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annotate create_features_from_gff3.py @ 0:b4a85d0c85b8 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:47:07 -0400
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 import argparse
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3 import logging
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4 import sys
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5 import time
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6
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7 from builtins import str
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9 from BCBio import GFF
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11 from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, featuresToFeatureSchema, retry
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12 logging.basicConfig(level=logging.INFO)
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13 log = logging.getLogger(__name__)
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16 if __name__ == '__main__':
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17 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
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18 WAAuth(parser)
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19 parser.add_argument('email', help='User Email')
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20 parser.add_argument('--source', help='URL where the input dataset can be found.')
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21 OrgOrGuess(parser)
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23 parser.add_argument('gff3', type=argparse.FileType('r'), help='GFF3 file')
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24 args = parser.parse_args()
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26 wa = WebApolloInstance(args.apollo, args.username, args.password)
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27 # User must have an account
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28 gx_user = AssertUser(wa.users.loadUsers(email=args.email))
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30 # Get organism
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31 org_cn = GuessOrg(args, wa)
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32 if isinstance(org_cn, list):
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33 org_cn = org_cn[0]
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34
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35 # TODO: Check user perms on org.
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36 org = wa.organisms.findOrganismByCn(org_cn)
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37
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38 bad_quals = ['date_creation', 'source', 'owner', 'date_last_modified', 'Name', 'ID']
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39
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40 sys.stdout.write('# ')
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41 sys.stdout.write('\t'.join(['Feature ID', 'Apollo ID', 'Success', 'Messages']))
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42 sys.stdout.write('\n')
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43 # print(wa.annotations.getFeatures())
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44 for rec in GFF.parse(args.gff3):
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45 wa.annotations.setSequence(rec.id, org['id'])
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46 for feature in rec.features:
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47 # We can only handle genes right now
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48 if feature.type not in ('gene', 'terminator'):
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49 continue
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50 # Convert the feature into a presentation that Apollo will accept
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51 featureData = featuresToFeatureSchema([feature])
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52 if 'children' in featureData[0] and any([child['type']['name'] == 'tRNA' for child in featureData[0]['children']]):
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53 # We're experiencing a (transient?) problem where gene_001 to
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54 # gene_025 will be rejected. Thus, hardcode to a known working
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55 # gene name and update later.
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56
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57 featureData[0]['name'] = 'tRNA_000'
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58 tRNA_sf = [child for child in feature.sub_features if child.type == 'tRNA'][0]
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59 tRNA_type = 'tRNA-' + tRNA_sf.qualifiers.get('Codon', ["Unk"])[0]
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60
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61 if 'Name' in feature.qualifiers:
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62 if feature.qualifiers['Name'][0].startswith('tRNA-'):
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63 tRNA_type = feature.qualifiers['Name'][0]
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64
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65 newfeature = wa.annotations.addFeature(featureData, trustme=True)
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66
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67 def func0():
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68 wa.annotations.setName(
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69 newfeature['features'][0]['uniquename'],
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70 tRNA_type,
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71 )
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72 retry(func0)
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73
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74 if args.source:
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75 gene_id = newfeature['features'][0]['parent_id']
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76
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77 def setSource():
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78 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]})
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79 retry(setSource)
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80
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81 sys.stdout.write('\t'.join([
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82 feature.id,
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83 newfeature['features'][0]['uniquename'],
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84 'success',
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85 ]))
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86 elif featureData[0]['type']['name'] == 'terminator':
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87 # We're experiencing a (transient?) problem where gene_001 to
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88 # gene_025 will be rejected. Thus, hardcode to a known working
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89 # gene name and update later.
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90 featureData[0]['name'] = 'terminator_000'
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91 newfeature = wa.annotations.addFeature(featureData, trustme=True)
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92
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93 def func0():
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94 wa.annotations.setName(
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95 newfeature['features'][0]['uniquename'],
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96 'terminator'
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97 )
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98
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99 retry(func0)
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100
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101 if args.source:
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102 gene_id = newfeature['features'][0]['parent_id']
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103
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104 def setSource():
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105 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]})
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106 retry(setSource)
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107
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108 sys.stdout.write('\t'.join([
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109 feature.id,
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110 newfeature['features'][0]['uniquename'],
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111 'success',
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112 ]))
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113 else:
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114 try:
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115 # We're experiencing a (transient?) problem where gene_001 to
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116 # gene_025 will be rejected. Thus, hardcode to a known working
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117 # gene name and update later.
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118 featureData[0]['name'] = 'gene_000'
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119 # Extract CDS feature from the feature data, this will be used
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120 # to set the CDS location correctly (apollo currently screwing
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121 # this up (2.0.6))
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122 CDS = featureData[0]['children'][0]['children']
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123 CDS = [x for x in CDS if x['type']['name'] == 'CDS'][0]['location']
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124 # Create the new feature
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125 newfeature = wa.annotations.addFeature(featureData, trustme=True)
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126 # Extract the UUIDs that apollo returns to us
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127 mrna_id = newfeature['features'][0]['uniquename']
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128 gene_id = newfeature['features'][0]['parent_id']
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129 # Sleep to give it time to actually persist the feature. Apollo
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130 # is terrible about writing + immediately reading back written
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131 # data.
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132 time.sleep(1)
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133 # Correct the translation start, but with strand specific log
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134 if CDS['strand'] == 1:
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135 wa.annotations.setTranslationStart(mrna_id, min(CDS['fmin'], CDS['fmax']))
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136 else:
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137 wa.annotations.setTranslationStart(mrna_id, max(CDS['fmin'], CDS['fmax']) - 1)
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138
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139 # Finally we set the name, this should be correct.
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140 time.sleep(0.5)
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141 wa.annotations.setName(mrna_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0])
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142 time.sleep(0.5)
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143
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144 def func():
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145 wa.annotations.setName(gene_id, feature.qualifiers.get('product', feature.qualifiers.get('Name', ["Unknown"]))[0])
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146 retry(func)
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147
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148 if args.source:
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149 gene_id = newfeature['features'][0]['parent_id']
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150
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151 def setSource():
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152 wa.annotations.addAttributes(gene_id, {'DatasetSource': [args.source]})
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153 retry(setSource)
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154 extra_attr = {}
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155 for (key, values) in feature.qualifiers.items():
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156 if key in bad_quals:
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157 continue
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158
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159 if key == 'Note':
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160 def func2():
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161 wa.annotations.addComments(gene_id, values)
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162 retry(func2)
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163 else:
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164 extra_attr[key] = values
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165
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166 def func3():
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167 wa.annotations.addAttributes(gene_id, extra_attr)
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168 retry(func3)
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169
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170 sys.stdout.write('\t'.join([
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171 feature.id,
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172 gene_id,
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173 'success',
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174 ]))
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175 except Exception as e:
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176 msg = str(e)
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177 if '\n' in msg:
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178 msg = msg[0:msg.index('\n')]
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179 sys.stdout.write('\t'.join([
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180 feature.id,
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181 '',
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182 'ERROR',
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183 msg
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184 ]))
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185 sys.stdout.write('\n')
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186 sys.stdout.flush()