search

sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
Other
18 stars 16 forks source link

AttributeError: 'Namespace' object has no attribute 'database_dir' #14

Closed tseemann closed 7 years ago

tseemann commented 7 years ago 
% 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 commented 7 years ago

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 commented 7 years ago

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 commented 7 years ago

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