Merge pull request #42 from yhoogstrate/3_0_6_arriba

changes to support arriba

Changelog

@@ -1,3 +1,7 @@
+2020-05-06  Youri Hoogstrate
+
+	* Version 3.0.6: Support for ARRIBA - thanks to Alexandre Rouette
+
 2016-07-11  Youri Hoogstrate
 
 	* Version 3.0.5: Changes in deployment & two fixes in export function

README.md

@@ -423,6 +423,7 @@ FuMa supports the following file formats:
 | Fusion Catcher     | final-list_cand*.txt  | fusion-catcher_final
 | FusionMap          |                       | fusionmap
 | JAFFA              | jaffa_results.cvs     | jaffa
+| ARRIBA             |                       | arriba
 | Trinity + GMAP     |                       | trinity-gmap
 | OncoFuse           |                       | oncofuse
 | RNA STAR           | Chimeric.out.junction | rna-star_chimeric

bin/fuma

@@ -152,6 +152,13 @@ if __name__ == "__main__":
 				except Exception as e:
 					raise Exception("Sample '"+sample_name+ "' could not be parsed as filetype: "+input_format+"\n\n"+str(e))
 
+			# ARRIBA
+			elif(input_format_stripped in ["arriba"]):
+				try:
+					samples[sample_name] = ReadArribaResults(sample_filename,sample_name)
+				except Exception as e:
+					raise Exception("Sample '"+sample_name+ "' could not be parsed as filetype: "+input_format+"\n\n"+str(e))
+
 			# 1-2-3-SV
 			elif(input_format_stripped in ["123sv"]):
 				try:

fuma/Readers.py

@@ -1539,3 +1539,58 @@ def parse_path(self,path_chunk):
 				m = re.search(self.regexes[key],line)
 				keys[key] = m.groups()
 		return keys
+
+
+
+
+
+
+class ReadArribaResults(FusionDetectionExperiment):
+	parse_left_column = 4
+	parse_right_column = 5
+
+	logger = logging.getLogger("FuMa::Readers::ReadArribaResults")
+
+	def __init__(self,arg_filename,name):
+		FusionDetectionExperiment.__init__(self,name)
+
+		self.filename = arg_filename
+
+		self.parse()
+
+	def parse(self):
+		self.logger.info("Parsing file: "+str(self.filename))
+
+		self.i = 0
+
+		with open(self.filename,"r") as fh:
+			for line in fh:
+				line = line.strip()
+				if(len(line) > 0):
+					if(self.i > 0):# otherwise it's the header
+						self.parse_line(line)
+
+					self.i += 1
+
+		self.logger.debug("Parsed fusion genes: "+str(len(self)))
+
+	def parse_line(self,line):
+		line = line.strip().split("\t")
+
+		left = line[self.parse_left_column].strip('"').split(':')
+		right = line[self.parse_right_column].strip('"').split(':')
+
+		f = Fusion( \
+			left[0], \
+			right[0], \
+			left[1], \
+			right[1], \
+			None, \
+			None, \
+			self.name, \
+			str(self.i), \
+			False # The authors claim that for this tool acceptator donor strand is not preserved - therefore this has to be false
+		)
+		self.add_fusion(f)
+
+

fuma/__init__.py

@@ -21,7 +21,7 @@
  <http://epydoc.sourceforge.net/manual-fields.html#fields-synonyms>
 """
 
-__version_info__ = ('3', '0', '5')
+__version_info__ = ('3', '0', '6')
 __version__ = '.'.join(__version_info__) if (len(__version_info__) == 3) else '.'.join(__version_info__[0:3])+"-"+__version_info__[3]
 __author__ = 'Youri Hoogstrate'
 __author_email__ = '_@.'

