Mercurial > repos > dfornika > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_standard.py @ 12:039a65ff445d draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author dfornika
date Tue, 05 Mar 2019 15:11:05 -0500
parents 1601703ae511
children
comparison
equal deleted inserted replaced
11:1dc93ae264e6 12:039a65ff445d
20 if return_code: 20 if return_code:
21 print("Error building database.", file=sys.stderr) 21 print("Error building database.", file=sys.stderr)
22 sys.exit( return_code ) 22 sys.exit( return_code )
23 23
24 def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): 24 def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
25 today = datetime.date.today().isoformat() 25 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
26 database_name = "_".join([ 26
27 today, 27 database_value = "_".join([
28 now,
28 "standard", 29 "standard",
29 "kmer-len=" + str(kraken2_args["kmer_len"]), 30 "kmer-len" + str(kraken2_args["kmer_len"]),
30 "minimizer-len=" + str(kraken2_args["minimizer_len"]), 31 "minimizer-len" + str(kraken2_args["minimizer_len"]),
31 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]), 32 "minimizer-spaces" + str(kraken2_args["minimizer_spaces"]),
32 ]) 33 ])
34
35 database_name = " ".join([
36 "Standard",
37 "(Created:",
38 now + ",",
39 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
40 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
41 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
42 ])
43
44 database_path = database_value
45
33 args = [ 46 args = [
34 '--threads', str(kraken2_args["threads"]), 47 '--threads', str(kraken2_args["threads"]),
35 '--standard', 48 '--standard',
36 '--kmer-len', str(kraken2_args["kmer_len"]), 49 '--kmer-len', str(kraken2_args["kmer_len"]),
37 '--minimizer-len', str(kraken2_args["minimizer_len"]), 50 '--minimizer-len', str(kraken2_args["minimizer_len"]),
38 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), 51 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
39 '--db', database_name 52 '--db', database_path
40 ] 53 ]
41 54
42 run(['kraken2-build'] + args, target_directory) 55 run(['kraken2-build'] + args, target_directory)
43 56
44 args = [ 57 args = [
45 '--threads', str(kraken2_args["threads"]), 58 '--threads', str(kraken2_args["threads"]),
46 '--clean', 59 '--clean',
47 '--db', database_name 60 '--db', database_path
48 ] 61 ]
49 62
50 run(['kraken2-build'] + args, target_directory) 63 run(['kraken2-build'] + args, target_directory)
51 64
52 data_table_entry = { 65 data_table_entry = {
53 "value": database_name, 66 "value": database_value,
54 "name": database_name, 67 "name": database_name,
55 "path": database_name 68 "path": database_path,
56 } 69 }
57 70
58 _add_data_table_entry(data_manager_dict, data_table_entry) 71 _add_data_table_entry(data_manager_dict, data_table_entry)
59 72
60 73