Ejemplo n.º 1
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 def test_build_a_sample(self):
     # tgt is C_SYNTHP53_22640_500_05_3_1-1-1.fastq
     source_read = parse_sam_file(
         "data/experimental_results/TP53/alignments/C_model_GMAPno40_NM_000546.5.sam"
     )
Ejemplo n.º 2
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	def test_parse_cigar_string(self):
		starting_file = data_dir + "/alignments/C_model_GMAPno40_NM_000546.5.sam"
		reads = parse_sam_file(starting_file)
		for i,r in enumerate(reads.CIGAR):
			print i,parse_cigar_string(r)
Ejemplo n.º 3
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	def test_build_a_sample(self):
		# tgt is C_SYNTHP53_22640_500_05_3_1-1-1.fastq
		source_read = parse_sam_file("data/experimental_results/TP53/alignments/C_model_GMAPno40_NM_000546.5.sam")
Ejemplo n.º 4
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 def test_parse_sam_file_original(self):
     starting_file = data_dir + "/alignments/C_model_GMAPno40_NM_000546.5.sam"
     reads = parse_sam_file(starting_file)
     # print reads
     print reads.sample(10)
Ejemplo n.º 5
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	def test_parse_sam_file(self):
		starting_file = data_dir + "/alignments/C_model_GMAPno40_NM_000546.5.sam"
		reads = parse_sam_file(starting_file)
		# print reads
		print reads.sample(10)
Ejemplo n.º 6
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 def test_parse_cigar_string(self):
     starting_file = data_dir + "/alignments/C_model_GMAPno40_NM_000546.5.sam"
     reads = parse_sam_file(starting_file)
     for i, r in enumerate(reads.CIGAR):
         print i, parse_cigar_string(r)