Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_download.py @ 9:08d7998c3afb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
author iuc
date Wed, 12 Feb 2020 18:33:53 -0500
parents d107d20dc6bd
children c6fbc5421697
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1 #!/usr/bin/env python
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2 import json
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3 import optparse
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4 import os
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5 import re
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6 import subprocess
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7 import sys
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8
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9
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10 def stop_err(msg):
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11 sys.stderr.write(msg)
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12 sys.exit(1)
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13
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14
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15 def fetch_databases(genome_list=None):
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16 snpDBs = dict()
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17 databases_path = 'databases.out'
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18 databases_output = open(databases_path, 'w')
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19 args = ['snpEff', 'databases']
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20 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno())
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21 if return_code:
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22 sys.exit(return_code)
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23 databases_output.close()
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24 try:
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25 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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26 for i, line in enumerate(fh):
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27 fields = line.split('\t')
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28 if len(fields) >= 2:
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29 genome_version = fields[0].strip()
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30 if genome_list and genome_version not in genome_list:
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31 continue
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32 if genome_version.startswith("Genome") or genome_version.startswith("-"):
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33 continue
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34 description = fields[1].strip()
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35 snpDBs[genome_version] = description
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36 except Exception as e:
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37 stop_err('Error parsing %s %s\n' % (databases_path, str(e)))
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38 else:
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39 fh.close()
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40 return snpDBs
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41
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43 def getOrganismNames(genomes, organisms):
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44 genome_list = genomes.split(',')
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45 organism_list = organisms.split(',') if organisms else []
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46 if len(genome_list) != len(organism_list):
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47 descriptions = []
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48 snpDBdict = fetch_databases(genome_list=genome_list)
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49 for genome in snpDBdict:
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50 descriptions.append(snpDBdict[genome] if genome in snpDBdict else genome)
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51 return ','.join(descriptions)
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52 return organisms
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55 def getSnpeffVersion():
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56 snpeff_version = 'SnpEff ?.?'
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57 stderr_path = 'snpeff.err'
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58 stderr_fh = open(stderr_path, 'w')
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59 args = ['snpEff', '-h']
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60 return_code = subprocess.call(args=args, shell=False, stderr=stderr_fh.fileno())
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61 if return_code != 255:
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62 sys.exit(return_code)
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63 stderr_fh.close()
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64 fh = open(stderr_path, 'r')
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65 for line in fh:
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66 m = re.match(r'^[Ss]npEff version (SnpEff)\s*(\d+\.\d+).*$', line)
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67 if m:
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68 snpeff_version = m.groups()[0] + m.groups()[1]
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69 break
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70 fh.close()
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71 return snpeff_version
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72
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74 # Download human database 'hg19'
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75 # java -jar snpEff.jar download -v hg19
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76 #
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77 # <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
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78 #
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79 # snpEffectPredictor.bin
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80 # regulation_HeLa-S3.bin
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81 # regulation_pattern = 'regulation_(.+).bin'
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82 def download_database(data_manager_dict, target_directory, genome_version, organism):
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83 # get data_dir from config
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84 # ---
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85 # Databases are stored here
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86 # E.g.: Information for 'hg19' is stored in data_dir/hg19/
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87 #
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88 # Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory
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89 data_dir = target_directory
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90 args = ['snpEff', 'download', '-dataDir', data_dir, '-v', genome_version]
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91 return_code = subprocess.call(args=args, shell=False)
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92 if return_code:
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93 sys.exit(return_code)
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94 # search data_dir/genome_version for files
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95 regulation_pattern = 'regulation_(.+).bin'
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96 genome_path = os.path.join(data_dir, genome_version)
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97 snpeff_version = getSnpeffVersion()
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98 key = snpeff_version + '_' + genome_version
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99 if os.path.isdir(genome_path):
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100 for root, dirs, files in os.walk(genome_path):
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101 for fname in files:
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102 if fname.startswith('snpEffectPredictor'):
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103 # if snpEffectPredictor.bin download succeeded
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104 name = genome_version + (' : ' + organism if organism else '')
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105 data_table_entry = dict(key=key, version=snpeff_version, value=genome_version, name=name, path=data_dir)
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106 _add_data_table_entry(data_manager_dict, 'snpeffv_genomedb', data_table_entry)
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107 else:
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108 m = re.match(regulation_pattern, fname)
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109 if m:
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110 name = m.groups()[0]
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111 data_table_entry = dict(key=key, version=snpeff_version, genome=genome_version, value=name, name=name)
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112 _add_data_table_entry(data_manager_dict, 'snpeffv_regulationdb', data_table_entry)
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113 return data_manager_dict
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116 def _add_data_table_entry(data_manager_dict, data_table, data_table_entry):
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117 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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118 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
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119 data_manager_dict['data_tables'][data_table].append(data_table_entry)
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120 return data_manager_dict
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122
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123 def main():
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124 parser = optparse.OptionParser()
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125 parser.add_option('-g', '--genome_version', dest='genome_version', action='store', type="string", default=None, help='genome_version')
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126 parser.add_option('-o', '--organism', dest='organism', action='store', type="string", default=None, help='organism name')
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127 (options, args) = parser.parse_args()
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128
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129 filename = args[0]
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130
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131 params = json.loads(open(filename).read())
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132 target_directory = params['output_data'][0]['extra_files_path']
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133 os.mkdir(target_directory)
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134 data_manager_dict = {}
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135
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136 # Create SnpEff Reference Data
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137 for genome_version, organism in zip(options.genome_version.split(','), getOrganismNames(options.genome_version, options.organism).split(',')):
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138 download_database(data_manager_dict, target_directory, genome_version, organism)
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139
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140 # save info to json file
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141 open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
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142
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143
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144 if __name__ == "__main__":
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145 main()