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annotate utils/correct-simple.py @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #!/usr/bin/env python
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2 from __future__ import division
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3 from __future__ import print_function
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4 from __future__ import absolute_import
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5 from __future__ import unicode_literals
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6 import sys
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7 import errno
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8 import logging
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9 import argparse
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10 import subprocess
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11
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12 ARG_DEFAULTS = {'nbarcodes':20, 'mapq_thres':25, 'log':sys.stderr, 'volume':logging.ERROR}
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13 DESCRIPTION = """"""
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14
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15
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16 def main(argv):
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17
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18 parser = argparse.ArgumentParser(description=DESCRIPTION)
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19 parser.set_defaults(**ARG_DEFAULTS)
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20
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21 parser.add_argument('nbarcodes', metavar='barcodes to try', type=int, nargs='?',
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22 help='')
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23 parser.add_argument('-s', '--summary', action='store_true',
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24 help='Only print the summary of how many families were rescued.')
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25 parser.add_argument('-m', '--mapq', type=int)
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26 parser.add_argument('-r', '--random', action='store_true')
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27 parser.add_argument('-l', '--log', type=argparse.FileType('w'),
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28 help='Print log messages to this file instead of to stderr. Warning: Will overwrite the file.')
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29 parser.add_argument('-q', '--quiet', dest='volume', action='store_const', const=logging.CRITICAL)
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30 parser.add_argument('-v', '--verbose', dest='volume', action='store_const', const=logging.INFO)
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31 parser.add_argument('-D', '--debug', dest='volume', action='store_const', const=logging.DEBUG)
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32
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33 args = parser.parse_args(argv[1:])
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34
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35 logging.basicConfig(stream=args.log, level=args.volume, format='%(message)s')
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36 tone_down_logger()
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37
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38 logging.info('Reading random barcodes from border-families.txt..')
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39 rand_arg = '--random-source=border-families.txt'
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40 if args.random:
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41 rand_arg = ''
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42 pipeline = 'cat border-families.txt | paste - - | shuf {} | head -n {}'.format(rand_arg,
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43 args.nbarcodes)
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44 commands = [cmd.split() for cmd in pipeline.split('|')]
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45 process = make_pipeline(*commands)
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46 families_by_barcode = {}
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47 for line_raw in process.stdout:
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48 line = line_raw.rstrip('\r\n')
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49 fields = line.split()
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50 family = {}
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51 count1, barcode, order1, count2, barcode2, order2 = fields
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52 assert barcode == barcode2, (barcode, barcode2)
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53 if order1 == 'ab':
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54 assert order2 == 'ba', barcode
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55 elif order1 == 'ba':
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56 assert order2 == 'ab', barcode
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57 count1, count2 = count2, count1
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58 else:
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59 fail(order1, order2, barcode)
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60 family['count1'] = int(count1)
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61 family['count2'] = int(count2)
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62 family['barcode'] = barcode
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63 families_by_barcode[barcode] = family
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64
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65 logging.info('Reading barcodes.fq to find read names..')
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66 hits = 0
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67 families_by_read_name = {}
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68 line_num = 0
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69 with open('barcodes.fq', 'rU') as barcodes_fq:
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70 for line in barcodes_fq:
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71 line_num += 1
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72 if line_num % 4 == 1:
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73 read_name = line[1:].rstrip('\r\n')
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74 elif line_num % 4 == 2:
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75 seq = line.rstrip('\r\n')
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76 family = families_by_barcode.get(seq)
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77 if family:
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78 hits += 1
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79 family['read_name'] = read_name
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80 families_by_read_name[read_name] = family
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81 logging.info('hits: {}'.format(hits))
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82
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83 logging.info('Reading barcodes.bam to find similar barcodes..')
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84 hits = 0
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85 neighbors_by_read_name = {}
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86 # samtools view -f 256 barcodes.bam | awk '$1 == '$read_name' && $5 > 25 {print $3}'
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87 process = subprocess.Popen(('samtools', 'view', '-f', '256', 'barcodes.bam'), stdout=subprocess.PIPE)
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88 for line in process.stdout:
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89 fields = line.split()
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90 mapq = int(fields[4])
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91 if mapq >= args.mapq_thres:
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92 read_name = fields[0]
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93 family = families_by_read_name.get(read_name)
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94 if family:
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95 hits += 1
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96 read_name2 = fields[2]
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97 neighbor = {'read_name':read_name2}
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98 neighbors = family.get('neighbors', [])
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99 neighbors.append(neighbor)
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100 family['neighbors'] = neighbors
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101 neighbors_by_read_name[read_name2] = neighbor
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102 logging.info('hits: {}'.format(hits))
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103
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104 logging.info('Reading barcodes.fq to find sequences of neighbors..')
