Mercurial > repos > iuc > variant_analyzer

comparison mut2sscs.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
54 if os.path.isfile(file2) is False: 54 if os.path.isfile(file2) is False:
55 sys.exit("Error: Could not find '{}'".format(file2)) 55 sys.exit("Error: Could not find '{}'".format(file2))
56 56
57 # 1. read mut file 57 # 1. read mut file
58 with open(file1, 'r') as mut: 58 with open(file1, 'r') as mut:
59 mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype='string') 59 mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str)
60 60
61 # 2 read SSCS bam file 61 # 2 read SSCS bam file
62 # pysam.index(file2) 62 # pysam.index(file2)
63 bam = pysam.AlignmentFile(file2, "rb") 63 bam = pysam.AlignmentFile(file2, "rb")
64 64
74 stop_pos = mut_array[m, 2].astype(int) 74 stop_pos = mut_array[m, 2].astype(int)
75 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) 75 chrom_stop_pos = str(chrom) + "#" + str(stop_pos)
76 ref = mut_array[m, 9] 76 ref = mut_array[m, 9]
77 alt = mut_array[m, 10] 77 alt = mut_array[m, 10]
78 78
79 for pileupcolumn in bam.pileup(chrom.tobytes(), stop_pos - 2, stop_pos, max_depth=1000000000): 79 for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=1000000000):
80 if pileupcolumn.reference_pos == stop_pos - 1: 80 if pileupcolumn.reference_pos == stop_pos - 1:
81 count_alt = 0 81 count_alt = 0
82 count_ref = 0 82 count_ref = 0
83 count_indel = 0 83 count_indel = 0
84 print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups), 84 print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups),