Mercurial > repos > iuc > variant_analyzer

comparison mut2read.py @ 1:3556001ff2db draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
author iuc
date Wed, 04 Dec 2019 16:21:17 -0500
parents 8d29173d49a9
children 3f1dbd2c59bf
comparison
equal deleted inserted replaced
0:8d29173d49a9 1:3556001ff2db
61 if os.path.isfile(file3) is False: 61 if os.path.isfile(file3) is False:
62 sys.exit("Error: Could not find '{}'".format(file3)) 62 sys.exit("Error: Could not find '{}'".format(file3))
63 63
64 # read mut file 64 # read mut file
65 with open(file1, 'r') as mut: 65 with open(file1, 'r') as mut:
66 mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype='string') 66 mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str)
67 67
68 # read dcs bam file 68 # read dcs bam file
69 # pysam.index(file2) 69 # pysam.index(file2)
70 bam = pysam.AlignmentFile(file2, "rb") 70 bam = pysam.AlignmentFile(file2, "rb")
71 71
84 ref = mut_array[m, 9] 84 ref = mut_array[m, 9]
85 alt = mut_array[m, 10] 85 alt = mut_array[m, 10]
86 86
87 dcs_len = [] 87 dcs_len = []
88 88
89 for pileupcolumn in bam.pileup(chrom.tobytes(), stop_pos - 2, stop_pos, max_depth=100000000): 89 for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=100000000):
90 90
91 if pileupcolumn.reference_pos == stop_pos - 1: 91 if pileupcolumn.reference_pos == stop_pos - 1:
92 count_alt = 0 92 count_alt = 0
93 count_ref = 0 93 count_ref = 0
94 count_indel = 0 94 count_indel = 0