Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_download.py @ 4:847b0f43c0e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:14:37 -0400
parents 85a23e2dd92b
children 3d9dd4b9fb09
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1 #!/usr/bin/env python
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2 import gzip
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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3 import json
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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4 import optparse
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5 import os
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6 import re
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7 import subprocess
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8 import sys
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9
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11 def stop_err(msg):
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12 sys.stderr.write(msg)
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13 sys.exit(1)
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14
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15
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16 def fetch_databases(jar_path, genome_list=None):
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17 snpDBs = dict()
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18 (snpEff_dir, snpEff_jar) = os.path.split(jar_path)
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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19 databases_path = 'databases.out'
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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20 databases_output = open(databases_path, 'w')
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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21 args = [ 'java', '-jar' ]
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22 args.append( snpEff_jar )
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23 args.append( 'databases' )
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24 # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" )
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25 # databases_output = open(databases_path)
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26 # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() )
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27 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() )
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28 return_code = proc.wait()
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29 if return_code:
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30 sys.exit( return_code )
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31 databases_output.close()
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32 try:
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33 fh = open(databases_path, 'r')
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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34 for i, line in enumerate(fh):
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35 fields = line.split('\t')
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36 if len(fields) >= 2:
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37 genome_version = fields[0].strip()
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38 if genome_list and genome_version not in genome_list:
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39 continue
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40 if genome_version.startswith("Genome") or genome_version.startswith("-"):
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41 continue
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42 description = fields[1].strip()
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43 snpDBs[genome_version] = description
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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44 except Exception as e:
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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45 stop_err( 'Error parsing %s %s\n' % (databases_path, str( e )) )
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46 else:
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47 fh.close()
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48 return snpDBs
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49
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51 def getOrganismNames(jar_path, genomes, organisms):
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52 genome_list = genomes.split(',')
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53 organism_list = organisms.split(',') if organisms else []
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54 if len(genome_list) != len(organism_list):
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55 descriptions = []
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56 snpDBdict = fetch_databases(jar_path, genome_list=genome_list)
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57 for genome in snpDBdict:
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58 descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome)
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59 return ','.join(descriptions)
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60 return organisms
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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61
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62
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63 def getSnpeffVersion(jar_path):
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64 snpeff_version = 'SnpEff ?.?'
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65 (snpEff_dir, snpEff_jar) = os.path.split(jar_path)
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66 stderr_path = 'snpeff.err'
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67 stderr_fh = open(stderr_path, 'w')
85a23e2dd92b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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68 args = [ 'java', '-jar' ]
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69 args.append( snpEff_jar )
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70 args.append( '-h' )
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71 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stderr=stderr_fh.fileno() )
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72 return_code = proc.wait()
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73 if return_code != 255:
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74 sys.exit( return_code )
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75 stderr_fh.close()
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76 fh = open(stderr_path, 'r')
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77 for line in fh:
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78 m = re.match('^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$', line)
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79 if m:
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80 snpeff_version = m.groups()[0] + m.groups()[1]
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81 break
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82 fh.close()
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83 return snpeff_version
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84
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85
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86 # Starting with SnpEff 4.1 the .bin files contain the SnpEff version:
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87 # Example - the first 3 line of GRCh37.75/snpEffectPredictor.bin (uncompressed):
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88 #
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89 # SnpEff 4.1
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90 # CHROMOSOME 2 1 0 179197 GL000219.1 false
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91 # CHROMOSOME 3 1 0 81347269 HSCHR17_1 false
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92 def getSnpeffVersionFromFile(path):
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93 snpeff_version = None
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94 try:
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95 fh = gzip.open(path, 'rb')
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96 buf = fh.read(100)
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97 lines = buf.splitlines()
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98 m = re.match('^(SnpEff)\s+(\d+\.\d+).*$', lines[0].strip())
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99 if m:
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100 snpeff_version = m.groups()[0] + m.groups()[1]
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101 fh.close()
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102 except Exception as e:
