Mercurial > repos > iuc > data_manager_fetch_busco

annotate data_manager/data_manager.py @ 2:2b4526fdf7fb draft

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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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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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1 #!/usr/bin/env python
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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2 #
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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3 # Data manager for reference data for the 'BUSCO' Galaxy tools
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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4 import argparse
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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5 import datetime
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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6 import json
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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7 import os
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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8 import shutil
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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9 import subprocess
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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10 from pathlib import Path
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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13 def main(args):
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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14 workdir = os.path.join(os.getcwd(), "busco_downloads")
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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15 cmd = "busco --download %s" % args.database
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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16 subprocess.check_call(cmd, shell=True)
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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17 with open(args.json) as fh:
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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18 params = json.load(fh)
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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19 target_directory = params["output_data"][0]["extra_files_path"]
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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20 data_manager_entry = {}
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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21 data_manager_entry["value"] = args.name.lower()
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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22 data_manager_entry["name"] = args.name
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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23 data_manager_entry["version"] = args.version
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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24 data_manager_entry["path"] = str(Path(target_directory))
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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25 data_manager_json = dict(data_tables=dict(busco_database=data_manager_entry))
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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27 os.mkdir(target_directory)
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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28 output_path = os.path.abspath(os.path.join(os.getcwd(), "busco_downloads"))
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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29 for filename in os.listdir(workdir):
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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30 shutil.move(os.path.join(output_path, filename), target_directory)
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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31 with open(args.json, "w") as fh:
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15b97817550a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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32 json.dump(data_manager_json, fh, sort_keys=True)
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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35 if __name__ == "__main__":
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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37 # Read command line
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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38 parser = argparse.ArgumentParser(description="Download BUSCO database")
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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39 parser.add_argument("--database", help="Database name")
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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40 parser.add_argument(
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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41 "--name", default=str(datetime.date.today()), help="Data table entry unique ID"
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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42 )
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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43 parser.add_argument("--version", help="BUSCO version")
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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44 parser.add_argument("--json", help="Path to JSON file")
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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45 args = parser.parse_args()
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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47 main(args)