Mercurial > repos > jjohnson > snpeff

comparison data_manager/data_manager_snpEff_download.py @ 2:6ad9205c1307

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Update to SnpEff version 3.3
author Jim Johnson <jj@umn.edu>
date Fri, 04 Oct 2013 09:09:29 -0500
parents e1d9f6a0ad53
children 8952990fcab9
comparison
equal deleted inserted replaced
1:bea875f081e8 2:6ad9205c1307
20 20
21 """ 21 """
22 # Download human database 'hg19' 22 # Download human database 'hg19'
23 java -jar snpEff.jar download -v hg19 23 java -jar snpEff.jar download -v hg19
24 24
25 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command> 25 <command>java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
26 26
27 snpEffectPredictor.bin 27 snpEffectPredictor.bin
28 regulation_HeLa-S3.bin 28 regulation_HeLa-S3.bin
29 regulation_pattern = 'regulation_(.+).bin' 29 regulation_pattern = 'regulation_(.+).bin'
30 30
63 return_code = proc.wait() 63 return_code = proc.wait()
64 if return_code: 64 if return_code:
65 sys.exit( return_code ) 65 sys.exit( return_code )
66 ## search data_dir/genome_version for files 66 ## search data_dir/genome_version for files
67 regulation_pattern = 'regulation_(.+).bin' 67 regulation_pattern = 'regulation_(.+).bin'
68 # annotation files that are included in snpEff by a flag
69 annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'}
68 genome_path = os.path.join(data_dir,genome_version) 70 genome_path = os.path.join(data_dir,genome_version)
69 if os.path.isdir(genome_path): 71 if os.path.isdir(genome_path):
70 for root, dirs, files in os.walk(genome_path): 72 for root, dirs, files in os.walk(genome_path):
71 for fname in files: 73 for fname in files:
72 if fname.startswith('snpEffectPredictor'): 74 if fname.startswith('snpEffectPredictor'):
76 _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry ) 78 _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry )
77 else: 79 else:
78 m = re.match(regulation_pattern,fname) 80 m = re.match(regulation_pattern,fname)
79 if m: 81 if m:
80 name = m.groups()[0] 82 name = m.groups()[0]
81 data_table_entry = dict(value=genome_version, name=name) 83 data_table_entry = dict(genome=genome_version,value=name, name=name)
82 _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry ) 84 _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry )
85 elif fname in annotations_dict:
86 value = annotations_dict[fname]
87 name = value.lstrip('-')
88 data_table_entry = dict(genome=genome_version,value=value, name=name)
89 _add_data_table_entry( data_manager_dict, 'snpeff_annotations', data_table_entry )
83 return data_manager_dict 90 return data_manager_dict
84 91
85 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ): 92 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ):
86 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) 93 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
87 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) 94 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )