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annotate ete_init_taxdb.py @ 15:1e85af7a29c4 draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 16:34:12 +0000
parents 03c10736e497
children
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03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
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diff changeset
1 import optparse
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1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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2 from urllib.request import urlretrieve
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03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
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1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
diff changeset
4 from ete3.ncbi_taxonomy.ncbiquery import update_db
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03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
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5
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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6 parser = optparse.OptionParser()
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1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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7 parser.add_option(
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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8 "-t",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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9 "--taxdump",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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10 dest="taxdump",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
diff changeset
11 default=None,
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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12 help="NCBI taxdump (tar.gz), will be downloaded if not given",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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13 )
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
diff changeset
14 parser.add_option(
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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15 "-d",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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16 "--database",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
diff changeset
17 dest="database",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
diff changeset
18 default=None,
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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19 help="ETE sqlite data base to create",
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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20 )
2
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
diff changeset
21 options, args = parser.parse_args()
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
diff changeset
22 if options.database is None:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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23 parser.error("-d option must be specified")
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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24 if options.taxdump is not None:
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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25 taxdump = options.taxdump
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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26 else:
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1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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27 urlretrieve(
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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28 "https://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz", "taxdump.tar.gz"
1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
diff changeset
29 )
2
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
diff changeset
30 taxdump = "taxdump.tar.gz"
03c10736e497 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 91b634b8f9b131045bbbbf43cc8edbea59ac686b-dirty
earlhaminst
parents:
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31
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1e85af7a29c4 planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/ete commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
earlhaminst
parents: 2
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32 update_db(dbfile=options.database, targz_file=taxdump)