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103 stop_err( 'Error parsing SnpEff version from: %s %s\n' % (path, str( e )) )
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104 return snpeff_version
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105
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106
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107 # Download human database 'hg19'
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108 # java -jar snpEff.jar download -v hg19
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109 #
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110 # <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
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111 #
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112 # snpEffectPredictor.bin
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113 # regulation_HeLa-S3.bin
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114 # regulation_pattern = 'regulation_(.+).bin'
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115 def download_database(data_manager_dict, target_directory, jar_path, config, genome_version, organism):
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116 # get data_dir from config
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117 # ---
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118 # Databases are stored here
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119 # E.g.: Information for 'hg19' is stored in data_dir/hg19/
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120 #
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121 # Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
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122 # ---
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123 # data_dir = ~/snpEff/data/
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124 data_dir = target_directory
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125 (snpEff_dir, snpEff_jar) = os.path.split(jar_path)
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126 args = [ 'java', '-jar' ]
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127 args.append( jar_path )
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128 args.append( 'download' )
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129 args.append( '-c' )
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130 args.append( config )
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131 args.append( '-dataDir' )
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132 args.append( data_dir )
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133 args.append( '-v' )
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134 args.append( genome_version )
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135 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir )
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136 return_code = proc.wait()
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137 if return_code:
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138 sys.exit( return_code )
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139 # search data_dir/genome_version for files
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140 regulation_pattern = 'regulation_(.+).bin'
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141 # annotation files that are included in snpEff by a flag
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142 annotations_dict = {'nextProt.bin': '-nextprot', 'motif.bin': '-motif'}
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143 genome_path = os.path.join(data_dir, genome_version)
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144 snpeff_version = getSnpeffVersion(jar_path)
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145 key = snpeff_version + '_' + genome_version
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146 if os.path.isdir(genome_path):
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147 for root, dirs, files in os.walk(genome_path):
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148 for fname in files:
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149 if fname.startswith('snpEffectPredictor'):
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150 # if snpEffectPredictor.bin download succeeded
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151 name = genome_version + (' : ' + organism if organism else '')
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152 # version = getSnpeffVersionFromFile(os.path.join(root,fname))
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153 data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
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154 _add_data_table_entry( data_manager_dict, 'snpeffv_genomedb', data_table_entry )
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155 else:
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156 m = re.match(regulation_pattern, fname)
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157 if m:
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158 name = m.groups()[0]
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159 data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
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160 _add_data_table_entry( data_manager_dict, 'snpeffv_regulationdb', data_table_entry )
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161 elif fname in annotations_dict:
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162 value = annotations_dict[fname]
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163 name = value.lstrip('-')
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164 data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=value, name=name)
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165 _add_data_table_entry( data_manager_dict, 'snpeffv_annotations', data_table_entry )
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166 return data_manager_dict
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167
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168
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169 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
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170 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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171 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
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172 data_manager_dict['data_tables'][data_table].append( data_table_entry )
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173 return data_manager_dict
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174
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175
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176 def main():
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177 # Parse Command Line
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178 parser = optparse.OptionParser()
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179 parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' )
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180 parser.add_option( '-c', '--config', dest='config', action='store', type="string", default=None, help='snpEff.config path' )
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181 parser.add_option( '-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version' )
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182 parser.add_option( '-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name' )
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183 (options, args) = parser.parse_args()
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184
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185 filename = args[0]
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186
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187 params = json.loads( open( filename ).read() )
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188 target_directory = params[ 'output_data' ][0]['extra_files_path']
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189 os.mkdir( target_directory )
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190 data_manager_dict = {}
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191
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192 # Create SnpEff Reference Data
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193 for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.jar_path, options.genome_version, options.organism).split(',')):
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194 download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism )
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195
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196 # save info to json file
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197 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
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198
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199
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200 if __name__ == "__main__":
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201 main()