Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath

annotate data_manager/data_manager_eggnog.py @ 3:e59a8fe169af draft default tip

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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 75035b2919ce95fa8d3b785d86c7c7c9da531db2
author galaxyp
date Mon, 20 Jun 2022 12:47:41 +0000
parents 3d12bbd5c0ba
children
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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)
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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():
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28 parser = argparse.ArgumentParser()
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29 parser.add_argument('--config_file')
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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()
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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)
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38
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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 = {}
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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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3d12bbd5c0ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
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45 # DB versionning was super confusing for eggnog-mapper 2.0.x:
1
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)
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3d12bbd5c0ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
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47 # eggnog-mapper 2.x needed a db v2.0 (based on eggnog v5.0)
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48 # (db v4.5 are not compatible with eggnog-mapper 2.0)
3d12bbd5c0ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
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49 # Starting with eggnog-mapper 2.1.* db versioning looks better: 2.1.0 requires db v5.0.2
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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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50 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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51 if "4.5" in db_version:
2
3d12bbd5c0ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
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52 # special case: eggnog-mapper 1.x
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53 version = "1.0"
2
3d12bbd5c0ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
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54 elif db_version.startswith('2.'):
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55 # special case: eggnog-mapper 2.0.x
3d12bbd5c0ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
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56 version = "2.0"
3d12bbd5c0ba "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
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57 else:
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58 # normal case or eggno-mapper >= 2.1
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59 version = db_version
1
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60 data_table_entry = dict(value=db_version, name=db_version,
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61 path=args.install_path, version=version)
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62 dm_dict['data_tables'][data_table].append(data_table_entry)
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64 # save info to json file
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65 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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68 if __name__ == "__main__":
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69 main()