Mercurial > repos > iuc > data_manager_fetch_busco

comparison data_manager/data_manager.py @ 2:2b4526fdf7fb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
author iuc
date Mon, 24 Apr 2023 12:26:46 +0000
parents 15b97817550a
children
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1:15b97817550a 2:2b4526fdf7fb
1 #!/usr/bin/env python
2 #
3 # Data manager for reference data for the 'BUSCO' Galaxy tools
1 import argparse 4 import argparse
2 import datetime 5 import datetime
3 import json 6 import json
4 import os 7 import os
5 import shutil 8 import shutil
6 import tarfile 9 import subprocess
7 import zipfile 10 from pathlib import Path
8 try:
9 # For Python 3.0 and later
10 from urllib.request import Request, urlopen
11 except ImportError:
12 # Fall back to Python 2 imports
13 from urllib2 import Request, urlopen
14
15
16 def url_download(url, workdir):
17 file_path = os.path.join(workdir, 'download.dat')
18 if not os.path.exists(workdir):
19 os.makedirs(workdir)
20 src = None
21 dst = None
22 try:
23 req = Request(url)
24 src = urlopen(req)
25 with open(file_path, 'wb') as dst:
26 while True:
27 chunk = src.read(2**10)
28 if chunk:
29 dst.write(chunk)
30 else:
31 break
32 finally:
33 if src:
34 src.close()
35 if tarfile.is_tarfile(file_path):
36 fh = tarfile.open(file_path, 'r:*')
37 elif zipfile.is_zipfile(file_path):
38 fh = zipfile.ZipFile(file_path, 'r')
39 else:
40 return
41 fh.extractall(workdir)
42 os.remove(file_path)
43 11
44 12
45 def main(args): 13 def main(args):
46 workdir = os.path.join(os.getcwd(), 'busco') 14 workdir = os.path.join(os.getcwd(), "busco_downloads")
47 url_download(args.url, workdir) 15 cmd = "busco --download %s" % args.database
16 subprocess.check_call(cmd, shell=True)
17 with open(args.json) as fh:
18 params = json.load(fh)
19 target_directory = params["output_data"][0]["extra_files_path"]
48 data_manager_entry = {} 20 data_manager_entry = {}
49 data_manager_entry['value'] = args.name.lower() 21 data_manager_entry["value"] = args.name.lower()
50 data_manager_entry['name'] = args.name 22 data_manager_entry["name"] = args.name
51 data_manager_entry['path'] = '.' 23 data_manager_entry["version"] = args.version
52 data_manager_json = dict(data_tables=dict(busco=data_manager_entry)) 24 data_manager_entry["path"] = str(Path(target_directory))
53 with open(args.output) as fh: 25 data_manager_json = dict(data_tables=dict(busco_database=data_manager_entry))
54 params = json.load(fh) 26
55 target_directory = params['output_data'][0]['extra_files_path']
56 os.mkdir(target_directory) 27 os.mkdir(target_directory)
57 output_path = os.path.abspath(os.path.join(os.getcwd(), 'busco')) 28 output_path = os.path.abspath(os.path.join(os.getcwd(), "busco_downloads"))
58 for filename in os.listdir(workdir): 29 for filename in os.listdir(workdir):
59 shutil.move(os.path.join(output_path, filename), target_directory) 30 shutil.move(os.path.join(output_path, filename), target_directory)
60 with open(args.output, 'w') as fh: 31 with open(args.json, "w") as fh:
61 json.dump(data_manager_json, fh, sort_keys=True) 32 json.dump(data_manager_json, fh, sort_keys=True)
62 33
63 34
64 if __name__ == '__main__': 35 if __name__ == "__main__":
65 parser = argparse.ArgumentParser(description='Create data manager json.') 36
66 parser.add_argument('--out', dest='output', action='store', help='JSON filename') 37 # Read command line
67 parser.add_argument('--name', dest='name', action='store', default=str(datetime.date.today()), help='Data table entry unique ID') 38 parser = argparse.ArgumentParser(description="Download BUSCO database")
68 parser.add_argument('--url', dest='url', action='store', help='Download URL') 39 parser.add_argument("--database", help="Database name")
40 parser.add_argument(
41 "--name", default=str(datetime.date.today()), help="Data table entry unique ID"
42 )
43 parser.add_argument("--version", help="BUSCO version")
44 parser.add_argument("--json", help="Path to JSON file")
69 args = parser.parse_args() 45 args = parser.parse_args()
70 46
71 main(args) 47 main(args)