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fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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MetaData.reflect() missing 1 required positional argument: 'bind' #151

Closed lpipes closed 1 year ago

lpipes commented 1 year ago

I can't seem to generate the 0_taxonomyfromtaxids.csv file from this command (I attached my two files 0.csv and 0_taxid.txt):

taxit taxtable ncbi_taxonomy.db -f 0_taxid.txt -i 0.csv -o 0_taxonomyfromtaxids.csv
Traceback (most recent call last):
  File "/space/s1/lenore/software/taxtastic/taxit.py", line 22, in <module>
    sys.exit(main(sys.argv[1:]))
             ^^^^^^^^^^^^^^^^^^
  File "/space/s1/lenore/software/taxtastic/taxtastic/scripts/taxit.py", line 51, in main
    return action(arguments)
           ^^^^^^^^^^^^^^^^^
  File "/space/s1/lenore/software/taxtastic/taxtastic/subcommands/taxtable.py", line 130, in action
    tax = Taxonomy(engine, schema=args.schema)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/space/s1/lenore/software/taxtastic/taxtastic/taxonomy.py", line 72, in __init__
    self.meta.reflect()
TypeError: MetaData.reflect() missing 1 required positional argument: 'bind'

0.csv 0_taxid.txt

nhoffman commented 1 year ago

This should be fixed in v0.10.0 - please reopen or submit a new issue if you still see the error.