AttributeError: 'Namespace' object has no attribute 'database_dir'

[tseemann]

% seroba getPneumocat db

Traceback (most recent call last):
  File "/home/linuxbrew/.linuxbrew/bin/seroba", line 4, in <module>
    __import__('pkg_resources').run_script('seroba==0.1.4', 'seroba')
  File "/home/linuxbrew/.linuxbrew/opt/python3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 742, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/home/linuxbrew/.linuxbrew/opt/python3/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1510, in run_script
    exec(script_code, namespace, namespace)
  File "/home/linuxbrew/.linuxbrew/opt/python3/lib/python3.6/site-packages/seroba-0.1.4-py3.6.egg/EGG-INFO/scripts/seroba", line 86, in <module>
  File "/home/linuxbrew/.linuxbrew/opt/python3/lib/python3.6/site-packages/seroba-0.1.4-py3.6.egg/seroba/tasks/getPneumocat.py", line 6, in run
AttributeError: 'Namespace' object has no attribute 'database_dir'

[eppinglen]

Thank you for reporting. The error has been fixed.
However, I would recommend you to use the database, thats provided in this repository.
It includes a couple of recently discovered serotypes.

[tseemann]

I wasn't aware a database was included?

The docs seem to tell me about getPneuomoCat as the first thing.

How do we use it?
Could you add some example command lines and an example contigs file to run it on?

[eppinglen]

Since version 0.1.3 we includes an extended database with novel serotypes.
(added serotypes: 6G, 6F, 11E, 10X, 39X and two NT references)
For a practical exercise with SeroBA, please have look here: https://github.com/sanger-pathogens/pathogen-informatics-training