tests/data/test_Readers.TestReadARRIBAfile.test_01.txt

@@ -0,0 +1,26 @@
+#gene1	gene2	strand1(gene/fusion)	strand2(gene/fusion)	breakpoint1	breakpoint2	site1	site2	type	direction1	direction2	split_reads1	split_reads2	discordant_mates	coverage1	coverage2	confidence	closest_genomic_breakpoint1	closest_genomic_breakpoint2	filters	fusion_transcript	reading_frame	peptide_sequence	read_identifiers
+KMT2A	MLLT10	+/+	+/+	11:118482495	10:21651673	splice-site	splice-site	translocation	downstream	upstream	13	2	0	99	302	high	.	.	duplicates(31)	ATCCAAACAGGCCACCACTCCAGCTTCCAGGAAGTCAAGCAAGCAGGTCTCCCAGCCAGCACTGGTCATCCCGCCTCAGCCACCTACTACAGGACCGCCAAGAAAAGAAGTTCCCAAAACCACTCCTAGTGAGCCCAAGAAAAAGCAGCCTCCACCACCAGAATCAG___GTCCAGAGCAGAGCAAACAGAAAAAAGTGGCTCCCCGCCCAAGTATCCCTGTAAAACAAAAACCAAAAGAAAAG|AAATATAAAGAGAAGGACAAACACAAACAGAAACACAAGAAGCAGCCAGAACCATCACCTGCATTGGTTCCATCCTTGACTGTTACTACAGAAAAA___ACTTATACAAGCACTAGCAAC	in-frame	SKQATTPASRKSSKQVSQPALVIPPQPPTTGPPRKEVPKTTPSEPKKKQPPPPESGPEQSKQKKVAPRPSIPVKQKPKEK|KYKEKDKHKQKHKKQPEPSPALVPSLTVTTEKTYTSTS	.
+KMT2A	MLLT10	+/+	+/+	11:118482092	10:21651673	splice-site	splice-site	translocation	downstream	upstream	1	0	0	194	302	low	.	.	.	CACTGGTCATCCCGCCTCAGCCACCTACTACAGGACCGCCAAGAAAAGAAGTTCCCAAAACCACTCCTAGTGAGCCCAAGAAAAAGCAGCCTCCACCACCAGAATCAG|AAATATAAAGAGAAGGACAAACACAAACAGAAACACAAGAAGCAGCC	out-of-frame	LVIPPQPPTTGPPRKEVPKTTPSEPKKKQPPPPES|ei*	.
+MLLT10	RP11-460I19.2(14723),RNF212(12555)	+/+	./+	10:21538912	4:1043695	splice-site	intergenic	translocation	downstream	upstream	1	7	2	138	42	high	.	.	duplicates(26)	ACCCGCTGGTTTATTGCGACGGGCACGGCTGCAGCGTCGCGGTGCATCAAG___CTTGCTATGGCATTGTTCAAGTACCCACTGGACCaTGGTTTTGCAGGAAATGTGAATCTCAGGAGAGAGCAGCCAGAGTG|CTCCTGCCAATTCCAACACTGAGAGTCTGTGTTTGGACGCCTCCAGTGACCACTGGCTCCGCGAGTGATGACTCACACCCATCACTCATCCCCTTCCTGAGTCAGCCGCGGGACCCTCTGCAGGGAGGCGTGCGAGTCATCGAG___AGAACAGCATTATTAGTGGC	out-of-frame	PLVYCDGHGCSVAVHQACYGIVQVPTGPWFCRKCESQERAARV|llpiptlrvcvwtppvttgsasddshpslipflsqprdplqggvrviertallv	.
+RP11-397P14.3	AKR1E2	-/+	+/+	10:4889923	10:4830675	exon	splice-site	duplication/3'-3'	downstream	upstream	5	2	2	60	445	high	.	.	duplicates(37)	AGAATATCCAG___GCTCTCTTTTTGCCTGCTGCCATCCATGTAAGACGCGACTTGTTTCTCCTTGCCTTCTGTCATGATTGTGAGGCTTCCCCAGACACTTGGAACT___TGCCGTTGGCAATCTTCTTTCGGATGGCCTGCCCGATGCCTTCTTCATTCAG|GCTTCTCCAGGGAAAGTGACCGAGGCAGTGAAAGAGGCCATTGACGCAGGGTACCGGCACTTCGACTGTGCTTACTTTTACCACAATGAGAGGGAGGTTGGAGCAGGGATCCGTTGCAAGATCAAGGAAGGCGCTGTAAGACGGGAG	.	.	.
