Mercurial > repos > artbio > lumpy_sv

comparison pairend_distro.py @ 5:6ae3a402b9af draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit e1bfc70a74f12ef8182d9afa0b3ab69d620fb3a8"
author artbio
date Sun, 24 May 2020 18:48:46 -0400
parents 093bb151a0a8
children
comparison
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4:093bb151a0a8 5:6ae3a402b9af
79 79
80 # warn if very few elements in distribution 80 # warn if very few elements in distribution
81 min_elements = 1000 81 min_elements = 1000
82 if len(L) < min_elements: 82 if len(L) < min_elements:
83 sys.stderr.write("Warning: only %s elements in distribution (min: %s)\n" % 83 sys.stderr.write("Warning: only %s elements in distribution (min: %s)\n" %
84 (len(L), min_elements)) 84 (str(len(L)), str(min_elements)))
85 mean = "NA" 85 mean = "NA"
86 stdev = "NA" 86 stdev = "NA"
87 87
88 else: 88 else:
89 # Remove outliers 89 # Remove outliers
92 med, umad = unscaled_upper_mad(L) 92 med, umad = unscaled_upper_mad(L)
93 upper_cutoff = med + options.mads * umad 93 upper_cutoff = med + options.mads * umad
94 L = L[L < upper_cutoff] 94 L = L[L < upper_cutoff]
95 new_len = len(L) 95 new_len = len(L)
96 removed = c - new_len 96 removed = c - new_len
97 sys.stderr.write("Removed %d outliers with isize >= %d\n" % 97 sys.stderr.write("Removed %s outliers with isize >= %s\n" %
98 (removed, upper_cutoff)) 98 (str(removed), str(upper_cutoff)))
99 c = new_len 99 c = new_len
100 100
101 mean = np.mean(L) 101 mean = np.mean(L)
102 stdev = np.std(L) 102 stdev = np.std(L)
103 103