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annotate pairend_distro.py @ 6:48e97429a749 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit 37c0f0938a5cad74c954a89827a6a08bbbb81cb0
author artbio
date Mon, 08 Jul 2024 22:23:10 +0000
parents 6ae3a402b9af
children
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796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
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1 #!/usr/bin/env python
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
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2 # (c) 2012 - Ryan M. Layer
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3 # Hall Laboratory
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4 # Quinlan Laboratory
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5 # Department of Computer Science
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6 # Department of Biochemistry and Molecular Genetics
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7 # Department of Public Health Sciences and Center for Public Health Genomics,
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8 # University of Virginia
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9 # rl6sf@virginia.edu
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11 import sys
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12 from optparse import OptionParser
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13
0
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14 import numpy as np
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16 # some constants for sam/bam field ids
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17 SAM_FLAG = 1
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18 SAM_REFNAME = 2
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19 SAM_MATE_REFNAME = 6
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20 SAM_ISIZE = 8
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22 parser = OptionParser()
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23 parser.add_option("-r", "--read_length", type="int", dest="read_length",
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24 help="Read length")
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25 parser.add_option("-X", dest="X", type="int",
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26 help="Number of stdevs from mean to extend")
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27 parser.add_option("-N", dest="N", type="int", help="Number to sample")
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28 parser.add_option("-o", dest="output_file", help="Output file")
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29 parser.add_option("-m", dest="mads", type="int", default=10,
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30 help='''Outlier cutoff in # of median absolute deviations
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31 (unscaled, upper only)''')
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34 def unscaled_upper_mad(xs):
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35 """Return a tuple consisting of the median of xs followed by the
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36 unscaled median absolute deviation of the values in xs that lie
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37 above the median.
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38 """
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39 med = np.median(xs)
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40 return med, np.median(xs[xs > med] - med)
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43 (options, args) = parser.parse_args()
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45 if not options.read_length:
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46 parser.error('Read length not given')
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47
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48 if not options.X:
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49 parser.error('X not given')
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50
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51 if not options.N:
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52 parser.error('N not given')
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53
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54 if not options.output_file:
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55 parser.error('Output file not given')
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56
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57
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58 required = 97
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59 restricted = 3484
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60 flag_mask = required | restricted
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61
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62 L = []
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63 c = 0
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64
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65 for length in sys.stdin:
0
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66 if c >= options.N:
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67 break
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68
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69 A = length.rstrip().split('\t')
0
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70 flag = int(A[SAM_FLAG])
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71 refname = A[SAM_REFNAME]
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72 mate_refname = A[SAM_MATE_REFNAME]
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73 isize = int(A[SAM_ISIZE])
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74
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75 want = mate_refname == "=" and flag & flag_mask == required and isize >= 0
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76 if want:
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77 c += 1
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78 L.append(isize)
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79
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80 # warn if very few elements in distribution
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81 min_elements = 1000
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82 if len(L) < min_elements:
1
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83 sys.stderr.write("Warning: only %s elements in distribution (min: %s)\n" %
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84 (str(len(L)), str(min_elements)))
0
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85 mean = "NA"
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86 stdev = "NA"
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87
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88 else:
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89 # Remove outliers
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90 L = np.array(L)
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91 L.sort()
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92 med, umad = unscaled_upper_mad(L)
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93 upper_cutoff = med + options.mads * umad
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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94 L = L[L < upper_cutoff]
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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95 new_len = len(L)
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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96 removed = c - new_len
5
6ae3a402b9af "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit e1bfc70a74f12ef8182d9afa0b3ab69d620fb3a8"
artbio
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97 sys.stderr.write("Removed %s outliers with isize >= %s\n" %
6ae3a402b9af "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit e1bfc70a74f12ef8182d9afa0b3ab69d620fb3a8"
artbio
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98 (str(removed), str(upper_cutoff)))
0
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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99 c = new_len
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
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100
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
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101 mean = np.mean(L)
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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102 stdev = np.std(L)
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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103
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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104 start = options.read_length
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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105 end = int(mean + options.X*stdev)
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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106
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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107 H = [0] * (end - start + 1)
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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108 s = 0
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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109
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
parents:
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110 for x in L:
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
parents:
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111 if (x >= start) and (x <= end):
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
parents:
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112 j = int(x - start)
1
1ed8619a5611 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit 0b55a106b1f76e3cc3d89932fef2cc8d3eb24e4f
artbio
parents: 0
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113 H[j] = H[int(x - start)] + 1
0
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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114 s += 1
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
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115
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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116 f = open(options.output_file, 'w')
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
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117
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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118 for i in range(end - start):
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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119 o = str(i) + "\t" + str(float(H[i])/float(s)) + "\n"
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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120 f.write(o)
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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121 f.close()
796552c157de planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy-sv commit d06124e8a097f3f665b4955281f40fe811eaee64
artbio
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122 print('mean:' + str(mean) + '\tstdev:' + str(stdev))