+KANSL1	RP11-707O23.1(5132),RP11-707O23.5(2368)	-/-	./-	17:46170855	17:45598501	splice-site	intergenic	deletion	upstream	downstream	1	2	1	470	90	high	.	.	duplicates(11)	AGAGATTTACAGCTAGTGGCATAGCCAACTTGAGGTGCAGTGAACAGGCATTTGATTCAGATGTCACTGACAGTAGTTCAGGAGGGGAGTCTGATATTGAAGAGGAAGAACTGACCAGAGCTGATCCCGAGCAGCGTCATGTACCCCT|AATTCTCAATCGCAATCCTCTGACAACTGTTGAAGATCCGTATCTCTTTAAATTACTGGCATTAAAATATCt___AGACGTGGGAACAACGCAAGTCCCACTTACAACACTTAAGAACATTCTCATG	out-of-frame	RFTASGIANLRCSEQAFDSDVTDSSSGGESDIEEEELTRADPEQRHVPl|ilnrnplttvedpylfkllalkyldvgttqvplttlknil	.
+HELLPAR	C12orf48	+/+	+/+	12:102205152	12:102148230	exon	splice-site	duplication	downstream	upstream	0	1	3	51	289	high	.	.	duplicates(27)	CTCTTGTTTTGCTCCAAGAATTGGAGTGG|CACAGTGGAGAATTTACAGTCTCTCTCAGTGATGTTTTATTGACATGGAAATACTTGCTCCATGAGAAATTG...TGGACGTGACTGACCATTATGAGGACGTTAGGAAGATTTATGATGATTTCTTGAAGAACAGTAATATGTTAGATCTGATTGATGTTTATCAAAAATGTAGG	.	.	.
+CDH12P3(63905),RP11-1415C14.4(377)	GUSBP3	./-	-/-	5:70196878	5:69642289	intergenic	splice-site	deletion	upstream	downstream	1	2	0	20	76	high	.	.	duplicates(9)	CCAAGGATGAAGGAAAAACTGGACCTCATTATGGATTTACTTTTGGGATACACTCATTATTCCAGAGGAGGGTAAAAGGCTGAGAAGCTTAAG|GATGGTGATTGCTCACACCAAAGCCTTGGACCCCTCCCAGCCTGTGACCTTTGTGACCAACTCCACCTACGCAGCAGACAAGGGGG	.	.	.
+RP11-524N5.1	CTC-436K13.2(38552),RP11-524N5.1(3318)	-/+	./+	5:158359646	5:158317365	intron	intergenic	duplication	downstream	upstream	27	14	3	104	470	medium	.	.	duplicates(134)	CGAGAAGGGAGGCAGATCAG___GTTTTTCCTTTTACCAGTGTGGACTAGAGGAAAAGTGATCGACAAAGAGGCAAGGAGAGAATGACAAACAGGAG___...CTTACATTCTAGCCAGGAAAAATGGATAGAAATAAGAAAATGAATACATGAATGATCTCAGAGAAGG___GTATATAGTATTGAGCAATGATAGCATTTTGCTTAAGGAAACTGACTGCATACAGTTGTTCCCAAG|ATGAGAAAACTGAGTCCCAAGGGGTTAAGTGATTTGCTCAAGGCAATGGCAGAGGAGGAACCAGGACCCAATTTTCTCAACTGTGAGCCAAG___GTTTTTCCTTTTACCAGTGTGGACTAGAGGAAAAGTGATCGACAAAGAGGCAAGGAGAGAATGACAAACAGGAG	.	.	.
