Mercurial > repos > dfornika > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_custom.py @ 5:1f6fe9dc5490 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
author dfornika
date Mon, 04 Mar 2019 18:59:44 -0500
parents 988c436ad798
children
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4:988c436ad798 5:1f6fe9dc5490
21 if return_code: 21 if return_code:
22 print("Error building database.", file=sys.stderr) 22 print("Error building database.", file=sys.stderr)
23 sys.exit( return_code ) 23 sys.exit( return_code )
24 24
25 25
26 def kraken2_build(data_manager_dict, kraken2_args, params, target_directory, data_table_name=DATA_TABLE_NAME): 26 def kraken2_build(data_manager_dict, kraken2_args, database_name, params, target_directory, data_table_name=DATA_TABLE_NAME):
27 today = datetime.date.today().isoformat() 27 today = datetime.date.today().isoformat()
28 database_name = "_".join([today, "custom"])
29 28
30 args = [ 29 args = [
31 'kraken2-build',
32 '--threads', str(kraken2_args["threads"]), 30 '--threads', str(kraken2_args["threads"]),
33 '--download-taxonomy', 31 '--download-taxonomy',
34 '--db', database_name 32 '--db', database_name
35 ] 33 ]
36 34
37 # run(args, target_directory) 35 run(['kraken2-build'] + args, target_directory)
38 36
39 args = [ 37 args = [
40 'kraken2-build',
41 '--threads', str(kraken2_args["threads"]), 38 '--threads', str(kraken2_args["threads"]),
42 '--add-to-library', kraken2_args["fasta"], 39 '--add-to-library', kraken2_args["fasta"],
43 '--db', database_name 40 '--db', database_name
44 ] 41 ]
45 42
46 run(args, target_directory) 43 run(['kraken2-build'] + args, target_directory)
47 44
48 args = [ 45 args = [
49 'kraken2-build', 46 '--threads', str(kraken2_args["threads"]),
47 '--build',
48 '--kmer-len', str(kraken2_args["kmer_len"]),
49 '--minimizer-len', str(kraken2_args["minimizer_len"]),
50 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
51 '--db', database_name
52 ]
53
54 run(['kraken2-build'] + args, target_directory)
55
56 args = [
50 '--threads', str(kraken2_args["threads"]), 57 '--threads', str(kraken2_args["threads"]),
51 '--clean', 58 '--clean',
52 '--db', database_name 59 '--db', database_name
53 ] 60 ]
54 61
55 run(args, target_directory) 62 run(['kraken2-build'] + args, target_directory)
56 63
57 data_table_entry = { 64 data_table_entry = {
58 "value": database_name, 65 "value": database_name,
59 "name": database_name, 66 "name": database_name,
60 "path": database_name 67 "path": database_name
71 78
72 79
73 def main(): 80 def main():
74 parser = argparse.ArgumentParser() 81 parser = argparse.ArgumentParser()
75 parser.add_argument('params') 82 parser.add_argument('params')
83 parser.add_argument( '-d', '--db', dest='database_name', help='database name' )
76 parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' ) 84 parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' )
77 parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' ) 85 parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' )
78 parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' ) 86 parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' )
79 parser.add_argument( '-f', '--fasta', dest='fasta', help='fasta' ) 87 parser.add_argument( '-f', '--fasta', dest='fasta', help='fasta' )
80 parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) 88 parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )