCTCCGTTCTTATGGAAGCCGGAAGGAAGTCTGTA	CCCCCC@CE>CC<CC@CB;;;;.;;;;;AC;::::+:92A:=CCAEE=?>;=:@<B?:<6<*/*/*/*/911112	XT:A:U	NM:i:3	X0:i:1	X1:i:0	XM:i:3	XO:i:1	XG:i:1	MD:Z:11C63")
+		assert_equal "TTTCgCTGGA", sub_mut.query(8,10)
+	end
+
+	def test_query_complex
+	complex	=	Bio::DB::Alignment.new	"MLF7W:00161:00415	0	1	226064342	70	121M30I32M1D52M7S	*	0	0	TCTCTGTACCATGGCTCGTACAAAGCAGACTGCCCGCAAATCGACCGGTGGTAAAGCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCGCAAGAGTGCGCCCTCTACTGGAGTGGTGAAGAAACCTCATCGTTAAAAAAACCTCATCGTTAAACCTCATCGTTACAGGTATTAAAAAACAGGAAAAAATGGGACAAAGTCTCTCTTGTATGTATCCATATAATTTAACAAAAAGAATGGAT	CC???ECCCACCCACBBCD>?@D=@@DCEEDDCC=CCDD;??;;;=@=;;0;66,65;5;1;@?C@CCCACCC=CCCCCCB.;;6;;;C;=:@:9:=2::>>52:BBCBCAD?>=ADCC?==:/:><<<=8884:CCCCC(B288::::C3=@8C?@:8888/*//0-'--.'-:;:;,><=288888)6BE?DCCC?DC@@>@;;7;00000<<DB@@@DC@CE?CA00000(0/*/;+;0	PG:Z:novoalign	AS:i:379	UQ:i:379	NM:i:33	MD:Z:113G39^A35C16	YH:m:1:g.[226064455G>T;226064462_226064463insAAACCTCATCGTTAAAAAAACCTCATCGTT;226064495delA]"
+		# offset 100, length 70
+		# MD:Z:113G39^A35C16      YH:m:1:g.[226064455G>T;226064462_226064463insAAACCTCATCGTTAAAAAAACCTCATCGTT;226064495delA]
+		assert_equal "GCCCTCTACTGGAGtGGTGAAG_aaacctcatcgttaaaaaaacctcatcgtt_AAACCTCATCGTTACAGGTATTAAAAAACAGG-", complex.query(100,70)
+	end
+
+	def test_query_with_preceding
+	pre = Bio::DB::Alignment.new	"MLF7W:00741:00261	0	1	226064342	70	32M1I127M2D33M1D34M1I14M36S	*	0	0	TCTCTGTACCATGGCTCGTACAAAGCAGACTGCCCCGCAAATCGACCGGTGGTAAAGCACCCAGGAAGCAACTGGCTACAAAAGCCGCTCGCAAGAGTGCGCCCTCTACTGGAGTGGTGAAGAAACCTCATCGTTACAGGTATTAAAAAACAGGAAAAAATGGACAAAGTCTCTCTTGTATGTATCCATATAATTAACAAAAAGATGGATAACAGGAAAACTTTTTGTCTTTAGAGAAACTTCATTTTGAACACTTAAACTTTACTGCTTAGCTGAGG	CC?>=CB@B>?@C@CCCDBB<66,<AA;;;;;;;;,6=CC,>>>>>@C@BC@;;;1;>;>C????@???DA???ACCCCCDC8@@ACCCFC??>?CCCCCCCC<CCCCCCE@CCCCACDCACCE:>=;:80:00*////)/??288888)8005:::::(0.).-61)133::BBC;????<<<882888?D20*/*/////(..66-.-------999-9;;99,0...8-:6:/88,8<7>?ABB1;:9888<288,888,88=88/*//0008:*	PG:Z:novoalign	AS:i:534	UQ:i:534	NM:i:8	MD:Z:113G45^AT0G27C4^T48	YH:m:1:g.[226064455G>T;226064501_226064502delAT;226064503G>T]"	
+	# MD:Z:113G45^AT0G27C4^T48        YH:m:1:g.[226064455G>T;226064501_226064502delAT;226064503G>T]
+	assert_equal "GCCCTCTACTGGAGtGGTGAAGAAACCTCATCGTTACAGGTATTAAAAAACAGGAAAAAA--tGGACAAA", pre.query(100,70)
+	end
+
+
+	def test_complex_mutation