+RP11-392E22.9	ANKRD18A	-/-	-/-	9:38575476	9:38588663	splice-site	splice-site	duplication	upstream	downstream	14	10	1	208	980	medium	.	.	duplicates(84),small_insert_size(3)	GGAAGCCTTTGCAGGAGCAGTGAAAGCTAACAATTCCATGTCAAAAAAATTAATGAA___ATCGGATAAGAAAATAGCAGTGATCAGCACCAAGCTCTTTACGGAGAAACAGCGGATGAAATATTTTCTCAGCACTCTTCCTACAAGGCCAGAACCAGAGTTACCTTGTGTTGAAAATCTTAATAGTATAGAACTCAACAGAAAATATATTCCCAAAACGGCCATAAGAATTCCTACTTCAAACCCACAGACTTCAAATAACTGCAAGAACTTCTTGACTGAG|CCTGAAGAAAAACATGAAGAATTCAGAAAACTTTTTGAATTAATATCATTACTGAACTATACTGCGGACCAAATAAGAAAGAAAAATCGTGAATTAGAAGAAGAGGCAACTGG___ATATAAGAAATGCCTAGAAATGACAATAAATATGTTAAATGCATTTGCAAATGAGGACTTCAGTTGCCATGGAGACTTAAATACAGACC	.	.	.
+RP11-392E22.9	ANKRD18A	-/-	-/-	9:38575476	9:38586312	splice-site	splice-site	duplication	upstream	downstream	6	12	0	208	262	medium	.	.	duplicates(40)	AGCAGTGATCAGCACCAAGCTCTTTACGGAGAAACAGCGGATGAAATATTTTCTCAGCACTCTTCCTACAAGGCCAGAACCAGAGTTACCTTGTGTTGAAAATCTTAATAGTATAGAACTCAACAGAAAATATATTCCCAAAACGGCCATAAGAATTCCTACTTCAAACCCACAGACTTCAAATAACTGCAAGAACTTCTTGACTGAG|ATATAAGAAATGCCTAGAAATGACAATAAATATGTTAAATGCATTTGCAAATGAGGACTTCAGTTGCCATGGAGACTTAAATACAGACC	out-of-frame	AVISTKLFTEKQRMKYFLSTLPTRPEPELPCVENLNSIELNRKYIPKTAIRIPTSNPQTSNNCKNFLTE|i*	.
+RP11-392E22.9	ANKRD18A	-/-	-/-	9:38575476	9:38578148	splice-site	splice-site	duplication	upstream	downstream	0	1	0	208	212	low	.	.	duplicates(5)	CAAATAACTGCAAGAACTTCTTGACTGAG|TTTAATGATCTTGTGGCCGAGAAGGAAGCTGTGTCTTCAGAATGTGTCAATTTGGCCAAAGACAATGAAGTTCTTCATCAGGAGTTATTATCTATGAGAAATGTACAAGAG	in-frame	NNCKNFLTE|FNDLVAEKEAVSSECVNLAKDNEVLHQELLSMRNVQ	.
+RNU6-3P	SNORA71B	-/-	-/-	X:141118029	20:38425322	splice-site	exon	translocation	upstream	downstream	25	0	0	866	3	medium	.	.	duplicates(69)	AGCACATATACTAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCAAATTCGTGAAGCGTTCCATATTTTTT|CGAAAGTGATCGTGGGCTGCCTTTGCCCTGGTCATTGATAGTGCAGGGAGAGGAATCAATGAAAGCGCTTCCCCGTGTTTGAAGG	.	.	.
+RNU6-3P	SNORA71D	-/-	-/-	X:141118029	20:38433989	splice-site	exon	translocation	upstream	downstream	19	0	0	866	13	medium	.	.	duplicates(49)	CAGCACATATACTAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCAAATTCGTGAAGCGTTCCATATTTTTT|CGAAAGTGATCGTGGGCTGCCTGTGCCCTGGTCATTGATAGTGCAGGGAGAG	.	.	.
+RNU6-9	SNORA20	+/+	-/-	19:893592	6:159780371	splice-site	exon	translocation	downstream	downstream	17	0	0	322	62	medium	.	.	duplicates(62)	CTTCGGCAGCACATATACTAAAATTGGAACGATACAGAGAAGATTAGCATGGCCCCTGCGCAAGGATGACACGCAAATTCGTGAAGCGTTCCATATTTTTTT|ATTTGCTGCTTGTAGTCTCACAGTGATACGAGCAGTTATACGCATGGGATAAAATAACATTGGGC	.	.	.
