AttributeError when parsing taxdump

[callumjethomas]

Problem description

I am getting an AttributeError message when trying to create a BlobDir, it appears there is an issue at the taxdump parsing stage.

Command used:

blobtools create --fasta USA_hap1.fa.gz \
> --meta USA_hap1.yaml \
> --taxid 343691  \
> --taxdump ncbi_dbs/taxdump \
> ./USA_ros3979_hap1

Error message

Loading sequences from USA_hap1.fa.gz
 - processing ScPul3w_1801;HRSCAF=1960: : 1801it [02:16, 13.23it/s]
Parsing taxdump
Traceback (most recent call last):
  File "/rds/user/hpc-work/miniforge3/envs/btk/bin/blobtools", line 8, in <module>
    sys.exit(cli())
  File "/rds/user/hpc-work/miniforge3/envs/btk/lib/python3.9/site-packages/blobtools/blobtools.py", line 105, in cli
    sys.exit(subcommand())
  File "/rds/user/hpc-work/miniforge3/envs/btk/lib/python3.9/site-packages/blobtools/lib/add.py", line 203, in cli
    main(args)
  File "/rds/user/hpc-work/miniforge3/envs/btk/lib/python3.9/site-packages/blobtools/lib/add.py", line 191, in main
    taxid.add(args["--taxid"], taxdump, meta)
  File "/rds/user/hpc-work/miniforge3/envs/btk/lib/python3.9/site-packages/blobtools/lib/taxid.py", line 13, in add
    meta.taxon.update({'taxid': taxid})
AttributeError: 'str' object has no attribute 'update'

Install information

• taxdump downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump
• blobtoolkit v4.4.5
• python v3.9.23 (hc30ae73_0_cpython)
• Rocky Linux 8.10 (Green Obsidian)

[rjchallis]

I think this may be being caused by the content of USA_hap1.yaml.

The taxon section should be an object, but when blobtools create is trying to set the taxid key, it can't add it to a string.

I'm guessing that you may have something like

taxon: "Taxon name"

instead of

taxon:
    name: "Taxon name"

If so, updating the taxon section to be an object should help.