Mercurial > repos > iuc > data_manager_snpeff
comparison data_manager/data_manager_snpEff_databases.py @ 5:3d9dd4b9fb09 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
author | iuc |
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date | Tue, 18 Apr 2017 09:40:03 -0400 |
parents | 847b0f43c0e5 |
children | 2107b4f40945 |
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4:847b0f43c0e5 | 5:3d9dd4b9fb09 |
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4 import os | 4 import os |
5 import subprocess | 5 import subprocess |
6 import sys | 6 import sys |
7 | 7 |
8 | 8 |
9 def stop_err(msg): | 9 def fetch_databases(data_manager_dict, target_directory): |
10 sys.stderr.write(msg) | |
11 sys.exit(1) | |
12 | |
13 | |
14 def fetch_databases(data_manager_dict, target_directory, jar_path): | |
15 (snpEff_dir, snpEff_jar) = os.path.split(jar_path) | |
16 if not os.path.exists(target_directory): | 10 if not os.path.exists(target_directory): |
17 os.makedirs(target_directory) | 11 os.makedirs(target_directory) |
18 databases_path = os.path.join( target_directory, 'databases.out' ) | 12 databases_path = os.path.join( target_directory, 'databases.out' ) |
19 databases_output = open(databases_path, 'w') | 13 databases_output = open(databases_path, 'w') |
20 args = [ 'java', '-jar' ] | 14 args = ['snpEff', 'databases'] |
21 args.append( snpEff_jar ) | 15 return_code = subprocess.call(args=args, shell=False, stdout=databases_output.fileno()) |
22 args.append( 'databases' ) | |
23 # tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-snpEff-stderr" ) | |
24 # databases_output = open(databases_path) | |
25 # proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno(), stderr=tmp_stderr.fileno() ) | |
26 proc = subprocess.Popen( args=args, shell=False, cwd=snpEff_dir, stdout=databases_output.fileno() ) | |
27 return_code = proc.wait() | |
28 if return_code: | 16 if return_code: |
29 sys.exit( return_code ) | 17 sys.exit( return_code ) |
30 databases_output.close() | 18 databases_output.close() |
31 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | 19 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) |
32 data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] ) | 20 data_manager_dict['data_tables']['snpeff4_databases'] = data_manager_dict['data_tables'].get( 'snpeff4_databases', [] ) |
33 data_table_entries = [] | 21 data_table_entries = [] |
34 try: | 22 with open(databases_path, 'r') as fh: |
35 fh = open(databases_path, 'r') | |
36 for i, line in enumerate(fh): | 23 for i, line in enumerate(fh): |
37 fields = line.split('\t') | 24 fields = line.split('\t') |
38 if len(fields) >= 2: | 25 if len(fields) >= 2: |
39 genome_version = fields[0].strip() | 26 genome_version = fields[0].strip() |
40 if genome_version.startswith("Genome") or genome_version.startswith("-"): | 27 if genome_version.startswith("Genome") or genome_version.startswith("-"): |
43 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): | 30 if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): |
44 continue | 31 continue |
45 description = fields[1].strip() + ' : ' + genome_version | 32 description = fields[1].strip() + ' : ' + genome_version |
46 data_table_entries.append(dict(value=genome_version, name=description)) | 33 data_table_entries.append(dict(value=genome_version, name=description)) |
47 data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries | 34 data_manager_dict['data_tables']['snpeff4_databases'] = data_table_entries |
48 except Exception as e: | |
49 stop_err( 'Error parsing %s %s\n' % (databases_path, str( e )) ) | |
50 else: | |
51 fh.close() | |
52 return data_manager_dict | 35 return data_manager_dict |
53 | 36 |
54 | 37 |
55 def main(): | 38 def main(): |
56 # Parse Command Line | |
57 parser = optparse.OptionParser() | 39 parser = optparse.OptionParser() |
58 parser.add_option( '-j', '--jar_path', dest='jar_path', action='store', type="string", default=None, help='snpEff.jar path' ) | |
59 (options, args) = parser.parse_args() | 40 (options, args) = parser.parse_args() |
60 | 41 |
61 filename = args[0] | 42 filename = args[0] |
62 | 43 |
63 params = json.loads( open( filename ).read() ) | 44 params = json.loads( open( filename ).read() ) |
64 target_directory = params[ 'output_data' ][0]['extra_files_path'] | 45 target_directory = params[ 'output_data' ][0]['extra_files_path'] |
65 os.mkdir( target_directory ) | 46 os.mkdir( target_directory ) |
66 data_manager_dict = {} | 47 data_manager_dict = {} |
67 | 48 |
68 # Create Defuse Reference Data | 49 # Create Defuse Reference Data |
69 data_manager_dict = fetch_databases( data_manager_dict, target_directory, options.jar_path) | 50 data_manager_dict = fetch_databases( data_manager_dict, target_directory) |
70 | 51 |
71 # save info to json file | 52 # save info to json file |
72 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) | 53 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) |
73 | 54 |
74 | 55 |