+OR10Z1	CTD-2341M24.1(92506),RP11-26L16.1(110092)	+/-	./-	1:158611080	14:86222284	3'UTR	intergenic	translocation	upstream	downstream	0	2	1	1155	10	medium	.	.	duplicates(9)	CGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCTTGTGTTTGTGTGCATATTACATTTATTGTAGGATCT?AAAAAATCTCAAG|TTTGGAAGGATGAGAAGGC...AAGACTAAGTAAGAACATGTATACAGGAAGCAATAAAGTATTGACAAGCCAATAATCATGACTGAGGGACAAATGAGATAACCCAAAGTCCAGCTCACATC	.	.	.
+ANKRD18A	ANKRD18A	-/-	-/-	9:38575476	9:38588663	splice-site	splice-site	duplication/non-canonical_splicing	upstream	downstream	14	10	1	208	980	low	.	.	duplicates(84)	GGAAGCCTTTGCAGGAGCAGTGAAAGCTAACAATTCCATGTCAAAAAAATTAATGAA___ATCGGATAAGAAAATAGCAGTGATCAGCACCAAGCTCTTTACGGAGAAACAGCGGATGAAATATTTTCTCAGCACTCTTCCTACAAGGCCAGAACCAGAGTTACCTTGTGTTGAAAATCTTAATAGTATAGAACTCAACAGAAAATATATTCCCAAAACGGCCATAAGAATTCCTACTTCAAACCCACAGACTTCAAATAACTGCAAGAACTTCTTGACTGAG|CCTGAAGAAAAACATGAAGAATTCAGAAAACTTTTTGAATTAATATCATTACTGAACTATACTGCGGACCAAATAAGAAAGAAAAATCGTGAATTAGAAGAAGAGGCAACTGG___ATATAAGAAATGCCTAGAAATGACAATAAATATGTTAAATGCATTTGCAAATGAGGACTTCAGTTGCCATGGAGACTTAAATACAGACC	in-frame	EAFAGAVKANNSMSKKLMKSDKKIAVISTKLFTEKQRMKYFLSTLPTRPEPELPCVENLNSIELNRKYIPKTAIRIPTSNPQTSNNCKNFLTE|PEEKHEEFRKLFELISLLNYTADQIRKKNRELEEEATGYKKCLEMTINMLNAFANEDFSCHGDLNTD	.
+WASHC2A	GLCCI1	+/+	+/+	10:50110138	7:8086902	CDS	3'UTR	translocation	downstream	upstream	0	0	4	74	402	low	.	.	duplicates(3)	GCAAAAGCCTCCGAGCTCTCCAAAAAGAAAGCATCTGCCCTGTTGTTCAGCAGTGATGAGGAG___GACCAGTGGAATATTCCTGCTTCACAGACCCACTTAGC...|...ATGGAAAATACTGTAATTCAGGATTATGTTTACAATTGATCCAGGTGTTTGTTTCTAACTTCTGTAATACATACAATGCAAAAAAAAAAAAAAAAAAATGGC	.	.	.
+COX7C	RP11-477B16.2(107232),RP11-74A12.2(91794)	+/+	./+	5:86620690	13:94868247	3'UTR	intergenic	translocation	downstream	upstream	0	0	4	5370	13	low	.	.	duplicates(2)	GCATTTGCTACACCCTTCCTTGTAGTAAGACACCAACTGCTTAAAACATAAGGATGTTTCAGTTCCTCCATTTAACAG___ATATGAAGAGCATTTTAAGAGGT...|...AACAAGTGCTGACAAGGATGTGTAGAAATTGAAACCCTCATGCATTCCTGGTGGGAATGCAAAATGGTGCATTCACTGCAAACCAAAAAAAAAAAAAAAGTTT	.	.	.
+CMTM6	AC093113.1(165002),RP11-638D14.1(79189)	-/-	./+	3:32483823	2:146754312	3'UTR	intergenic	translocation	upstream	upstream	0	0	4	4080	17	low	.	.	.	CCTGCATTGTGGTGCCTGAGCCCTGGCAGAAGCTCTTGTAAAATTTGTTAATTGTTTAAACCACTTCTTTTGGAGAGCAAGGGGAAGGTCAAGAAGGCAGT...|...ATgGAGAAGTAGTGGGAGAAAAAAAGTTCAAATGATAGAAGTTGGCAAATGCCAATCTAAGGATTTCAAATTTATCTTTTTTTTTTTTTTTTTTTTTT	.	.	.