+		sub_del_ins = Bio::DB::Alignment.new "OR1FQ:00021:00043	0	ENST00000366794	936	70	128M1D16M1I38M	*	0	0	ACTCATCTTCAACAAGCAGCAAGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCCGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGTGCCTATTACTGCACTGGGGGACGTCACTGCCTGGACCAAGTGTATGGTCAAGAC	CCCCCCCDB@?=<B7;;<<<A7?@FCDDABBCCD;C???BAB?@@?CAC@CC>??C@;;;7;;;/8/000+.;;8/@7<;;;1;;7;7;;1>BBCCDAD;???;;;C:;;C;;;?@@BC=;;7;;<00...)-55357DC<<6;;;;;,66;;;;;;6606606<:@@;5;44--)--.)---	PG:Z:novoalign	AS:i:121	UQ:i:121	NM:i:3	MD:Z:60T67^A54"
+		# MD:Z:60T67^A54
+		# Old "manual" method:
+		assert_equal "996T>C;1064delA;1080_1081insG", sub_del_ins.mutations.map{|m| m.to_hgvs}.join(";")
+	end
+
+	def test_really_complex_mutation
+		omg = Bio::DB::Alignment.new "MLF7W:01389:01808	0	ENST00000366794	957	70	153M45D46M1I83M1I13M4S	*	0	0	AGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCCGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGATGCCTATTACTGCACTGGGGACGTCACTGCCTGGACCAAGTGTATGGAATTCCGAGAAATCTCTTACCTCAAGAAATTGAAGGTTAAAAAAGCAGGACCGTATATTCCCCCCAGAAACCAGCGCCTCCGTGGCGGCCACGCCTCCGCCCTCCACAGCCTCGGCTCCTGCTGCTGTCGAACTCCTCTGCTGAGG	0666606066666,66@//*//----)-)--)666@6666B@@<666660---)--)----)660606C<65>5;;6;4;BCCCCD>CCC??>B7;;C7;;@AAAA<<<<<7<<<7<;DA;;;;---%-------6BB6??=;D<@7;;;;;;A6;7;7;7;;<6D:6<B<<7;;7;;;7;;;1<><;7;@C7;;;;;+;BCCA?><<;BB;;7;;;;;+;;;;160666.-)-.)--6)-4.;6;;AB>;;7;;;1;C7;;5;;0666066<0555<?6;;/.-.).8==CCCCCA;:/6	PG:Z:novoalign	AS:i:504	UQ:i:504	NM:i:48	MD:Z:39T113^GGTCAAGACACAGACACCCAACCGGAAGGAGTGGGTAACCCCAAA142"
+		# MDZ MD:Z:39T113^GGTCAAGACACAGACACCCAACCGGAAGGAGTGGGTAACCCCAAA142
+		# translation start 145
+		assert_equal "ENST00000366794:c.[852T>C;966_1010delGGTCAAGACACAGACACCCAACCGGAAGGAGTGGGTAACCCCAAA;1056_1057insG;1139_1140insC]", omg.mutations(1,nil,145).to_hgvs
+
+		#This one (wrong mutant base retrieved for substition) seems to be a problem with novoalign? Mutation is CT>TC but aligned as a single T substition
+		#wtf = Bio::DB::Alignment.new "MLF7W:00090:00609\t0\tENST00000366794\t957\t70\t25M1I314M4S\t*\t0\t0\tAGTGCCTTCTGGGGAGTCGGCGATCTTTGGACCGAGTAGTCGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGATGCCTATTACTGCACTGGGGACGTCACTGCCTGGACCAAGTGTATGGTCAAGACACAGACACCCAACCGGAAGGAGTGGGTAACCCCAAAGGAATTCCGAGAAATCTCTTACCTCAAGAAATTGAAGGTTAAAAAGCAGGACCGTATATTCCCCCCAGAAACCAGCGCCTCCGTGGCGGCCACGCCTCCGCCCTCCACAGCCTCGGCTCCTGCTGCTGTGAACTCCTCTGCGAGG\t?AA<<7;7>>DDC;@@@DCAB;;;;;;1;7;@?;;;;;;;6;;;@@C;<<7<<;7<?7<CBB:<;7;7;;1;;B;;;7;=@BCCCCC1>>;;>BC@CCDACDACC;;<<<<<7?FEADCDGDDA;?;;/;<<;;CCB@CA@@>?DAC???DCCFDAD??>?CCCDDCD@??C9@<B;>=?@C@CFCCD>CC6;;;/;C;CAD>?>?ACCCDC?DDCCCACCACCCA@@@:>6;E>A@C<;;;;-;CCCADD<;;C>??ACGGGE+;<<<1;>ACCDDADC7<;B7/0+0+////8;;7?AA9<<66<6;<66CC?C?><;<<;;;;>;ACA>??A>>;;>>;;7\tPG:Z:novoalign\tAS:i:164\tUQ:i:164\tNM:i:3\tMD:Z:39T203A95"
+		# MD:Z:39T203A95