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105 hits = 0
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106 line_num = 0
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107 neighbors_by_barcode = {}
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108 with open('barcodes.fq', 'rU') as barcodes_fq:
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109 for line in barcodes_fq:
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110 line_num += 1
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111 if line_num % 4 == 1:
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112 read_name = line[1:].rstrip('\r\n')
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113 neighbor = neighbors_by_read_name.get(read_name)
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114 if line_num % 4 == 2 and neighbor:
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115 seq = line.rstrip('\r\n')
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116 neighbor['barcode'] = seq
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117 neighbors_by_barcode[seq] = neighbor
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118 logging.info('hits: {}'.format(hits))
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119
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120 logging.info('Reading families.uniq.txt to get counts of neighbors..')
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121 hits = 0
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122 with open('families.uniq.txt', 'rU') as families_uniq:
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123 for line in families_uniq:
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124 fields = line.split()
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125 barcode = fields[1]
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126 neighbor = neighbors_by_barcode.get(barcode)
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127 if neighbor:
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128 hits += 1
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129 count = int(fields[0])
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130 order = fields[2].rstrip('\r\n')
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131 alpha = barcode[:len(seq)//2]
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132 beta = barcode[len(seq)//2:]
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133 swap = alpha >= beta
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134 if (not swap and order == 'ab') or (swap and order == 'ba'):
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135 neighbor['count1'] = count
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136 neighbor['count2'] = 0
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137 elif (not swap and order == 'ba') or (swap and order == 'ab'):
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138 neighbor['count1'] = 0
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139 neighbor['count2'] = count
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140 else:
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141 fail(order, barcode, swap)
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142 logging.info('hits: {}'.format(hits))
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143
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144 logging.info('Printing results..')
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145 total = 0
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146 passing = 0
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147 for family in families_by_barcode.values():
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148 total += 1
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149 count1 = family['count1']
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150 count2 = family['count2']
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151 if not args.summary:
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152 print('{barcode}\t{count1}\t{count2}\t{read_name}'.format(**family))
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153 neighbors = family.get('neighbors')
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154 if neighbors:
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155 for neighbor in neighbors:
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156 if not args.summary:
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157 print('{barcode}\t{count1}\t{count2}\t{read_name}'.format(**neighbor))
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158 count1 += neighbor['count1']
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159 count2 += neighbor['count2']
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160 if count1 >= 3 and count2 >= 3:
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161 if not args.summary:
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162 print('PASS!')
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163 passing += 1
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164 elif not args.summary:
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165 print('fail')
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166
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167 print('{} families rescued out of {} ({:0.2f}%)'.format(passing, total, 100*passing/total))
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168
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169
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170 def make_pipeline(*commands):
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171 processes = []
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172 for command in commands:
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173 if not processes:
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174 processes.append(subprocess.Popen(command, stdout=subprocess.PIPE))
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175 else:
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176 processes.append(subprocess.Popen(command, stdin=processes[-1].stdout, stdout=subprocess.PIPE))
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177 processes[0].stdout.close()
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178 return processes[-1]
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179
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180
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181 def tone_down_logger():
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182 """Change the logging level names from all-caps to capitalized lowercase.
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183 E.g. "WARNING" -> "Warning" (turn down the volume a bit in your log files)"""
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184 for level in (logging.CRITICAL, logging.ERROR, logging.WARNING, logging.INFO, logging.DEBUG):
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185 level_name = logging.getLevelName(level)
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186 logging.addLevelName(level, level_name.capitalize())
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187
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188
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189 def fail(message):
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190 sys.stderr.write(message+"\n")
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191 sys.exit(1)
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192
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193
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194 if __name__ == '__main__':
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195 try:
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196 sys.exit(main(sys.argv))
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197 except IOError as ioe:
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198 if ioe.errno != errno.EPIPE:
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199 raise