+PYURF	KDM6A(32878),CXorf36(2894)	-/-	./+	4:88521038	X:45145480	3'UTR	intergenic	translocation	upstream	upstream	0	0	3	186	8	low	.	.	duplicates(1)	CGAATGTGATATAAAACCACATAATCAAATAGAAACTTCATGTACTTACAAAAACTGAGTTTGTAAAATTACCTTCATTTCTTTGACATTAAATGCTTATA...|...TACAAAAAAATTTTAAAAAATTAGCCAGGCGTGGTGCTACCACTGCACTCCAGCCTGGACAAAGCCCTGTCTCcAAAAAAAAAAAAAAAAAAAAGAGTG	.	.	.
+AC006369.3(15150),AC010878.3(54719)	CDC42EP3	./-	-/-	2:37762196	2:37719944	intergenic	splice-site	deletion/read-through	upstream	downstream	1	2	0	13	14	low	.	.	duplicates(10)	CACCGTGATCCTTAACCAGAAGTCATTTTGTGCTCTTTCAACTGCATTCTGCAAATTTGTATTCCACAGTGCAGGAAAGATC|GCAGAAACGAGTAATGTGAGAGCCTGCAATTGTAATCTTCATAAAGTATATCACATACCGTTCAAAAACATCAAGTGGCATGTTAAATAAGCTTTTGGAGAATAAGTTGAGCGTGAC	.	.	.
+SMARCA5	RP1-241P17.1(12064),RP11-761E20.1(62157)	+/+	./+	4:143546801	X:115855114	CDS	intergenic	translocation	downstream	upstream	0	0	3	5123	1	low	.	.	.	AACAGCTTAAAATTGATGAAGCTGAATCCCTTAATGATGAAGAGTTAGAGGAAAAAGAGAAGCTTCTAACACAG___GGATTTACCAATTGGAATAAGAGAGA...|...TTcTGAGtgTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAAAGAGAGAGAGAAAGAGAAAGAGACAGAGAAAAGAAACTATGTTG	.	.	.
+CKAP4	SGCB	-/-	-/-	12:106238010	4:52031703	3'UTR	intron	translocation	upstream	downstream	0	3	0	207	8	low	.	.	.	CTGAGCTGTATTGTTCTTTAATGGCTGTCTTGCCCTTCCAAAAAAAATTGAAAA|CTCCTAAACCATGGAAAAAATAGAAACTCATGGAATAGAGAAAATGC...TCAATGAAACAAGAATAACATGCCATTTAAAAGGCACAAGCCAGGCACAGTGGCTCATGCCTGATAAAGTGAGACCCTGTCTCTACCAAAAAAAAAAAAAAT	.	.	.
+CTD-2013M15.1(4379018),EMB(121204)	EMB	./-	-/-	5:50274988	5:50410965	intergenic	splice-site	duplication	upstream	downstream	1	2	0	83	16723	low	.	.	duplicates(6)	TACTAAAGGCTTACTATTGGTAAGACCTATAGAACAGTGCGTTTGGAAGCGGACTCACCcAGCATTCTATTTAATCACTCTGTAGAAGCTAAG|GTTCACCATCATTAATAGCAAACAAATGGGAAGTTATTCTTGTTTCTTTCGAGAGGAAAAGGAACAAAGGGGAACATTTAATTTCAAAG___TCCCTGAACTTCATG	.	.	.
+KIAA1586(4626),ZNF451(26979)	KIAA1586	./+	+/+	6:57059865	6:57052686	intergenic	splice-site	duplication	downstream	upstream	1	0	0	16	373	low	.	.	duplicates(3)	TAAACAGACTCAAAGAAG___GCATTTTAAACTGAATAGGTCCAAAGCTGAATTTATTCATCTCTCATCATATCTGTTTTGAAAAATGGCCCAACCATTTCCCTTGATGCTCAAACTAGAAAG|ATTCTGTTTCCTAAAATGCCAAAACGACAG	.	.	.

