vispr test

[Janine Lux]

Dear all,

running vispr test, I have the following error shown below. I would be very grateful if anyone knows what the problem is.

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\$ vispr test
/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/server.py:23: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
CAPTIONS = yaml.load(f)
Loading data.
/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/cli.py:40: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
config = yaml.load(f)
Traceback (most recent call last):
File "/home/jl2113/miniconda3/envs/mageck-vispr2/bin/vispr", line 10, in <module>
sys.exit(main())
File "/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/cli.py", line 209, in main
test_server(port=args.port, host=args.host, update=args.update)
File "/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/cli.py", line 80, in test_server
port=port)
File "/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/cli.py", line 42, in init_server
app.screens.add(config, parentdir=os.path.dirname(path))
File "/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/results/init.py", line 29, in add
self.screens[screen] = Screen(config, parentdir=parentdir)
File "/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/results/init.py", line 114, in init
self.target_clustering = target_clustering.TargetClustering(self.targets)
File "/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/vispr/results/target_clustering.py", line 21, in init
self.df = self.df.ix[mean[:topn].index]
File "/home/jl2113/miniconda3/envs/mageck-vispr2/lib/python3.7/site-packages/pandas/core/generic.py", line 5274, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'

[John Reeves]

Pandas 1.0.0 breaks vispr. You need to downgrade to pandas 0.25.3. In an existing environment, you can try…

conda activate your_environment
conda install pandas=0.25.3

Say “yes” when asked if you are OK with downgrading. Depending on your environment, you might need to make other adjustment as well.

We found that installing mageck-vispr following instructions failed, suggesting that the dependency definitions on bioconda need to be updated. The following environment definition file appears to be working (so far so good!)

# environment definition for mageck-vispr
name: mv

channels:
  - bioconda
  - conda-forge
  - r
  - defaults

dependencies:
  - mageck-vispr
  - python=3.6.8
  - snakemake=3.13.3
  - r-base=3.5.1
  - pandas=0.25.3

Save as “environment.yml” and install using…

conda env create --file environment.yml

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