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" )
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)
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")
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)
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)
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)