tests/test_Readers.py

@@ -38,6 +38,7 @@
 from fuma.Readers import ReadSOAPFuseTranscripts
 from fuma.Readers import ReadEricScriptResultsTotal
 from fuma.Readers import ReadJaffaResults
+from fuma.Readers import ReadArribaResults
 
 
 class TestReadChimeraScanAbsoluteBEDPE(unittest.TestCase):
@@ -225,41 +226,19 @@ def test_01(self):
 		self.assertEqual(fusions[1].right_strand , STRAND_FORWARD )
 
 
-class TestReadJaffaResults(unittest.TestCase):
+class TestReadArribaResults(unittest.TestCase):
 	def test_01(self):
-		""" Tests whether files of input format from SOAPFusion can
-		be parsed
-		
-		Fusion (from dataset 'test'): chr20:46365686(?)<->chr20:47538547(?)
-		Fusion (from dataset 'test'): chr17:59445688(?)<->chr20:49411710(?)
-		Fusion (from dataset 'test'): chr17:37793484(?)<->chr20:53259997(?)
-		Fusion (from dataset 'test'): chr17:57917129(?)<->chr17:57992064(?)
-		"""
+		fusions = ReadArribaResults("tests/data/test_Readers.TestReadARRIBAfile.test_01.txt","test")
+		self.assertEqual(len(fusions) , 25)
 
-		fusions = ReadJaffaResults("tests/data/test_Readers.TestReadJaffaResults.test_01.txt","test")
-
-		self.assertEqual(len(fusions) , 4)
-
-		self.assertEqual(fusions[0].get_left_chromosome(True) , 'chr20')
-		self.assertEqual(fusions[0].get_right_chromosome(True) , 'chr20')
-		self.assertEqual(fusions[0].left_break_position , 46365686)
-		self.assertEqual(fusions[0].right_break_position , 47538547)
+		self.assertEqual(fusions[0].get_left_chromosome(True) , 'chr10')
+		self.assertEqual(fusions[0].get_right_chromosome(True) , 'chr11')
+		self.assertEqual(fusions[0].left_break_position , 21651673)
+		self.assertEqual(fusions[0].right_break_position , 118482495)
 		self.assertEqual(fusions[0].left_strand , None)
 		self.assertEqual(fusions[0].right_strand , None)
 		self.assertEqual(fusions[0].acceptor_donor_direction , None)
-
-		#dataset 'test'): chr17:59445688(?)<-chr20:49411710(?)
-		self.assertEqual(fusions[1].get_left_chromosome(True) , 'chr17')
-		self.assertEqual(fusions[1].get_right_chromosome(True) , 'chr20')
-		self.assertEqual(fusions[1].left_break_position , 59445688)
-		self.assertEqual(fusions[1].right_break_position , 49411710)
-		self.assertEqual(fusions[1].left_strand , None)
-		self.assertEqual(fusions[1].right_strand , None)
-		self.assertEqual(fusions[0].acceptor_donor_direction , None)
-
-		# @todo
-		# comparing 2x test read jaffa results should give a exception:
-		# raise Exception("A fusion gene without an annotated acceptor-donor direction was used for acceptor-donor-order-specific-matching.\n\n"+fusion_1.__str__()+"\n"+fusion_2.__str__())
+
 
 
 def main():