+		#assert_equal "ENST00000366794:c.[981_982insT;996T>T;1200A>A]", wtf.mutations.to_hgvs
+
+	end
+
+	def test_add_tag
+		sub_del_ins = Bio::DB::Alignment.new "OR1FQ:00021:00043	0	ENST00000366794	936	70	128M1D16M1I38M	*	0	0	ACTCATCTTCAACAAGCAGCAAGTGCCTTCTGGGGAGTCGGCGATCTTGGACCGAGTAGCCGATGGCATGGTGTTCGGTGCCCTCCTTCCCTGCGAGGAATGCTCGGGTCAGCTGGTCTTCAAGAGCGTGCCTATTACTGCACTGGGGGACGTCACTGCCTGGACCAAGTGTATGGTCAAGAC	CCCCCCCDB@?=<B7;;<<<A7?@FCDDABBCCD;C???BAB?@@?CAC@CC>??C@;;;7;;;/8/000+.;;8/@7<;;;1;;7;7;;1>BBCCDAD;???;;;C:;;C;;;?@@BC=;;7;;<00...)-55357DC<<6;;;;;,66;;;;;;6606606<:@@;5;44--)--.)---	PG:Z:novoalign	AS:i:121	UQ:i:121	NM:i:3	MD:Z:60T67^A54"
+		sub_del_ins.add_tag!("TE:s:TTAG")
+		assert_equal "TTAG", sub_del_ins.tags["TE"].value
+
+		tag_obj = Bio::DB::Tag.new
+		tag_obj.set("TA:g:Object")
+		sub_del_ins.add_tag!(tag_obj)
+		assert_equal "Object", sub_del_ins.tags["TA"].value
+
+		 assert_match "TA:g:Object", sub_del_ins.sam_string
+	end
+
+end

data/test/test_vep_hgvs.rb

@@ -0,0 +1,9 @@
+require 'helper'
+class VepHgvsTest < Test::Unit::TestCase
+  def test_vep_parsing
+   json_obj = JSON.parse "[{\"assembly_name\":\"GRCh38\",\"end\":226392243,\"seq_region_name\":\"1\",\"transcript_consequences\":[{\"gene_id\":\"ENSG00000143799\",\"distance\":15,\"biotype\":\"protein_coding\",\"gene_symbol_source\":\"HGNC\",\"consequence_terms\":[\"downstream_gene_variant\"],\"strand\":-1,\"hgnc_id\":\"HGNC:270\",\"gene_symbol\":\"PARP1\",\"transcript_id\":\"ENST00000366792\",\"impact\":\"MODIFIER\"},{\"gene_id\":\"ENSG00000143799\",\"distance\":697,\"biotype\":\"protein_coding\",\"gene_symbol_source\":\"HGNC\",\"consequence_terms\":[\"downstream_gene_variant\"],\"strand\":-1,\"hgnc_id\":\"HGNC:270\",\"gene_symbol\":\"PARP1\",\"transcript_id\":\"ENST00000629232\",\"impact\":\"MODIFIER\"},{\"gene_id\":\"ENSG00000143799\",\"cdna_end\":227,\"biotype\":\"processed_transcript\",\"gene_symbol_source\":\"HGNC\",\"consequence_terms\":[\"non_coding_transcript_exon_variant\",\"non_coding_transcript_variant\"],\"strand\":-1,\"hgnc_id\":\"HGNC:270\",\"gene_symbol\":\"PARP1\",\"cdna_start\":225,\"transcript_id\":\"ENST00000469663\",\"impact\":\"MODIFIER\"},{\"cdna_end\":504,\"codons\":\"TCC/-\",\"protein_end\":120,\"strand\":-1,\"hgnc_id\":\"HGNC:270\",\"amino_acids\":\"S/-\",\"gene_symbol\":\"PARP1\",\"cdna_start\":502,\"transcript_id\":\"ENST00000366794\",\"cds_start\":358,\"gene_id\":\"ENSG00000143799\",\"protein_start\":120,\"biotype\":\"protein_coding\",\"gene_symbol_source\":\"HGNC\",\"cds_end\":360,\"consequence_terms\":[\"inframe_deletion\"],\"impact\":\"MODERATE\"}],\"strand\":-1,\"id\":\"ENST00000366794:c.358_360delTCC\",\"allele_string\":\"TCC/-\",\"most_severe_consequence\":\"inframe_deletion\",\"start\":226392241}]"
