Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath

annotate data_manager/data_manager_eggnog.py @ 1:46d2e3ed9530 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
author galaxyp
date Fri, 19 Feb 2021 18:52:23 +0000
parents 48893cfa76a8
children 3d12bbd5c0ba
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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1 #!/usr/bin/env python
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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3 from __future__ import print_function
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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5 import argparse
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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6 import json
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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7 import os.path
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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8 import sqlite3
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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9 import sys
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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10 from sqlite3 import OperationalError
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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13 def _get_db_version(sqlitedb_path):
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46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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14 version = '5.0'
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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15 try:
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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16 query = 'select version from version'
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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17 conn = sqlite3.connect(sqlitedb_path)
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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18 cur = conn.cursor()
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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19 cur.execute(query)
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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20 version = cur.fetchone()[0]
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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21 except OperationalError as e:
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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22 print('Assuming eggnog version %s because %s %s' %
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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23 (version, sqlitedb_path, e), file=sys.stderr)
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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24 return version
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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27 def main():
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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28 parser = argparse.ArgumentParser()
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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29 parser.add_argument('--config_file')
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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30 parser.add_argument('--install_path')
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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31 args = parser.parse_args()
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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33 eggnog_db_path = os.path.join(args.install_path, 'eggnog.db')
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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34 if not os.path.exists(eggnog_db_path):
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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35 print('Can not open: %s' % eggnog_db_path, file=sys.stderr)
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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36 exit(1)
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37 db_version = _get_db_version(eggnog_db_path)
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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38
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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39 # params = json.loads(open(args.config_file).read())
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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40 dm_dict = {}
48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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41 dm_dict['data_tables'] = dm_dict.get('data_tables', {})
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46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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42 data_table = 'eggnog_mapper_db_versioned'
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43 dm_dict['data_tables'][data_table]\
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44 = dm_dict['data_tables'].get(data_table, [])
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46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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45 # Versionning is super confusing:
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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46 # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5)
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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47 # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0)
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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48 # db v4.5 are not compatible with eggnog-mapper 2.0
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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49 version = "2.0"
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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50 if "4.5" in db_version:
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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51 version = "1.0"
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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52 data_table_entry = dict(value=db_version, name=db_version,
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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53 path=args.install_path, version=version)
46d2e3ed9530 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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54 dm_dict['data_tables'][data_table].append(data_table_entry)
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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56 # save info to json file
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57 open(args.config_file, 'w').write(json.dumps(dm_dict))
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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48893cfa76a8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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60 if __name__ == "__main__":
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61 main()