Mercurial > repos > jjohnson > eggnog_mapper_data_manager

annotate data_manager/data_manager_eggnog.py @ 0:2909815b6a01 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
author jjohnson
date Thu, 07 Nov 2019 12:41:50 -0500
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2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
parents:
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1 #!/usr/bin/env python
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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3 from __future__ import print_function
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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jjohnson
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5 import argparse
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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6 import json
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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7 import os.path
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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8 import sqlite3
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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9 import sys
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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10 from sqlite3 import OperationalError
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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13 def _get_db_version(sqlitedb_path):
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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14 version = '4.5'
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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15 try:
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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16 query = 'select version from version'
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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17 conn = sqlite3.connect(sqlitedb_path)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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18 cur = conn.cursor()
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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19 cur.execute(query)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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20 version = cur.fetchone()[0]
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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21 except OperationalError as e:
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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22 print('Assuming eggnog version %s because %s %s' %
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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23 (version, sqlitedb_path, e), file=sys.stderr)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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24 return version
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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27 def main():
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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28 parser = argparse.ArgumentParser()
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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29 parser.add_argument('--config_file')
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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30 parser.add_argument('--install_path')
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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31 parser.add_argument('--dbs', default='')
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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32 args = parser.parse_args()
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34 eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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35 if not os.path.exists(eggnog_db_path):
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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36 print('Can not open: %s' % eggnog_db_path, file=sys.stderr)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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37 exit(1)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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38 db_version = _get_db_version(eggnog_db_path)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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39
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40 # params = json.loads(open(args.config_file).read())
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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41 dm_dict = {}
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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42 dm_dict['data_tables'] = dm_dict.get('data_tables', {})
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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43 data_table = 'eggnog_mapper_db'
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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44 dm_dict['data_tables'][data_table]\
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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45 = dm_dict['data_tables'].get(data_table, [])
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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46 data_table_entry = dict(value=db_version, name=db_version,
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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47 path=args.install_path)
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48 dm_dict['data_tables'][data_table].append(data_table_entry)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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49 data_table = 'eggnog_mapper_hmm_dbs'
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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50 dm_dict['data_tables'][data_table]\
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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51 = dm_dict['data_tables'].get(data_table, [])
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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52 if args.dbs:
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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53 dbs = [x.strip() for x in args.dbs.split(',')]
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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54 for db in dbs:
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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55 key = '%s_%s' % (db_version, db)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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56 data_table_entry = dict(key=key, db_version=db_version,
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57 value=db, name=db, path=db)
2909815b6a01 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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58 dm_dict['data_tables'][data_table].append(data_table_entry)
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59
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60 # save info to json file
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61 open(args.config_file, 'wb').write(json.dumps(dm_dict))
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62
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63
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64 if __name__ == "__main__":
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65 main()