+   #test result from hg18
+   assert_equal [{"Allele"=>"TCC/-", "CDS position"=>358, "Protein start"=>120, "Mutation"=>"S/-", "Consequence"=>["inframe_deletion"]}], VepHgvs.consequences_for_transcript(json_obj,"ENST00000366794")
+
+  end
+end

metadata

@@ -0,0 +1,247 @@
+--- !ruby/object:Gem::Specification
+name: bio-sam-mutation
+version: !ruby/object:Gem::Version
+  version: 0.4.1
+platform: ruby
+authors:
+- Stephen Pettitt
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-02-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: bio-samtools
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.3.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.3.4
+- !ruby/object:Gem::Dependency
+  name: oj
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.14'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.14'
+- !ruby/object:Gem::Dependency
+  name: bio-ensembl-rest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.9'
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: Simple classes for parsing SAM, CIGAR and MD:Z strings, including slices.
+  Methods for calling mutations in HGVS format and looking up consequences using Ensembl
+  VEP REST API. Developed for calling mutations at an expected position in an alignment
+  - e.g. Amplicon sequencing of CRISPR-induced mutations.
+email: spettitt@gmail.com
+executables:
+- mutations
+- sam-mutation
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- ".document"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- bin/mutations
+- bin/sam-mutation
+- lib/bio-sam-mutation.rb
+- lib/bio-sam-mutation/bio/alignment/cigar.rb
+- lib/bio-sam-mutation/bio/alignment/iterate_pairs.rb
+- lib/bio-sam-mutation/bio/db/alignment.rb
+- lib/bio-sam-mutation/bio/db/tag.rb
+- lib/bio-sam-mutation/bio/db/tag/md.rb
+- lib/bio-sam-mutation/bio/mutantallele.rb
+- lib/bio-sam-mutation/bio/mutation.rb
+- lib/bio-sam-mutation/bio/mutation_array.rb
+- lib/bio-sam-mutation/bio/vephgvs.rb
+- lib/bio-sam-mutation/mutationscli.rb
+- test/helper.rb
+- test/test_cigar.rb
+- test/test_mdtag.rb
+- test/test_mutant_allele.rb
+- test/test_mutation.rb
+- test/test_mutation_array.rb
+- test/test_sam.rb
+- test/test_vep_hgvs.rb
+homepage: http://github.com/stveep/bioruby-sam-mutation
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.5
+signing_key: 
+specification_version: 4
+summary: Parsing and mutation calling from SAM, CIGAR and MD:Z.
+test_files: []